WorldWideScience

Sample records for biomedical information extraction

  1. Extracting laboratory test information from biomedical text

    Directory of Open Access Journals (Sweden)

    Yanna Shen Kang

    2013-01-01

    Full Text Available Background: No previous study reported the efficacy of current natural language processing (NLP methods for extracting laboratory test information from narrative documents. This study investigates the pathology informatics question of how accurately such information can be extracted from text with the current tools and techniques, especially machine learning and symbolic NLP methods. The study data came from a text corpus maintained by the U.S. Food and Drug Administration, containing a rich set of information on laboratory tests and test devices. Methods: The authors developed a symbolic information extraction (SIE system to extract device and test specific information about four types of laboratory test entities: Specimens, analytes, units of measures and detection limits. They compared the performance of SIE and three prominent machine learning based NLP systems, LingPipe, GATE and BANNER, each implementing a distinct supervised machine learning method, hidden Markov models, support vector machines and conditional random fields, respectively. Results: Machine learning systems recognized laboratory test entities with moderately high recall, but low precision rates. Their recall rates were relatively higher when the number of distinct entity values (e.g., the spectrum of specimens was very limited or when lexical morphology of the entity was distinctive (as in units of measures, yet SIE outperformed them with statistically significant margins on extracting specimen, analyte and detection limit information in both precision and F-measure. Its high recall performance was statistically significant on analyte information extraction. Conclusions: Despite its shortcomings against machine learning methods, a well-tailored symbolic system may better discern relevancy among a pile of information of the same type and may outperform a machine learning system by tapping into lexically non-local contextual information such as the document structure.

  2. NAMED ENTITY RECOGNITION FROM BIOMEDICAL TEXT -AN INFORMATION EXTRACTION TASK

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    N. Kanya

    2016-07-01

    Full Text Available Biomedical Text Mining targets the Extraction of significant information from biomedical archives. Bio TM encompasses Information Retrieval (IR and Information Extraction (IE. The Information Retrieval will retrieve the relevant Biomedical Literature documents from the various Repositories like PubMed, MedLine etc., based on a search query. The IR Process ends up with the generation of corpus with the relevant document retrieved from the Publication databases based on the query. The IE task includes the process of Preprocessing of the document, Named Entity Recognition (NER from the documents and Relationship Extraction. This process includes Natural Language Processing, Data Mining techniques and machine Language algorithm. The preprocessing task includes tokenization, stop word Removal, shallow parsing, and Parts-Of-Speech tagging. NER phase involves recognition of well-defined objects such as genes, proteins or cell-lines etc. This process leads to the next phase that is extraction of relationships (IE. The work was based on machine learning algorithm Conditional Random Field (CRF.

  3. Construction of an annotated corpus to support biomedical information extraction

    Directory of Open Access Journals (Sweden)

    McNaught John

    2009-10-01

    Full Text Available Abstract Background Information Extraction (IE is a component of text mining that facilitates knowledge discovery by automatically locating instances of interesting biomedical events from huge document collections. As events are usually centred on verbs and nominalised verbs, understanding the syntactic and semantic behaviour of these words is highly important. Corpora annotated with information concerning this behaviour can constitute a valuable resource in the training of IE components and resources. Results We have defined a new scheme for annotating sentence-bound gene regulation events, centred on both verbs and nominalised verbs. For each event instance, all participants (arguments in the same sentence are identified and assigned a semantic role from a rich set of 13 roles tailored to biomedical research articles, together with a biological concept type linked to the Gene Regulation Ontology. To our knowledge, our scheme is unique within the biomedical field in terms of the range of event arguments identified. Using the scheme, we have created the Gene Regulation Event Corpus (GREC, consisting of 240 MEDLINE abstracts, in which events relating to gene regulation and expression have been annotated by biologists. A novel method of evaluating various different facets of the annotation task showed that average inter-annotator agreement rates fall within the range of 66% - 90%. Conclusion The GREC is a unique resource within the biomedical field, in that it annotates not only core relationships between entities, but also a range of other important details about these relationships, e.g., location, temporal, manner and environmental conditions. As such, it is specifically designed to support bio-specific tool and resource development. It has already been used to acquire semantic frames for inclusion within the BioLexicon (a lexical, terminological resource to aid biomedical text mining. Initial experiments have also shown that the corpus may

  4. Introducing meta-services for biomedical information extraction

    OpenAIRE

    Leitner, Florian; Krallinger, Martin; Johnson, Calvin A.; Saetre, Rune; Yoshida, Kazuhiro; Chen, Yan Hua; Kim, Sun; Shin, Soo-Yong; Zhang, Byoung-Tak; Baumgartner, William A.; Hunter, Lawrence; Haddow, Barry; Rodriguez-Penagos, Carlos; Matthews, Michael; Wang, Xinglong

    2008-01-01

    We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://bcms.bioinfo.cnio.es/). This prototype platform is a joint effort of 13 research groups and provides automatically generated annotations for PubMed/Medline abstracts. Annotation types cover gene names, gene IDs, species, and protein-protein interactions. The annotations are distributed by the meta-server in both human and machine readable formats (HTML/XML). This servi...

  5. BioSimplify: an open source sentence simplification engine to improve recall in automatic biomedical information extraction

    CERN Document Server

    Jonnalagadda, Siddhartha

    2011-01-01

    BioSimplify is an open source tool written in Java that introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction (as opposed to sentence simplification for improving human readability). The model is based on a "shot-gun" approach that produces many different (simpler) versions of the original sentence by combining variants of its constituent elements. This tool is optimized for processing biomedical scientific literature such as the abstracts indexed in PubMed. We tested our tool on its impact to the task of PPI extraction and it improved the f-score of the PPI tool by around 7%, with an improvement in recall of around 20%. The BioSimplify tool and test corpus can be downloaded from https://biosimplify.sourceforge.net.

  6. Towards Evidence-based Precision Medicine: Extracting Population Information from Biomedical Text using Binary Classifiers and Syntactic Patterns.

    Science.gov (United States)

    Raja, Kalpana; Dasot, Naman; Goyal, Pawan; Jonnalagadda, Siddhartha R

    2016-01-01

    Precision Medicine is an emerging approach for prevention and treatment of disease that considers individual variability in genes, environment, and lifestyle for each person. The dissemination of individualized evidence by automatically identifying population information in literature is a key for evidence-based precision medicine at the point-of-care. We propose a hybrid approach using natural language processing techniques to automatically extract the population information from biomedical literature. Our approach first implements a binary classifier to classify sentences with or without population information. A rule-based system based on syntactic-tree regular expressions is then applied to sentences containing population information to extract the population named entities. The proposed two-stage approach achieved an F-score of 0.81 using a MaxEnt classifier and the rule- based system, and an F-score of 0.87 using a Nai've-Bayes classifier and the rule-based system, and performed relatively well compared to many existing systems. The system and evaluation dataset is being released as open source. PMID:27570671

  7. Figure text extraction in biomedical literature.

    Directory of Open Access Journals (Sweden)

    Daehyun Kim

    Full Text Available BACKGROUND: Figures are ubiquitous in biomedical full-text articles, and they represent important biomedical knowledge. However, the sheer volume of biomedical publications has made it necessary to develop computational approaches for accessing figures. Therefore, we are developing the Biomedical Figure Search engine (http://figuresearch.askHERMES.org to allow bioscientists to access figures efficiently. Since text frequently appears in figures, automatically extracting such text may assist the task of mining information from figures. Little research, however, has been conducted exploring text extraction from biomedical figures. METHODOLOGY: We first evaluated an off-the-shelf Optical Character Recognition (OCR tool on its ability to extract text from figures appearing in biomedical full-text articles. We then developed a Figure Text Extraction Tool (FigTExT to improve the performance of the OCR tool for figure text extraction through the use of three innovative components: image preprocessing, character recognition, and text correction. We first developed image preprocessing to enhance image quality and to improve text localization. Then we adapted the off-the-shelf OCR tool on the improved text localization for character recognition. Finally, we developed and evaluated a novel text correction framework by taking advantage of figure-specific lexicons. RESULTS/CONCLUSIONS: The evaluation on 382 figures (9,643 figure texts in total randomly selected from PubMed Central full-text articles shows that FigTExT performed with 84% precision, 98% recall, and 90% F1-score for text localization and with 62.5% precision, 51.0% recall and 56.2% F1-score for figure text extraction. When limiting figure texts to those judged by domain experts to be important content, FigTExT performed with 87.3% precision, 68.8% recall, and 77% F1-score. FigTExT significantly improved the performance of the off-the-shelf OCR tool we used, which on its own performed with 36

  8. Enhancing biomedical text summarization using semantic relation extraction.

    Directory of Open Access Journals (Sweden)

    Yue Shang

    Full Text Available Automatic text summarization for a biomedical concept can help researchers to get the key points of a certain topic from large amount of biomedical literature efficiently. In this paper, we present a method for generating text summary for a given biomedical concept, e.g., H1N1 disease, from multiple documents based on semantic relation extraction. Our approach includes three stages: 1 We extract semantic relations in each sentence using the semantic knowledge representation tool SemRep. 2 We develop a relation-level retrieval method to select the relations most relevant to each query concept and visualize them in a graphic representation. 3 For relations in the relevant set, we extract informative sentences that can interpret them from the document collection to generate text summary using an information retrieval based method. Our major focus in this work is to investigate the contribution of semantic relation extraction to the task of biomedical text summarization. The experimental results on summarization for a set of diseases show that the introduction of semantic knowledge improves the performance and our results are better than the MEAD system, a well-known tool for text summarization.

  9. A Unified Active Learning Framework for Biomedical Relation Extraction

    Institute of Scientific and Technical Information of China (English)

    Hong-Tao Zhang; Min-Lie Huang; Xiao-Yan Zhu

    2012-01-01

    Supervised machine learning methods have been employed with great success in the task of biomedical relation extraction.However,existing methods are not practical enough,since manual construction of large training data is very expensive.Therefore,active learning is urgently needed for designing practical relation extraction methods with little human effort.In this paper,we describe a unified active learning framework.Particularly,our framework systematically addresses some practical issues during active learning process,including a strategy for selecting informative data,a data diversity selection algorithm,an active feature acquisition method,and an informative feature selection algorithm,in order to meet the challenges due to the immense amount of complex and diverse biomedical text.The framework is evaluated on protein-protein interaction (PPI) extraction and is shown to achieve promising results with a significant reduction in editorial effort and labeling time.

  10. Biomedical information retrieval across languages.

    Science.gov (United States)

    Daumke, Philipp; Markü, Kornél; Poprat, Michael; Schulz, Stefan; Klar, Rüdiger

    2007-06-01

    This work presents a new dictionary-based approach to biomedical cross-language information retrieval (CLIR) that addresses many of the general and domain-specific challenges in current CLIR research. Our method is based on a multilingual lexicon that was generated partly manually and partly automatically, and currently covers six European languages. It contains morphologically meaningful word fragments, termed subwords. Using subwords instead of entire words significantly reduces the number of lexical entries necessary to sufficiently cover a specific language and domain. Mediation between queries and documents is based on these subwords as well as on lists of word-n-grams that are generated from large monolingual corpora and constitute possible translation units. The translations are then sent to a standard Internet search engine. This process makes our approach an effective tool for searching the biomedical content of the World Wide Web in different languages. We evaluate this approach using the OHSUMED corpus, a large medical document collection, within a cross-language retrieval setting. PMID:17541863

  11. Mining biomedical images towards valuable information retrieval in biomedical and life sciences

    Science.gov (United States)

    Ahmed, Zeeshan; Zeeshan, Saman; Dandekar, Thomas

    2016-01-01

    Biomedical images are helpful sources for the scientists and practitioners in drawing significant hypotheses, exemplifying approaches and describing experimental results in published biomedical literature. In last decades, there has been an enormous increase in the amount of heterogeneous biomedical image production and publication, which results in a need for bioimaging platforms for feature extraction and analysis of text and content in biomedical images to take advantage in implementing effective information retrieval systems. In this review, we summarize technologies related to data mining of figures. We describe and compare the potential of different approaches in terms of their developmental aspects, used methodologies, produced results, achieved accuracies and limitations. Our comparative conclusions include current challenges for bioimaging software with selective image mining, embedded text extraction and processing of complex natural language queries. PMID:27538578

  12. Document Exploration and Automatic Knowledge Extraction for Unstructured Biomedical Text

    Science.gov (United States)

    Chu, S.; Totaro, G.; Doshi, N.; Thapar, S.; Mattmann, C. A.; Ramirez, P.

    2015-12-01

    We describe our work on building a web-browser based document reader with built-in exploration tool and automatic concept extraction of medical entities for biomedical text. Vast amounts of biomedical information are offered in unstructured text form through scientific publications and R&D reports. Utilizing text mining can help us to mine information and extract relevant knowledge from a plethora of biomedical text. The ability to employ such technologies to aid researchers in coping with information overload is greatly desirable. In recent years, there has been an increased interest in automatic biomedical concept extraction [1, 2] and intelligent PDF reader tools with the ability to search on content and find related articles [3]. Such reader tools are typically desktop applications and are limited to specific platforms. Our goal is to provide researchers with a simple tool to aid them in finding, reading, and exploring documents. Thus, we propose a web-based document explorer, which we called Shangri-Docs, which combines a document reader with automatic concept extraction and highlighting of relevant terms. Shangri-Docsalso provides the ability to evaluate a wide variety of document formats (e.g. PDF, Words, PPT, text, etc.) and to exploit the linked nature of the Web and personal content by performing searches on content from public sites (e.g. Wikipedia, PubMed) and private cataloged databases simultaneously. Shangri-Docsutilizes Apache cTAKES (clinical Text Analysis and Knowledge Extraction System) [4] and Unified Medical Language System (UMLS) to automatically identify and highlight terms and concepts, such as specific symptoms, diseases, drugs, and anatomical sites, mentioned in the text. cTAKES was originally designed specially to extract information from clinical medical records. Our investigation leads us to extend the automatic knowledge extraction process of cTAKES for biomedical research domain by improving the ontology guided information extraction

  13. Enhancing Biomedical Text Summarization Using Semantic Relation Extraction

    OpenAIRE

    Yue Shang; Yanpeng Li; Hongfei Lin; Zhihao Yang

    2011-01-01

    Automatic text summarization for a biomedical concept can help researchers to get the key points of a certain topic from large amount of biomedical literature efficiently. In this paper, we present a method for generating text summary for a given biomedical concept, e.g., H1N1 disease, from multiple documents based on semantic relation extraction. Our approach includes three stages: 1) We extract semantic relations in each sentence using the semantic knowledge representation tool SemRep. 2) W...

  14. Combining C-value and Keyword Extraction Methods for Biomedical Terms Extraction

    OpenAIRE

    Lossio-Ventura, Juan Antonio; Jonquet, Clement; Roche, Mathieu; Teisseire, Maguelonne

    2013-01-01

    The objective of this work is to extract and to rank biomedical terms from free text. We present new extraction methods that use linguistic patterns specialized for the biomedical field, and use term extraction measures, such as C-value, and keyword extraction measures, such as Okapi BM25, and TFIDF. We propose several combinations of these measures to improve the extraction and ranking process. Our experiments show that an appropriate harmonic mean of C-value used with keyword extraction mea...

  15. Electromembrane extraction for pharmaceutical and biomedical analysis

    DEFF Research Database (Denmark)

    Huang, Chuixiu; Seip, Knut Fredrik; Gjelstad, Astrid;

    2015-01-01

    present paper discusses recent development of EME. The paper focuses on the principles of EME, and discusses how to optimize operational parameters. In addition, pharmaceutical and biomedical applications of EME are reviewed, with emphasis on basic drugs, acidic drugs, amino acids, and peptides. Finally...

  16. DeTEXT: A Database for Evaluating Text Extraction from Biomedical Literature Figures.

    Directory of Open Access Journals (Sweden)

    Xu-Cheng Yin

    Full Text Available Hundreds of millions of figures are available in biomedical literature, representing important biomedical experimental evidence. Since text is a rich source of information in figures, automatically extracting such text may assist in the task of mining figure information. A high-quality ground truth standard can greatly facilitate the development of an automated system. This article describes DeTEXT: A database for evaluating text extraction from biomedical literature figures. It is the first publicly available, human-annotated, high quality, and large-scale figure-text dataset with 288 full-text articles, 500 biomedical figures, and 9308 text regions. This article describes how figures were selected from open-access full-text biomedical articles and how annotation guidelines and annotation tools were developed. We also discuss the inter-annotator agreement and the reliability of the annotations. We summarize the statistics of the DeTEXT data and make available evaluation protocols for DeTEXT. Finally we lay out challenges we observed in the automated detection and recognition of figure text and discuss research directions in this area. DeTEXT is publicly available for downloading at http://prir.ustb.edu.cn/DeTEXT/.

  17. An unsupervised text mining method for relation extraction from biomedical literature.

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    Changqin Quan

    Full Text Available The wealth of interaction information provided in biomedical articles motivated the implementation of text mining approaches to automatically extract biomedical relations. This paper presents an unsupervised method based on pattern clustering and sentence parsing to deal with biomedical relation extraction. Pattern clustering algorithm is based on Polynomial Kernel method, which identifies interaction words from unlabeled data; these interaction words are then used in relation extraction between entity pairs. Dependency parsing and phrase structure parsing are combined for relation extraction. Based on the semi-supervised KNN algorithm, we extend the proposed unsupervised approach to a semi-supervised approach by combining pattern clustering, dependency parsing and phrase structure parsing rules. We evaluated the approaches on two different tasks: (1 Protein-protein interactions extraction, and (2 Gene-suicide association extraction. The evaluation of task (1 on the benchmark dataset (AImed corpus showed that our proposed unsupervised approach outperformed three supervised methods. The three supervised methods are rule based, SVM based, and Kernel based separately. The proposed semi-supervised approach is superior to the existing semi-supervised methods. The evaluation on gene-suicide association extraction on a smaller dataset from Genetic Association Database and a larger dataset from publicly available PubMed showed that the proposed unsupervised and semi-supervised methods achieved much higher F-scores than co-occurrence based method.

  18. BRONCO: Biomedical entity Relation ONcology COrpus for extracting gene-variant-disease-drug relations

    Science.gov (United States)

    Lee, Kyubum; Lee, Sunwon; Park, Sungjoon; Kim, Sunkyu; Kim, Suhkyung; Choi, Kwanghun; Tan, Aik Choon; Kang, Jaewoo

    2016-01-01

    Comprehensive knowledge of genomic variants in a biological context is key for precision medicine. As next-generation sequencing technologies improve, the amount of literature containing genomic variant data, such as new functions or related phenotypes, rapidly increases. Because numerous articles are published every day, it is almost impossible to manually curate all the variant information from the literature. Many researchers focus on creating an improved automated biomedical natural language processing (BioNLP) method that extracts useful variants and their functional information from the literature. However, there is no gold-standard data set that contains texts annotated with variants and their related functions. To overcome these limitations, we introduce a Biomedical entity Relation ONcology COrpus (BRONCO) that contains more than 400 variants and their relations with genes, diseases, drugs and cell lines in the context of cancer and anti-tumor drug screening research. The variants and their relations were manually extracted from 108 full-text articles. BRONCO can be utilized to evaluate and train new methods used for extracting biomedical entity relations from full-text publications, and thus be a valuable resource to the biomedical text mining research community. Using BRONCO, we quantitatively and qualitatively evaluated the performance of three state-of-the-art BioNLP methods. We also identified their shortcomings, and suggested remedies for each method. We implemented post-processing modules for the three BioNLP methods, which improved their performance. Database URL: http://infos.korea.ac.kr/bronco PMID:27074804

  19. BRONCO: Biomedical entity Relation ONcology COrpus for extracting gene-variant-disease-drug relations.

    Science.gov (United States)

    Lee, Kyubum; Lee, Sunwon; Park, Sungjoon; Kim, Sunkyu; Kim, Suhkyung; Choi, Kwanghun; Tan, Aik Choon; Kang, Jaewoo

    2016-01-01

    Comprehensive knowledge of genomic variants in a biological context is key for precision medicine. As next-generation sequencing technologies improve, the amount of literature containing genomic variant data, such as new functions or related phenotypes, rapidly increases. Because numerous articles are published every day, it is almost impossible to manually curate all the variant information from the literature. Many researchers focus on creating an improved automated biomedical natural language processing (BioNLP) method that extracts useful variants and their functional information from the literature. However, there is no gold-standard data set that contains texts annotated with variants and their related functions. To overcome these limitations, we introduce a Biomedical entity Relation ONcology COrpus (BRONCO) that contains more than 400 variants and their relations with genes, diseases, drugs and cell lines in the context of cancer and anti-tumor drug screening research. The variants and their relations were manually extracted from 108 full-text articles. BRONCO can be utilized to evaluate and train new methods used for extracting biomedical entity relations from full-text publications, and thus be a valuable resource to the biomedical text mining research community. Using BRONCO, we quantitatively and qualitatively evaluated the performance of three state-of-the-art BioNLP methods. We also identified their shortcomings, and suggested remedies for each method. We implemented post-processing modules for the three BioNLP methods, which improved their performance.Database URL:http://infos.korea.ac.kr/bronco. PMID:27074804

  20. Information extraction system

    Science.gov (United States)

    Lemmond, Tracy D; Hanley, William G; Guensche, Joseph Wendell; Perry, Nathan C; Nitao, John J; Kidwell, Paul Brandon; Boakye, Kofi Agyeman; Glaser, Ron E; Prenger, Ryan James

    2014-05-13

    An information extraction system and methods of operating the system are provided. In particular, an information extraction system for performing meta-extraction of named entities of people, organizations, and locations as well as relationships and events from text documents are described herein.

  1. BelSmile: a biomedical semantic role labeling approach for extracting biological expression language from text.

    Science.gov (United States)

    Lai, Po-Ting; Lo, Yu-Yan; Huang, Ming-Siang; Hsiao, Yu-Cheng; Tsai, Richard Tzong-Han

    2016-01-01

    Biological expression language (BEL) is one of the most popular languages to represent the causal and correlative relationships among biological events. Automatically extracting and representing biomedical events using BEL can help biologists quickly survey and understand relevant literature. Recently, many researchers have shown interest in biomedical event extraction. However, the task is still a challenge for current systems because of the complexity of integrating different information extraction tasks such as named entity recognition (NER), named entity normalization (NEN) and relation extraction into a single system. In this study, we introduce our BelSmile system, which uses a semantic-role-labeling (SRL)-based approach to extract the NEs and events for BEL statements. BelSmile combines our previous NER, NEN and SRL systems. We evaluate BelSmile using the BioCreative V BEL task dataset. Our system achieved an F-score of 27.8%, ∼7% higher than the top BioCreative V system. The three main contributions of this study are (i) an effective pipeline approach to extract BEL statements, and (ii) a syntactic-based labeler to extract subject-verb-object tuples. We also implement a web-based version of BelSmile (iii) that is publicly available at iisrserv.csie.ncu.edu.tw/belsmile. PMID:27173520

  2. BelSmile: a biomedical semantic role labeling approach for extracting biological expression language from text

    Science.gov (United States)

    Lai, Po-Ting; Lo, Yu-Yan; Huang, Ming-Siang; Hsiao, Yu-Cheng; Tsai, Richard Tzong-Han

    2016-01-01

    Biological expression language (BEL) is one of the most popular languages to represent the causal and correlative relationships among biological events. Automatically extracting and representing biomedical events using BEL can help biologists quickly survey and understand relevant literature. Recently, many researchers have shown interest in biomedical event extraction. However, the task is still a challenge for current systems because of the complexity of integrating different information extraction tasks such as named entity recognition (NER), named entity normalization (NEN) and relation extraction into a single system. In this study, we introduce our BelSmile system, which uses a semantic-role-labeling (SRL)-based approach to extract the NEs and events for BEL statements. BelSmile combines our previous NER, NEN and SRL systems. We evaluate BelSmile using the BioCreative V BEL task dataset. Our system achieved an F-score of 27.8%, ∼7% higher than the top BioCreative V system. The three main contributions of this study are (i) an effective pipeline approach to extract BEL statements, and (ii) a syntactic-based labeler to extract subject–verb–object tuples. We also implement a web-based version of BelSmile (iii) that is publicly available at iisrserv.csie.ncu.edu.tw/belsmile. PMID:27173520

  3. Electromembrane extraction for pharmaceutical and biomedical analysis - Quo vadis.

    Science.gov (United States)

    Huang, Chuixiu; Seip, Knut Fredrik; Gjelstad, Astrid; Pedersen-Bjergaard, Stig

    2015-09-10

    Electromembrane extraction (EME) was presented as a new microextraction concept in 2006, and since the introduction, substantial research has been conducted to develop this concept in different areas of analytical chemistry. To date, more than 100 research papers have been published on EME. The present paper discusses recent development of EME. The paper focuses on the principles of EME, and discusses how to optimize operational parameters. In addition, pharmaceutical and biomedical applications of EME are reviewed, with emphasis on basic drugs, acidic drugs, amino acids, and peptides. Finally, pros and cons of EME are discussed and future directions for EME are identified. Compared with other reviews focused on EME, the authors have especially highlighted their personal views about the most promising directions for the future, and identified the areas where more fundamental work is required. PMID:25669728

  4. Classifying and identifying servers for biomedical information retrieval.

    OpenAIRE

    Patrick, T. B.; Springer, G K

    1994-01-01

    Useful retrieval of biomedical information from network information sources requires methods for organized access to those information sources. This access must be organized in terms of the information content of information sources and in terms of the discovery of the network location of those information sources. We have developed an approach to providing organized access to information sources based on a scheme of hierarchical classifiers and identifiers of the servers providing access to ...

  5. Biomedical and Environmental Sciences INFORMATION FOR AUTHORS

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    @@ Biomedical and Environmental Sciences, an international journal with emphasis on scientific findings in China, publishes articles dealing with biologic and toxic effects of environmental pollutants on man and other forms of life. The effects may be measured with pharmacological, biochemical, pathological, and immunological techniques. The journal also publishes reports dealing with the entry, transport, and fate of natural and anthropogenic chemicals in the biosphere, and their impact on human health and well-being.Papers describing biochemical, pharmacological, pathological, toxicological and immunological studies of pharmaceuticals (biotechnological products) are also welcome.

  6. Multimedia Information Extraction

    CERN Document Server

    Maybury, Mark T

    2012-01-01

    The advent of increasingly large consumer collections of audio (e.g., iTunes), imagery (e.g., Flickr), and video (e.g., YouTube) is driving a need not only for multimedia retrieval but also information extraction from and across media. Furthermore, industrial and government collections fuel requirements for stock media access, media preservation, broadcast news retrieval, identity management, and video surveillance.  While significant advances have been made in language processing for information extraction from unstructured multilingual text and extraction of objects from imagery and vid

  7. Integration and Querying of Genomic and Proteomic Semantic Annotations for Biomedical Knowledge Extraction.

    Science.gov (United States)

    Masseroli, Marco; Canakoglu, Arif; Ceri, Stefano

    2016-01-01

    Understanding complex biological phenomena involves answering complex biomedical questions on multiple biomolecular information simultaneously, which are expressed through multiple genomic and proteomic semantic annotations scattered in many distributed and heterogeneous data sources; such heterogeneity and dispersion hamper the biologists' ability of asking global queries and performing global evaluations. To overcome this problem, we developed a software architecture to create and maintain a Genomic and Proteomic Knowledge Base (GPKB), which integrates several of the most relevant sources of such dispersed information (including Entrez Gene, UniProt, IntAct, Expasy Enzyme, GO, GOA, BioCyc, KEGG, Reactome, and OMIM). Our solution is general, as it uses a flexible, modular, and multilevel global data schema based on abstraction and generalization of integrated data features, and a set of automatic procedures for easing data integration and maintenance, also when the integrated data sources evolve in data content, structure, and number. These procedures also assure consistency, quality, and provenance tracking of all integrated data, and perform the semantic closure of the hierarchical relationships of the integrated biomedical ontologies. At http://www.bioinformatics.deib.polimi.it/GPKB/, a Web interface allows graphical easy composition of queries, although complex, on the knowledge base, supporting also semantic query expansion and comprehensive explorative search of the integrated data to better sustain biomedical knowledge extraction. PMID:27045824

  8. PIMiner: A web tool for extraction of protein interactions from biomedical literature

    KAUST Repository

    Chowdhary, Rajesh

    2013-01-01

    Information on Protein Interactions (PIs) is valuable for biomedical research, but often lies buried in the scientific literature and cannot be readily retrieved. While much progress has been made over the years in extracting PIs from the literature using computational methods, there is a lack of free, public, user-friendly tools for the discovery of PIs. We developed an online tool for the extraction of PI relationships from PubMed-abstracts, which we name PIMiner. Protein pairs and the words that describe their interactions are reported by PIMiner so that new interactions can be easily detected within text. The interaction likelihood levels are reported too. The option to extract only specific types of interactions is also provided. The PIMiner server can be accessed through a web browser or remotely through a client\\'s command line. PIMiner can process 50,000 PubMed abstracts in approximately 7 min and thus appears suitable for large-scale processing of biological/biomedical literature. Copyright © 2013 Inderscience Enterprises Ltd.

  9. Early progress of the Biomedical Computing Technology Information Center (BCTIC)

    International Nuclear Information System (INIS)

    Through five years of effort by the Society of Nuclear Medicine Computer Committee, the Biomedical Computing Technology Information Center (BCTIC) was established by the Division of Biomedical and Environmental Research (DBER) of the U. S. Energy Research and Development Administration (ERDA) at the Oak Ridge National Laboratory in July of 1975. BCTIC forged ahead into the tasks of designing guidelines and procedures, acquisition and packaging of computer codes, data, and interface designs; building a bibliographic data base; and maintaining a directory of the user community. Important contacts were made with societies and individuals involved in biomedical computing; and BCTIC was publicized through news releases, the BCTIC newsletter (bimonthly, since October, 1975), presentations at meetings, and personal contacts. This paper presents the response BCTIC has received in its initial months, gives a progress report on the developmental phase, and takes a look to the future of BCTIC as a national technology resource in nuclear medicine computing

  10. Popularizing biomedical information on an online health forum

    Directory of Open Access Journals (Sweden)

    Patrizia Anesa

    2015-04-01

    Full Text Available Given the increasing importance assumed by online health forums as a form of doctor-patient communication, this study describes the types of dialogic and polylogic interactions that develop in this type of communicative event, focusing on a corpus of threads drawn from an “Ask a Doctor” forum in the area of cardiology. Adopting a discourse analytical approach, the investigation illustrates how these forums may popularize biomedical knowledge. After describing the shifting conceptualization of popularization, we present a new conceptualization of Web 2.0 popularization which we call “oblique popularization”, as it is indirect, user-generated, dialogic and polylogic, and targeted. In particular, this study characterizes the online health forum as a Web 2.0-style popularization tool. It does so not only because biomedical information communicated to a single inquirer is also available to the whole population, but also because the function of the online forum as a medium of popularization is discursively acknowledged by the participants. The study also explores what explanatory tools (such as definitions, analogies, exemplifications, and generalizations are used by the experts to present complex or technical information. The analysis shows that biomedical information is circulated on a health forum by a complex network of participants, and that e-patients’ posts may also serve as prompters of popularization

  11. Challenges in Managing Information Extraction

    Science.gov (United States)

    Shen, Warren H.

    2009-01-01

    This dissertation studies information extraction (IE), the problem of extracting structured information from unstructured data. Example IE tasks include extracting person names from news articles, product information from e-commerce Web pages, street addresses from emails, and names of emerging music bands from blogs. IE is all increasingly…

  12. Evaluation methods for retrieving information from interferograms of biomedical objects

    Science.gov (United States)

    Podbielska, Halina; Rottenkolber, Matthias

    1996-04-01

    Interferograms in the form of fringe patterns can be produced in two-beam interferometers, holographic or speckle interferometers, in setups realizing moire techniques or in deflectometers. Optical metrology based on the principle of interference can be applied as a testing tool in biomedical research. By analyzing of the fringe pattern images, information about the shape or mechanical behavior of the object under study can be retrieved. Here, some of the techniques for creating fringe pattern images were presented along with methods of analysis. Intensity based analysis as well as methods of phase measurements, are mentioned. Applications of inteferometric methods, especially in the field of experimental orthopedics, endoscopy and ophthalmology are pointed out.

  13. Information-theoretic evaluation for computational biomedical ontologies

    CERN Document Server

    Clark, Wyatt Travis

    2014-01-01

    The development of effective methods for the prediction of ontological annotations is an important goal in computational biology, yet evaluating their performance is difficult due to problems caused by the structure of biomedical ontologies and incomplete annotations of genes. This work proposes an information-theoretic framework to evaluate the performance of computational protein function prediction. A Bayesian network is used, structured according to the underlying ontology, to model the prior probability of a protein's function. The concepts of misinformation and remaining uncertainty are

  14. Information bottleneck based incremental fuzzy clustering for large biomedical data.

    Science.gov (United States)

    Liu, Yongli; Wan, Xing

    2016-08-01

    Incremental fuzzy clustering combines advantages of fuzzy clustering and incremental clustering, and therefore is important in classifying large biomedical literature. Conventional algorithms, suffering from data sparsity and high-dimensionality, often fail to produce reasonable results and may even assign all the objects to a single cluster. In this paper, we propose two incremental algorithms based on information bottleneck, Single-Pass fuzzy c-means (spFCM-IB) and Online fuzzy c-means (oFCM-IB). These two algorithms modify conventional algorithms by considering different weights for each centroid and object and scoring mutual information loss to measure the distance between centroids and objects. spFCM-IB and oFCM-IB are used to group a collection of biomedical text abstracts from Medline database. Experimental results show that clustering performances of our approaches are better than such prominent counterparts as spFCM, spHFCM, oFCM and oHFCM, in terms of accuracy. PMID:27260783

  15. Extracting Biomolecular Interactions Using Semantic Parsing of Biomedical Text

    OpenAIRE

    Garg, Sahil; Galstyan, Aram; Hermjakob, Ulf; Marcu, Daniel

    2015-01-01

    We advance the state of the art in biomolecular interaction extraction with three contributions: (i) We show that deep, Abstract Meaning Representations (AMR) significantly improve the accuracy of a biomolecular interaction extraction system when compared to a baseline that relies solely on surface- and syntax-based features; (ii) In contrast with previous approaches that infer relations on a sentence-by-sentence basis, we expand our framework to enable consistent predictions over sets of sen...

  16. Approximate Grammar for Information Extraction

    OpenAIRE

    Sriram, V; Reddy, B. Ravi Sekar; Sangal, R.

    2003-01-01

    In this paper, we present the concept of Approximate grammar and how it can be used to extract information from a documemt. As the structure of informational strings cannot be defined well in a document, we cannot use the conventional grammar rules to represent the information. Hence, the need arises to design an approximate grammar that can be used effectively to accomplish the task of Information extraction. Approximate grammars are a novel step in this direction. The rules of an approximat...

  17. Extraction of semantic biomedical relations from text using conditional random fields

    Directory of Open Access Journals (Sweden)

    Stetter Martin

    2008-04-01

    Full Text Available Abstract Background The increasing amount of published literature in biomedicine represents an immense source of knowledge, which can only efficiently be accessed by a new generation of automated information extraction tools. Named entity recognition of well-defined objects, such as genes or proteins, has achieved a sufficient level of maturity such that it can form the basis for the next step: the extraction of relations that exist between the recognized entities. Whereas most early work focused on the mere detection of relations, the classification of the type of relation is also of great importance and this is the focus of this work. In this paper we describe an approach that extracts both the existence of a relation and its type. Our work is based on Conditional Random Fields, which have been applied with much success to the task of named entity recognition. Results We benchmark our approach on two different tasks. The first task is the identification of semantic relations between diseases and treatments. The available data set consists of manually annotated PubMed abstracts. The second task is the identification of relations between genes and diseases from a set of concise phrases, so-called GeneRIF (Gene Reference Into Function phrases. In our experimental setting, we do not assume that the entities are given, as is often the case in previous relation extraction work. Rather the extraction of the entities is solved as a subproblem. Compared with other state-of-the-art approaches, we achieve very competitive results on both data sets. To demonstrate the scalability of our solution, we apply our approach to the complete human GeneRIF database. The resulting gene-disease network contains 34758 semantic associations between 4939 genes and 1745 diseases. The gene-disease network is publicly available as a machine-readable RDF graph. Conclusion We extend the framework of Conditional Random Fields towards the annotation of semantic relations from

  18. Extracting useful information from images

    DEFF Research Database (Denmark)

    Kucheryavskiy, Sergey

    2011-01-01

    The paper presents an overview of methods for extracting useful information from digital images. It covers various approaches that utilized different properties of images, like intensity distribution, spatial frequencies content and several others. A few case studies including isotropic and...

  19. Extracting information from noise

    OpenAIRE

    Baptie, Brian

    2010-01-01

    Seismic waves created by sources such as wind, the ocean and human activity propagate inside the Earth all the time. Such waves are often regarded as ‘noise’ by seismologists, however, they travel through the Earth in exactly the same way as those waves from earthquakes. Recent advances in theory have shown that ambient noise recorded at two seismic stations can be combined to provide information about the properties of the Earth between the two stations. This is known as seism...

  20. Informed consent among nursing students participating in biomedical research.

    Science.gov (United States)

    Nambiar, Anupama; Christopher, D J; Mammen, Joy; David, Thambu; Kang, Gagandeep; David, Shirley

    2012-01-01

    For consent in biomedical research, it is essential that research participants understand the need for research, the study protocol, the risk and benefits of participation, the freedom to participate or decline and the right to leave the study at any time. A structured questionnaire was used to assess understanding and knowledge among nursing trainees participating in a cohort study investigating exposure and latent tuberculosis at a tertiary care hospital. Data were collected for 138 participants. While 97% were aware of their enrollment into a research protocol, only 78% could state that it was a study on tuberculosis. Approximately two-thirds were aware of plans for blood collection, but not all of them knew the timings or number of samples. The majority (59%) participants had consulted others before making the decision to participate, and only 73% felt that their participation was completely voluntary. Even among healthcare trainees, emphasis needs to be placed on testing both the knowledge and understanding of participants to ensure the principle and practice of truly informed consent. PMID:22864079

  1. MIMI: multimodality, multiresource, information integration environment for biomedical core facilities.

    Science.gov (United States)

    Szymanski, Jacek; Wilson, David L; Zhang, Guo-Qiang

    2009-10-01

    The rapid expansion of biomedical research has brought substantial scientific and administrative data management challenges to modern core facilities. Scientifically, a core facility must be able to manage experimental workflow and the corresponding set of large and complex scientific data. It must also disseminate experimental data to relevant researchers in a secure and expedient manner that facilitates collaboration and provides support for data interpretation and analysis. Administratively, a core facility must be able to manage the scheduling of its equipment and to maintain a flexible and effective billing system to track material, resource, and personnel costs and charge for services to sustain its operation. It must also have the ability to regularly monitor the usage and performance of its equipment and to provide summary statistics on resources spent on different categories of research. To address these informatics challenges, we introduce a comprehensive system called MIMI (multimodality, multiresource, information integration environment) that integrates the administrative and scientific support of a core facility into a single web-based environment. We report the design, development, and deployment experience of a baseline MIMI system at an imaging core facility and discuss the general applicability of such a system in other types of core facilities. These initial results suggest that MIMI will be a unique, cost-effective approach to addressing the informatics infrastructure needs of core facilities and similar research laboratories. PMID:17999114

  2. Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature.

    Science.gov (United States)

    Ozyurt, Ibrahim Burak; Grethe, Jeffrey S; Martone, Maryann E; Bandrowski, Anita E

    2016-01-01

    The NIF Registry developed and maintained by the Neuroscience Information Framework is a cooperative project aimed at cataloging research resources, e.g., software tools, databases and tissue banks, funded largely by governments and available as tools to research scientists. Although originally conceived for neuroscience, the NIF Registry has over the years broadened in the scope to include research resources of general relevance to biomedical research. The current number of research resources listed by the Registry numbers over 13K. The broadening in scope to biomedical science led us to re-christen the NIF Registry platform as SciCrunch. The NIF/SciCrunch Registry has been cataloging the resource landscape since 2006; as such, it serves as a valuable dataset for tracking the breadth, fate and utilization of these resources. Our experience shows research resources like databases are dynamic objects, that can change location and scope over time. Although each record is entered manually and human-curated, the current size of the registry requires tools that can aid in curation efforts to keep content up to date, including when and where such resources are used. To address this challenge, we have developed an open source tool suite, collectively termed RDW: Resource Disambiguator for the (Web). RDW is designed to help in the upkeep and curation of the registry as well as in enhancing the content of the registry by automated extraction of resource candidates from the literature. The RDW toolkit includes a URL extractor from papers, resource candidate screen, resource URL change tracker, resource content change tracker. Curators access these tools via a web based user interface. Several strategies are used to optimize these tools, including supervised and unsupervised learning algorithms as well as statistical text analysis. The complete tool suite is used to enhance and maintain the resource registry as well as track the usage of individual resources through an

  3. Informed consent in dental extractions.

    Directory of Open Access Journals (Sweden)

    José Luis Capote Femenías

    2009-07-01

    Full Text Available When performing any oral intervention, particularly dental extractions, the specialist should have the oral or written consent of the patient. This consent includes the explanation of all possible complications, whether typical, very serious or personalized associated with the previous health condition, age, profession, religion or any other characteristic of the patient, as well as the possi.ble benefits of the intervention. This article is related with the bioethical aspects related with dental extractions, in order to determine the main elements that the informed consent should include.

  4. Proposal for a new LEIR Slow Extraction Scheme dedicated to Biomedical Research

    CERN Document Server

    Garonna, A; Carli, C

    2014-01-01

    This report presents a proposal for a new slow extraction scheme for the Low Energy Ion Ring (LEIR) in the context of the feasibility study for a biomedical research facility at CERN. LEIR has to be maintained as a heavy ion accumulator ring for LHC and for fixed-target experiments with the SPS. In parallel to this on-going operation for physics experiments, an additional secondary use of LEIR for a biomedical research facility was proposed [Dosanjh2013, Holzscheiter2012, PHE2010]. This facility would complement the existing research beam-time available at other laboratories for studies related to ion beam therapy. The new slow extraction [Abler2013] is based on the third-integer resonance. The reference beam is composed of fully stripped carbon ions with extraction energies of 20-440 MeV/u, transverse physical emittances of 5-25 µm and momentum spreads of ±2-9•10-4. Two resonance driving mechanisms have been studied: the quadrupole-driven method and the RF-knockout technique. Both were made compatible...

  5. Organization of Biomedical Data for Collaborative Scientific Research: A Research Information Management System

    OpenAIRE

    Myneni, Sahiti; Patel, Vimla L.

    2010-01-01

    Biomedical researchers often work with massive, detailed and heterogeneous datasets. These datasets raise new challenges of information organization and management for scientific interpretation, as they demand much of the researchers’ time and attention. The current study investigated the nature of the problems that researchers face when dealing with such data. Four major problems identified with existing biomedical scientific information management methods were related to data organization, ...

  6. Information Extraction and Webpage Understanding

    OpenAIRE

    M.Sharmila Begum; L. Dinesh; P.Aruna

    2011-01-01

    The two most important tasks in information extraction from the Web are webpage structure understanding and natural language sentences processing. However, little work has been done toward an integrated statistical model for understanding webpage structures and processing natural language sentences within the HTML elements. Our recent work on webpage understanding introduces a joint model of Hierarchical Conditional Random Fields (HCRFs) and extended Semi-Markov Conditional Random Fields (Sem...

  7. Down syndrome screening information in midwifery practices in the Netherlands: Strategies to integrate biomedical information.

    Science.gov (United States)

    Rosman, Sophia

    2016-03-01

    The aim of this qualitative study was to analyse counselling with regard to prenatal screening in midwifery consultations in the Netherlands where a national prenatal screening programme has only existed since 2007, after years of social and political debates. The methodology is based on in situ observations of 25 counselling consultations in four midwifery practices in two main cities in the Netherlands. The results of this study show that, since midwives are obliged to offer information on Down syndrome screening to all pregnant women (2007), they have to deal with the communication of medical screening information using biostatistical concepts to explain risks, calculations, probabilities and chromosomal anomalies. In order to avoid the risk of medicalization of their consultation, midwives develop strategies that allow them to integrate this new biomedical discourse while maintaining their low medicalized approach of midwife-led care. One of their main strategies is to switch from 'alarming' biomedical messages to 'reassuring words' in order to manage the anxiety induced by the information and to keep the control over their low medicalized consultation. They also tend to distance themselves from the obligation to talk about screening. The way midwives handle these counselling consultations allows them to respect their obligation to propose information, and to remain faithful to their struggle to protect the natural process of pregnancy as well as their professional autonomy. PMID:25504473

  8. Information based universal feature extraction

    Science.gov (United States)

    Amiri, Mohammad; Brause, Rüdiger

    2015-02-01

    In many real world image based pattern recognition tasks, the extraction and usage of task-relevant features are the most crucial part of the diagnosis. In the standard approach, they mostly remain task-specific, although humans who perform such a task always use the same image features, trained in early childhood. It seems that universal feature sets exist, but they are not yet systematically found. In our contribution, we tried to find those universal image feature sets that are valuable for most image related tasks. In our approach, we trained a neural network by natural and non-natural images of objects and background, using a Shannon information-based algorithm and learning constraints. The goal was to extract those features that give the most valuable information for classification of visual objects hand-written digits. This will give a good start and performance increase for all other image learning tasks, implementing a transfer learning approach. As result, in our case we found that we could indeed extract features which are valid in all three kinds of tasks.

  9. Web-Based Information Extraction Technology

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Information extraction techniques on the Web are the current research hotspot. Now many information extraction techniques based on different principles have appeared and have different capabilities. We classify the existing information extraction techniques by the principle of information extraction and analyze the methods and principles of semantic information adding, schema defining,rule expression, semantic items locating and object locating in the approaches. Based on the above survey and analysis,several open problems are discussed.

  10. Personalized Web Services for Web Information Extraction

    OpenAIRE

    Jarir, Zahi; Quafafou, Mohamed; Erradi, Mahammed

    2011-01-01

    The field of information extraction from the Web emerged with the growth of the Web and the multiplication of online data sources. This paper is an analysis of information extraction methods. It presents a service oriented approach for web information extraction considering both web data management and extraction services. Then we propose an SOA based architecture to enhance flexibility and on-the-fly modification of web extraction services. An implementation of the proposed architecture is p...

  11. A Computer Based Biomedical Information System. I. Logic Foundation and Techniques

    Science.gov (United States)

    Syner, James C.

    A digital computer based biomedical information system was designed to service the needs of physicians engaged in patient care and clinical research, and scientists engaged in laboratory research. The system embraces all functions of information processing which include information collection, storage, retrieval, analyses and display. The…

  12. TAKES: Two-step Approach for Knowledge Extraction in Biomedical Digital Libraries

    Directory of Open Access Journals (Sweden)

    Song, Min

    2014-03-01

    Full Text Available This paper proposes a novel knowledge extraction system, TAKES (Two-step Approach for Knowledge Extraction System, which integrates advanced techniques from Information Retrieval (IR, Information Extraction (IE, and Natural Language Processing (NLP. In particular, TAKES adopts a novel keyphrase extraction-based query expansion technique to collect promising documents. It also uses a Conditional Random Field-based machine learning technique to extract important biological entities and relations. TAKES is applied to biological knowledge extraction, particularly retrieving promising documents that contain Protein-Protein Interaction (PPI and extracting PPI pairs. TAKES consists of two major components: DocSpotter, which is used to query and retrieve promising documents for extraction, and a Conditional Random Field (CRF-based entity extraction component known as FCRF. The present paper investigated research problems addressing the issues with a knowledge extraction system and conducted a series of experiments to test our hypotheses. The findings from the experiments are as follows: First, the author verified, using three different test collections to measure the performance of our query expansion technique, that DocSpotter is robust and highly accurate when compared to Okapi BM25 and SLIPPER. Second, the author verified that our relation extraction algorithm, FCRF, is highly accurate in terms of F-Measure compared to four other competitive extraction algorithms: Support Vector Machine, Maximum Entropy, Single POS HMM, and Rapier.

  13. Information Extraction and Webpage Understanding

    Directory of Open Access Journals (Sweden)

    M.Sharmila Begum

    2011-11-01

    Full Text Available The two most important tasks in information extraction from the Web are webpage structure understanding and natural language sentences processing. However, little work has been done toward an integrated statistical model for understanding webpage structures and processing natural language sentences within the HTML elements. Our recent work on webpage understanding introduces a joint model of Hierarchical Conditional Random Fields (HCRFs and extended Semi-Markov Conditional Random Fields (Semi-CRFs to leverage the page structure understanding results in free text segmentation and labeling. In this top-down integration model, the decision of the HCRF model could guide the decision making of the Semi-CRF model. However, the drawback of the topdown integration strategy is also apparent, i.e., the decision of the Semi-CRF model could not be used by the HCRF model to guide its decision making. This paper proposed a novel framework called WebNLP, which enables bidirectional integration of page structure understanding and text understanding in an iterative manner. We have applied the proposed framework to local business entity extraction and Chinese person and organization name extraction. Experiments show that the WebNLP framework achieved significantly better performance than existing methods.

  14. A Semantics-Based Approach to Retrieving Biomedical Information

    DEFF Research Database (Denmark)

    Andreasen, Troels; Bulskov, Henrik; Zambach, Sine;

    2011-01-01

    This paper describes an approach to representing, organising, and accessing conceptual content of biomedical texts using a formal ontology. The ontology is based on UMLS resources supplemented with domain ontologies developed in the project. The approach introduces the notion of ‘generative ontol...... data mining of texts identifying paraphrases and concept relations and measuring distances between key concepts in texts. Thus, the project is distinct in its attempt to provide a formal underpinning of conceptual similarity or relatedness of meaning.......This paper describes an approach to representing, organising, and accessing conceptual content of biomedical texts using a formal ontology. The ontology is based on UMLS resources supplemented with domain ontologies developed in the project. The approach introduces the notion of ‘generative...... ontologies’, i.e., ontologies providing increasingly specialised concepts reflecting the phrase structure of natural language. Furthermore, we propose a novel so called ontological semantics which maps noun phrases from texts and queries into nodes in the generative ontology. This enables an advanced form of...

  15. Generic information can retrieve known biological associations: implications for biomedical knowledge discovery.

    Directory of Open Access Journals (Sweden)

    Herman H H B M van Haagen

    Full Text Available MOTIVATION: Weighted semantic networks built from text-mined literature can be used to retrieve known protein-protein or gene-disease associations, and have been shown to anticipate associations years before they are explicitly stated in the literature. Our text-mining system recognizes over 640,000 biomedical concepts: some are specific (i.e., names of genes or proteins others generic (e.g., 'Homo sapiens'. Generic concepts may play important roles in automated information retrieval, extraction, and inference but may also result in concept overload and confound retrieval and reasoning with low-relevance or even spurious links. Here, we attempted to optimize the retrieval performance for protein-protein interactions (PPI by filtering generic concepts (node filtering or links to generic concepts (edge filtering from a weighted semantic network. First, we defined metrics based on network properties that quantify the specificity of concepts. Then using these metrics, we systematically filtered generic information from the network while monitoring retrieval performance of known protein-protein interactions. We also systematically filtered specific information from the network (inverse filtering, and assessed the retrieval performance of networks composed of generic information alone. RESULTS: Filtering generic or specific information induced a two-phase response in retrieval performance: initially the effects of filtering were minimal but beyond a critical threshold network performance suddenly drops. Contrary to expectations, networks composed exclusively of generic information demonstrated retrieval performance comparable to unfiltered networks that also contain specific concepts. Furthermore, an analysis using individual generic concepts demonstrated that they can effectively support the retrieval of known protein-protein interactions. For instance the concept "binding" is indicative for PPI retrieval and the concept "mutation abnormality" is

  16. Strategies for Disseminating Information on Biomedical Research on Autism to Hispanic Parents

    Science.gov (United States)

    Lajonchere, Clara M.; Wheeler, Barbara Y.; Valente, Thomas W.; Kreutzer, Cary; Munson, Aron; Narayanan, Shrikanth; Kazemzadeh, Abe; Cruz, Roxana; Martinez, Irene; Schrager, Sheree M.; Schweitzer, Lisa; Chklovski, Tara; Hwang, Darryl

    2016-01-01

    Low income Hispanic families experience multiple barriers to accessing evidence-based information on Autism Spectrum Disorders (ASD). This study utilized a mixed-strategy intervention to create access to information in published bio-medical research articles on ASD by distilling the content into parent-friendly English- and Spanish-language ASD…

  17. Extracting information from multiplex networks

    Science.gov (United States)

    Iacovacci, Jacopo; Bianconi, Ginestra

    2016-06-01

    Multiplex networks are generalized network structures that are able to describe networks in which the same set of nodes are connected by links that have different connotations. Multiplex networks are ubiquitous since they describe social, financial, engineering, and biological networks as well. Extending our ability to analyze complex networks to multiplex network structures increases greatly the level of information that is possible to extract from big data. For these reasons, characterizing the centrality of nodes in multiplex networks and finding new ways to solve challenging inference problems defined on multiplex networks are fundamental questions of network science. In this paper, we discuss the relevance of the Multiplex PageRank algorithm for measuring the centrality of nodes in multilayer networks and we characterize the utility of the recently introduced indicator function Θ ˜ S for describing their mesoscale organization and community structure. As working examples for studying these measures, we consider three multiplex network datasets coming for social science.

  18. Extracting Information from Multiplex Networks

    CERN Document Server

    Iacovacci, Jacopo

    2016-01-01

    Multiplex networks are generalized network structures that are able to describe networks in which the same set of nodes are connected by links that have different connotations. Multiplex networks are ubiquitous since they describe social, financial, engineering and biological networks as well. Extending our ability to analyze complex networks to multiplex network structures increases greatly the level of information that is possible to extract from Big Data. For these reasons characterizing the centrality of nodes in multiplex networks and finding new ways to solve challenging inference problems defined on multiplex networks are fundamental questions of network science. In this paper we discuss the relevance of the Multiplex PageRank algorithm for measuring the centrality of nodes in multilayer networks and we characterize the utility of the recently introduced indicator function $\\widetilde{\\Theta}^{S}$ for describing their mesoscale organization and community structure. As working examples for studying thes...

  19. Biomedical Information Extraction: Mining Disease Associated Genes from Literature

    Science.gov (United States)

    Huang, Zhong

    2014-01-01

    Disease associated gene discovery is a critical step to realize the future of personalized medicine. However empirical and clinical validation of disease associated genes are time consuming and expensive. In silico discovery of disease associated genes from literature is therefore becoming the first essential step for biomarker discovery to…

  20. An integrated biomedical knowledge extraction and analysis platform: using federated search and document clustering technology.

    Science.gov (United States)

    Taylor, Donald P

    2007-01-01

    High content screening (HCS) requires time-consuming and often complex iterative information retrieval and assessment approaches to optimally conduct drug discovery programs and biomedical research. Pre- and post-HCS experimentation both require the retrieval of information from public as well as proprietary literature in addition to structured information assets such as compound libraries and projects databases. Unfortunately, this information is typically scattered across a plethora of proprietary bioinformatics tools and databases and public domain sources. Consequently, single search requests must be presented to each information repository, forcing the results to be manually integrated for a meaningful result set. Furthermore, these bioinformatics tools and data repositories are becoming increasingly complex to use; typically they fail to allow for more natural query interfaces. Vivisimo has developed an enterprise software platform to bridge disparate silos of information. The platform automatically categorizes search results into descriptive folders without the use of taxonomies to drive the categorization. A new approach to information retrieval for HCS experimentation is proposed. PMID:16988412

  1. Use of systematic review to inform the infection risk for biomedical engineers and technicians servicing biomedical devices

    International Nuclear Information System (INIS)

    Full text: Many microorganisms responsible for hospital acquired infections are able to stay viable on surfaces with no visible sign of contamination, in dry conditions and on non-porous surfaces. The infection risk to biomedical staff when servicing biomedical devices is not documented. An indirect approach has been used to examine the different aspects that will affect the risk of infection including a systematic review of microbial contamination and transmission relating to biomedical devices. A systematic review found 58% of biomedical devices have microbial contamination with 13% having at least one pathogenic organism. These microbes can persist for some months. Occupational-infections of biomedical service staff are low compared to other healthcare workers. A biomedical device with contaminated surface or dust was identified as the source of patient outbreaks in 13 papers. The cleaning agent most tested for removal of micro-organisms from devices was alcohol swabs, but sterile water swabs were also effective. However, manufacturers mainly recommend (74%) cleaning devices with water and detergent. Biomedical engineers and technicians have a small risk of being exposed to dangerous micro-organisms on most biomedical devices, but without skin breakage, this exposure is unlikely to cause ill-health. It is recommended that biomedical staff follow good infection control practices, wipe devices with detergent, sterile water or alcohol swabs as recommended by the manufacturer before working on them, and keep alcohol hand rubs accessible at all benches. (author)

  2. Biosynthesis of silver nanoparticle from leaf extract of Desmodium gangeticum (L.) DC. and its biomedical potential

    Science.gov (United States)

    Thirunavoukkarasu, M.; Balaji, U.; Behera, S.; Panda, P. K.; Mishra, B. K.

    2013-12-01

    An aqueous leaf extract of Desmodium gangeticum was employed to synthesize silver nano particles. Rapid formation of stable silver nanoparticles were observed on exposure of the aqueous leaf extract with solution of silver nitrate. The silver nanoparticles were characterized by UV-visible spectroscopy, scanning electron microscopy, energy dispersive X-ray analysis and transmission electron microscopy (TEM), and Fourier Transform Infra-Red spectroscopy (FTIR) UV-visible spectroscopy, scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDAX), transmission electron microscopy (TEM), and Fourier Transform Infra-Red spectroscopy (FTIR). UV-visible spectrum of the aqueous medium peaked at 450 nm corresponding to the plasmon absorbance of silver nanoparticles. SEM analysis revealed the spherical shape of the particles with sizes ranging from 18 to 39 nm and the EDAX spectrum confirmed the presence of silver along with other elements in the plant metabolite. Further, these biologically synthesized nanoparticles were found to be highly toxic against pathogenic bacteria Escherichia coli, thus implying significance of the present study in production of biomedical products.

  3. Using Hypertext to Facilitate Information Sharing in Biomedical Research Groups

    OpenAIRE

    Chaney, R. Jesse; Shipman, Frank M.; Gorry, G. Anthony

    1989-01-01

    As part of our effort to create an Integrated Academic Information Management System at Baylor College of Medicine, we are developing information technology to support the efforts of scientific work groups. Many of our ideas in this regard are embodied in a system called the Virtual Notebook which is intended to facilitate information sharing and management in such groups. Here we discuss the foundations of that system - a hypertext system that we have developed using a relational data base a...

  4. Ontology-based retrieval of bio-medical information based on microarray text corpora

    DEFF Research Database (Denmark)

    Hansen, Kim Allan; Zambach, Sine; Have, Christian Theil

    Microarray technology is often used in gene expression exper- iments. Information retrieval in the context of microarrays has mainly been concerned with the analysis of the numeric data produced; how- ever, the experiments are often annotated with textual metadata. Al- though biomedical resources...

  5. Chrysopogon zizanioides aqueous extract mediated synthesis, characterization of crystalline silver and gold nanoparticles for biomedical applications.

    Science.gov (United States)

    Arunachalam, Kantha D; Annamalai, Sathesh Kumar

    2013-01-01

    The exploitation of various plant materials for the biosynthesis of nanoparticles is considered a green technology as it does not involve any harmful chemicals. The aim of this study was to develop a simple biological method for the synthesis of silver and gold nanoparticles using Chrysopogon zizanioides. To exploit various plant materials for the biosynthesis of nanoparticles was considered a green technology. An aqueous leaf extract of C. zizanioides was used to synthesize silver and gold nanoparticles by the bioreduction of silver nitrate (AgNO3) and chloroauric acid (HAuCl4) respectively. Water-soluble organics present in the plant materials were mainly responsible for reducing silver or gold ions to nanosized Ag or Au particles. The synthesized silver and gold nanoparticles were characterized by ultraviolet (UV)-visible spectroscopy, scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDAX), Fourier transform infrared spectroscopy (FTIR), and X-ray diffraction (XRD) analysis. The kinetics decline reactions of aqueous silver/gold ion with the C. zizanioides crude extract were determined by UV-visible spectroscopy. SEM analysis showed that aqueous gold ions, when exposed to the extract were reduced and resulted in the biosynthesis of gold nanoparticles in the size range 20-50 nm. This eco-friendly approach for the synthesis of nanoparticles is simple, can be scaled up for large-scale production with powerful bioactivity as demonstrated by the synthesized silver nanoparticles. The synthesized nanoparticles can have clinical use as antibacterial, antioxidant, as well as cytotoxic agents and can be used for biomedical applications. PMID:23861583

  6. Chrysopogon zizanioides aqueous extract mediated synthesis characterization of crystalline silver and gold nanoparticles for biomedical applications

    Directory of Open Access Journals (Sweden)

    Arunachalam KD

    2013-07-01

    Full Text Available Kantha D Arunachalam, Sathesh Kumar Annamalai Center for Environmental Nuclear Research, Directorate of Research, SRM University, Chennai, Tamil Nadu, India Abstract: The exploitation of various plant materials for the biosynthesis of nanoparticles is considered a green technology as it does not involve any harmful chemicals. The aim of this study was to develop a simple biological method for the synthesis of silver and gold nanoparticles using Chrysopogon zizanioides. To exploit various plant materials for the biosynthesis of nanoparticles was considered a green technology. An aqueous leaf extract of C. zizanioides was used to synthesize silver and gold nanoparticles by the bioreduction of silver nitrate (AgNO3 and chloroauric acid (HAuCl4 respectively. Water-soluble organics present in the plant materials were mainly responsible for reducing silver or gold ions to nanosized Ag or Au particles. The synthesized silver and gold nanoparticles were characterized by ultraviolet (UV-visible spectroscopy, scanning electron microscopy (SEM, energy dispersive X-ray analysis (EDAX, Fourier transform infrared spectroscopy (FTIR, and X-ray diffraction (XRD analysis. The kinetics decline reactions of aqueous silver/gold ion with the C. zizanioides crude extract were determined by UV-visible spectroscopy. SEM analysis showed that aqueous gold ions, when exposed to the extract were reduced and resulted in the biosynthesis of gold nanoparticles in the size range 20–50 nm. This eco-friendly approach for the synthesis of nanoparticles is simple, can be scaled up for large-scale production with powerful bioactivity as demonstrated by the synthesized silver nanoparticles. The synthesized nanoparticles can have clinical use as antibacterial, antioxidant, as well as cytotoxic agents and can be used for biomedical applications. Keywords: nanoparticles, bioreduction, SEM, silver, gold

  7. Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation.

    Science.gov (United States)

    Huang, Chung-Chi; Lu, Zhiyong

    2016-01-01

    Identifying relevant papers from the literature is a common task in biocuration. Most current biomedical literature search systems primarily rely on matching user keywords. Semantic search, on the other hand, seeks to improve search accuracy by understanding the entities and contextual relations in user keywords. However, past research has mostly focused on semantically identifying biological entities (e.g. chemicals, diseases and genes) with little effort on discovering semantic relations. In this work, we aim to discover biomedical semantic relations in PubMed queries in an automated and unsupervised fashion. Specifically, we focus on extracting and understanding the contextual information (or context patterns) that is used by PubMed users to represent semantic relations between entities such as 'CHEMICAL-1 compared to CHEMICAL-2' With the advances in automatic named entity recognition, we first tag entities in PubMed queries and then use tagged entities as knowledge to recognize pattern semantics. More specifically, we transform PubMed queries into context patterns involving participating entities, which are subsequently projected to latent topics via latent semantic analysis (LSA) to avoid the data sparseness and specificity issues. Finally, we mine semantically similar contextual patterns or semantic relations based on LSA topic distributions. Our two separate evaluation experiments of chemical-chemical (CC) and chemical-disease (CD) relations show that the proposed approach significantly outperforms a baseline method, which simply measures pattern semantics by similarity in participating entities. The highest performance achieved by our approach is nearly 0.9 and 0.85 respectively for the CC and CD task when compared against the ground truth in terms of normalized discounted cumulative gain (nDCG), a standard measure of ranking quality. These results suggest that our approach can effectively identify and return related semantic patterns in a ranked order

  8. [Biomedical information on the internet using search engines. A one-year trial].

    Science.gov (United States)

    Corrao, Salvatore; Leone, Francesco; Arnone, Sabrina

    2004-01-01

    The internet is a communication medium and content distributor that provide information in the general sense but it could be of great utility regarding as the search and retrieval of biomedical information. Search engines represent a great deal to rapidly find information on the net. However, we do not know whether general search engines and meta-search ones are reliable in order to find useful and validated biomedical information. The aim of our study was to verify the reproducibility of a search by key-words (pediatric or evidence) using 9 international search engines and 1 meta-search engine at the baseline and after a one year period. We analysed the first 20 citations as output of each searching. We evaluated the formal quality of Web-sites and their domain extensions. Moreover, we compared the output of each search at the start of this study and after a one year period and we considered as a criterion of reliability the number of Web-sites cited again. We found some interesting results that are reported throughout the text. Our findings point out an extreme dynamicity of the information on the Web and, for this reason, we advice a great caution when someone want to use search and meta-search engines as a tool for searching and retrieve reliable biomedical information. On the other hand, some search and meta-search engines could be very useful as a first step searching for defining better a search and, moreover, for finding institutional Web-sites too. This paper allows to know a more conscious approach to the internet biomedical information universe. PMID:15032337

  9. Strategies for Disseminating Information on Biomedical Research on Autism to Hispanic Parents.

    Science.gov (United States)

    Lajonchere, Clara M; Wheeler, Barbara Y; Valente, Thomas W; Kreutzer, Cary; Munson, Aron; Narayanan, Shrikanth; Kazemzadeh, Abe; Cruz, Roxana; Martinez, Irene; Schrager, Sheree M; Schweitzer, Lisa; Chklovski, Tara; Hwang, Darryl

    2016-03-01

    Low income Hispanic families experience multiple barriers to accessing evidence-based information on Autism Spectrum Disorders (ASD). This study utilized a mixed-strategy intervention to create access to information in published bio-medical research articles on ASD by distilling the content into parent-friendly English- and Spanish-language ASD Science Briefs and presenting them to participants using two socially-oriented dissemination methods. There was a main effect for short-term knowledge gains associated with the Science Briefs but no effect for the dissemination method. After 5 months, participants reported utilizing the information learned and 90 % wanted to read more Science Briefs. These preliminary findings highlight the potential benefits of distilling biomedical research articles on ASD into parent-friendly educational products for currently underserved Hispanic parents. PMID:26563948

  10. Organization of Biomedical Data for Collaborative Scientific Research: A Research Information Management System

    Science.gov (United States)

    Myneni, Sahiti; Patel, Vimla L.

    2010-01-01

    Biomedical researchers often work with massive, detailed and heterogeneous datasets. These datasets raise new challenges of information organization and management for scientific interpretation, as they demand much of the researchers’ time and attention. The current study investigated the nature of the problems that researchers face when dealing with such data. Four major problems identified with existing biomedical scientific information management methods were related to data organization, data sharing, collaboration, and publications. Therefore, there is a compelling need to develop an efficient and user-friendly information management system to handle the biomedical research data. This study evaluated the implementation of an information management system, which was introduced as part of the collaborative research to increase scientific productivity in a research laboratory. Laboratory members seemed to exhibit frustration during the implementation process. However, empirical findings revealed that they gained new knowledge and completed specified tasks while working together with the new system. Hence, researchers are urged to persist and persevere when dealing with any new technology, including an information management system in a research laboratory environment. PMID:20543892

  11. Automated Extraction Of Associations Between Methylated Genes and Diseases From Biomedical Literature

    KAUST Repository

    Bin Res, Arwa A.

    2012-12-01

    Associations between methylated genes and diseases have been investigated in several studies, and it is critical to have such information available for better understanding of diseases and clinical decisions. However, such information is scattered in a large number of electronic publications and it is difficult to manually search for it. Therefore, the goal of the project is to develop a machine learning model that can efficiently extract such information. Twelve machine learning algorithms were applied and compared in application to this problem based on three approaches that involve: document-term frequency matrices, position weight matrices, and a hybrid approach that uses the combination of the previous two. The best results we obtained by the hybrid approach with a random forest model that, in a 10-fold cross-validation, achieved F-score and accuracy of nearly 85% and 84%, respectively. On a completely separate testing set, F-score and accuracy of 89% and 88%, respectively, were obtained. Based on this model, we developed a tool that automates extraction of associations between methylated genes and diseases from electronic text. Our study contributed an efficient method for extracting specific types of associations from free text and the methodology developed here can be extended to other similar association extraction problems.

  12. Method for Detecting Core Malware Sites Related to Biomedical Information Systems

    Directory of Open Access Journals (Sweden)

    Dohoon Kim

    2015-01-01

    Full Text Available Most advanced persistent threat attacks target web users through malicious code within landing (exploit or distribution sites. There is an urgent need to block the affected websites. Attacks on biomedical information systems are no exception to this issue. In this paper, we present a method for locating malicious websites that attempt to attack biomedical information systems. Our approach uses malicious code crawling to rearrange websites in the order of their risk index by analyzing the centrality between malware sites and proactively eliminates the root of these sites by finding the core-hub node, thereby reducing unnecessary security policies. In particular, we dynamically estimate the risk index of the affected websites by analyzing various centrality measures and converting them into a single quantified vector. On average, the proactive elimination of core malicious websites results in an average improvement in zero-day attack detection of more than 20%.

  13. Method for detecting core malware sites related to biomedical information systems.

    Science.gov (United States)

    Kim, Dohoon; Choi, Donghee; Jin, Jonghyun

    2015-01-01

    Most advanced persistent threat attacks target web users through malicious code within landing (exploit) or distribution sites. There is an urgent need to block the affected websites. Attacks on biomedical information systems are no exception to this issue. In this paper, we present a method for locating malicious websites that attempt to attack biomedical information systems. Our approach uses malicious code crawling to rearrange websites in the order of their risk index by analyzing the centrality between malware sites and proactively eliminates the root of these sites by finding the core-hub node, thereby reducing unnecessary security policies. In particular, we dynamically estimate the risk index of the affected websites by analyzing various centrality measures and converting them into a single quantified vector. On average, the proactive elimination of core malicious websites results in an average improvement in zero-day attack detection of more than 20%. PMID:25821511

  14. A System for Information Management in BioMedical Studies—SIMBioMS

    Science.gov (United States)

    Krestyaninova, Maria; Zarins, Andris; Viksna, Juris; Kurbatova, Natalja; Rucevskis, Peteris; Neogi, Sudeshna Guha; Gostev, Mike; Perheentupa, Teemu; Knuuttila, Juha; Barrett, Amy; Lappalainen, Ilkka; Rung, Johan; Podnieks, Karlis; Sarkans, Ugis; McCarthy, Mark I; Brazma, Alvis

    2009-01-01

    Summary: SIMBioMS is a web-based open source software system for managing data and information in biomedical studies. It provides a solution for the collection, storage, management and retrieval of information about research subjects and biomedical samples, as well as experimental data obtained using a range of high-throughput technologies, including gene expression, genotyping, proteomics and metabonomics. The system can easily be customized and has proven to be successful in several large-scale multi-site collaborative projects. It is compatible with emerging functional genomics data standards and provides data import and export in accepted standard formats. Protocols for transferring data to durable archives at the European Bioinformatics Institute have been implemented. Availability: The source code, documentation and initialization scripts are available at http://simbioms.org. Contact: support@simbioms.org; mariak@ebi.ac.uk PMID:19633095

  15. The Biomedical Computing Technology Information Center. An international resource for technology sharing

    International Nuclear Information System (INIS)

    The expense of developing and maintaining special software and interfaces has been prohibitive to many clinical installations desiring to perform computer-assisted studies. Also, existing developmental groups have been economically unable to adequately transfer their work to such smaller installations. In response to this need and through the efforts of the Society of Nuclear Medicine Computer Committee, the US Energy Research and Development Administration (ERDA) has established the Biomedical Computing Technology Information Center (BCTIC) at the Oak Ridge National Laboratory (ORNL). BCTIC collects, organizes, evaluates and disseminates information on computing technology pertinent to biomedicine in general and nuclear medicine in particular, providing the needed routes of communication between installations and serving as a clearinghouse for the exchange of biomedical computing software, data and interface designs. BCTIC services are available to its sponsors and their contractors and to any individual or group willing to participate in mutual exchange. (author)

  16. Enhanced Pattern Representation in Information Extraction

    Institute of Scientific and Technical Information of China (English)

    廖乐健; 曹元大; 张映波

    2004-01-01

    Traditional pattern representation in information extraction lack in the ability of representing domain-specific concepts and are therefore devoid of flexibility. To overcome these restrictions, an enhanced pattern representation is designed which includes ontological concepts, neighboring-tree structures and soft constraints. An information-extraction inference engine based on hypothesis-generation and conflict-resolution is implemented. The proposed technique is successfully applied to an information extraction system for Chinese-language query front-end of a job-recruitment search engine.

  17. Information- Theoretic Analysis for the Difficulty of Extracting Hidden Information

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wei-ming; LI Shi-qu; CAO Jia; LIU Jiu-fen

    2005-01-01

    The difficulty of extracting hidden information,which is essentially a kind of secrecy, is analyzed by information-theoretic method. The relations between key rate, message rate, hiding capacity and difficulty of extraction are studied in the terms of unicity distance of stego-key, and the theoretic conclusion is used to analyze the actual extracting attack on Least Significant Bit(LSB) steganographic algorithms.

  18. Implementation and management of a biomedical observation dictionary in a large healthcare information system

    Science.gov (United States)

    Vandenbussche, Pierre-Yves; Cormont, Sylvie; André, Christophe; Daniel, Christel; Delahousse, Jean; Charlet, Jean; Lepage, Eric

    2013-01-01

    Objective This study shows the evolution of a biomedical observation dictionary within the Assistance Publique Hôpitaux Paris (AP-HP), the largest European university hospital group. The different steps are detailed as follows: the dictionary creation, the mapping to logical observation identifier names and codes (LOINC), the integration into a multiterminological management platform and, finally, the implementation in the health information system. Methods AP-HP decided to create a biomedical observation dictionary named AnaBio, to map it to LOINC and to maintain the mapping. A management platform based on methods used for knowledge engineering has been put in place. It aims at integrating AnaBio within the health information system and improving both the quality and stability of the dictionary. Results This new management platform is now active in AP-HP. The AnaBio dictionary is shared by 120 laboratories and currently includes 50 000 codes. The mapping implementation to LOINC reaches 40% of the AnaBio entries and uses 26% of LOINC records. The results of our work validate the choice made to develop a local dictionary aligned with LOINC. Discussion and Conclusions This work constitutes a first step towards a wider use of the platform. The next step will support the entire biomedical production chain, from the clinician prescription, through laboratory tests tracking in the laboratory information system to the communication of results and the use for decision support and biomedical research. In addition, the increase in the mapping implementation to LOINC ensures the interoperability allowing communication with other international health institutions. PMID:23635601

  19. System for Information Extraction from News Sites

    OpenAIRE

    Stefanov, Tihomir

    2015-01-01

    The present paper deals with a system for crawling and content extraction from news sites. The system of web crawlers extracts textual and graphic information and checks for multimedia content availability. A part of the programming code and the database have been presented.

  20. A New Approach for Web Information Extraction

    Directory of Open Access Journals (Sweden)

    R.Gunasundari

    2012-01-01

    Full Text Available With the exponentially growing amount of information available on the Internet, an effective technique for users to discern the useful information from the unnecessary information is urgently required. Cleaning web pages for web data extraction becomes critical for improving performance of information retrieval and information extraction. So, we investigate to remove various noise patterns in Web pages instead of extracting relevant content from Web pages to get main content information. To solve this problem, we put forward an extracting main content method which firstly removes the usual noise and the candidate nodes without any main content information from web pages, and makes use of the relation of content text length, the length of anchor text and the number of punctuation marks to extract the main content. In this paper, we focus on removing noise and utilization of all kinds of content-characteristics, experiments show that this approach can enhance the universality and accuracy in extracting the body text of web pages

  1. Battling the biomedical information explosion: a plan for implementing a quality filtered database.

    Science.gov (United States)

    Moore, M

    1989-01-01

    In 1980 an article appeared in the Archives of Internal Medicine stating that two-thirds of the studies appearing in the best medical journals contain unwarranted conclusions. In order to deal with the ever increasing mass of biomedical information (termed a "journalistic blastoma" by one editor), IAIMS has extolled the use of quality filters, devices to sort through the literature and sift the good from the bad. The complexity of the task is staggering. Quality is obviously subjective, and its nature raises the question of whether our users can be taught the necessary skills to systematically evaluate the literature. This report is based on a research project that grew into an elective course for medical students at Texas Tech University School of Medicine on "Critical Appraisal of the Biomedical Literature." PMID:10303951

  2. Information Extraction From Chemical Patents

    Directory of Open Access Journals (Sweden)

    Sandra Bergmann

    2012-01-01

    Full Text Available The development of new chemicals or pharmaceuticals is preceded by an indepth analysis of published patents in this field. This information retrieval is a costly and time inefficient step when done by a human reader, yet it is mandatory for potential success of an investment. The goal of the research project UIMA-HPC is to automate and hence speed-up the process of knowledge mining about patents. Multi-threaded analysis engines, developed according to UIMA (Unstructured Information Management Architecture standards, process texts and images in thousands of documents in parallel. UNICORE (UNiform Interface to COmputing Resources workflow control structures make it possible to dynamically allocate resources for every given task to gain best cpu-time/realtime ratios in an HPC environment.

  3. Language Engineering for Information Extraction

    OpenAIRE

    Schierle, Martin

    2012-01-01

    Accompanied by the cultural development to an information society and knowledge economy and driven by the rapid growth of the World Wide Web and decreasing prices for technology and disk space, the world\\'s knowledge is evolving fast, and humans are challenged with keeping up. Despite all efforts on data structuring, a large part of this human knowledge is still hidden behind the ambiguities and fuzziness of natural language. Especially domain language poses new challenges by having specif...

  4. Application of GIS to Geological Information Extraction

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    GIS. a powerful tool for processing spatial data, is advantageous in its spatial overlaying. In this paper, GIS is applied to the extraction of geological information. Information associated with mineral resources is chosen to delineate the geo-anomalies, the basis of ore-forming anomalies and of mineral-deposit location. This application is illustrated with an example in Weixi area, Yunnan Province.

  5. Testbed for Information Extraction from Deep Web

    OpenAIRE

    Yamada, Yasuhiro; Nakatoh, Tetsuya; Hirokawa, Sachio

    2004-01-01

    Search results generated by searchable databases are served dynamically and far larger than the static documents on the Web. These results pages have been referred to as the Deep Web [1]. We need to extract the target data in results pages to integrate them on different searchable databases. We propose a testbed for information extraction from search results. We chose 100 databases randomly from 114,540 pages with search forms. Therefore, these databases have a good variety. We selected 51 da...

  6. A sentence sliding window approach to extract protein annotations from biomedical articles

    OpenAIRE

    2005-01-01

    Background Within the emerging field of text mining and statistical natural language processing (NLP) applied to biomedical articles, a broad variety of techniques have been developed during the past years. Nevertheless, there is still a great ned of comparative assessment of the performance of the proposed methods and the development of common evaluation criteria. This issue was addressed by the Critical Assessment of Text Mining Methods in Molecular Biology (BioCreative) contest. The aim of...

  7. Synonym set extraction from the biomedical literature by lexical pattern discovery

    OpenAIRE

    Collier Nigel; McCrae John

    2008-01-01

    Abstract Background Although there are a large number of thesauri for the biomedical domain many of them lack coverage in terms and their variant forms. Automatic thesaurus construction based on patterns was first suggested by Hearst 1, but it is still not clear how to automatically construct such patterns for different semantic relations and domains. In particular it is not certain which patterns are useful for capturing synonymy. The assumption of extant resources such as parsers is also a ...

  8. DKIE: Open Source Information Extraction for Danish

    DEFF Research Database (Denmark)

    Derczynski, Leon; Field, Camilla Vilhelmsen; Bøgh, Kenneth Sejdenfaden

    2014-01-01

    Danish is a major Scandinavian language spoken daily by around six million people. However, it lacks a unified, open set of NLP tools. This demonstration will introduce DKIE, an extensible open-source toolkit for processing Danish text. We implement an information extraction architecture for Danish...

  9. Assessing the impact of case sensitivity and term information gain on biomedical concept recognition.

    Directory of Open Access Journals (Sweden)

    Tudor Groza

    Full Text Available Concept recognition (CR is a foundational task in the biomedical domain. It supports the important process of transforming unstructured resources into structured knowledge. To date, several CR approaches have been proposed, most of which focus on a particular set of biomedical ontologies. Their underlying mechanisms vary from shallow natural language processing and dictionary lookup to specialized machine learning modules. However, no prior approach considers the case sensitivity characteristics and the term distribution of the underlying ontology on the CR process. This article proposes a framework that models the CR process as an information retrieval task in which both case sensitivity and the information gain associated with tokens in lexical representations (e.g., term labels, synonyms are central components of a strategy for generating term variants. The case sensitivity of a given ontology is assessed based on the distribution of so-called case sensitive tokens in its terms, while information gain is modelled using a combination of divergence from randomness and mutual information. An extensive evaluation has been carried out using the CRAFT corpus. Experimental results show that case sensitivity awareness leads to an increase of up to 0.07 F1 against a non-case sensitive baseline on the Protein Ontology and GO Cellular Component. Similarly, the use of information gain leads to an increase of up to 0.06 F1 against a standard baseline in the case of GO Biological Process and Molecular Function and GO Cellular Component. Overall, subject to the underlying token distribution, these methods lead to valid complementary strategies for augmenting term label sets to improve concept recognition.

  10. A service-oriented distributed semantic mediator: integrating multiscale biomedical information.

    Science.gov (United States)

    Mora, Oscar; Engelbrecht, Gerhard; Bisbal, Jesus

    2012-11-01

    Biomedical research continuously generates large amounts of heterogeneous and multimodal data spread over multiple data sources. These data, if appropriately shared and exploited, could dramatically improve the research practice itself, and ultimately the quality of health care delivered. This paper presents DISMED (DIstributed Semantic MEDiator), an open source semantic mediator that provides a unified view of a federated environment of multiscale biomedical data sources. DISMED is a Web-based software application to query and retrieve information distributed over a set of registered data sources, using semantic technologies. It also offers a userfriendly interface specifically designed to simplify the usage of these technologies by non-expert users. Although the architecture of the software mediator is generic and domain independent, in the context of this paper, DISMED has been evaluated for managing biomedical environments and facilitating research with respect to the handling of scientific data distributed in multiple heterogeneous data sources. As part of this contribution, a quantitative evaluation framework has been developed. It consist of a benchmarking scenario and the definition of five realistic use-cases. This framework, created entirely with public datasets, has been used to compare the performance of DISMED against other available mediators. It is also available to the scientific community in order to evaluate progress in the domain of semantic mediation, in a systematic and comparable manner. The results show an average improvement in the execution time by DISMED of 55% compared to the second best alternative in four out of the five use-cases of the experimental evaluation. PMID:22929464

  11. Information extraction and CT reconstruction of liver images based on diffraction enhanced imaging

    Institute of Scientific and Technical Information of China (English)

    Chunhong Hu; Tao Zhao; Lu Zhang; Hui Li; Xinyan Zhao; Shuqian Luo

    2009-01-01

    X-ray phase-contrast imaging (PCI) is a new emerging imaging technique that generates a high spatial resolution and high contrast of biological soft tissues compared to conventional radiography. Herein a biomedical application of diffraction enhanced imaging (DEI) is presented. As one of the PCI methods, DEI derives contrast from many different kinds of sample information, such as the sample's X-ray absorption, refraction gradient and ultra-small-angle X-ray scattering (USAXS) properties, and the sample information is expressed by three parametric images. Combined with computed tomography (CT), DEI-CT can produce 3D volumetric images of the sample and can be used for investigating micro-structures of biomedical samples. Our DEI experiments for fiver samples were implemented at the topog-raphy station of Beijing Synchrotron Radiation Facility (BSRF). The results show that by using our provided information extraction method and DEI-CT reconstruction approach, the obtained parametric images clearly display the inner structures of liver tissues and the morphology of blood vessels. Furthermore, the reconstructed 3D view of the fiver blood vessels exhibits the micro blood vessels whose minimum diameter is on the order of about tens of microns, much better than its conventional CT reconstruction at a millimeter resolution.In conclusion, both the information extraction method and DEI-CT have the potential for use in biomedical micro-structures analysis.

  12. Web Information Extraction Systems for Web Semantization

    Czech Academy of Sciences Publication Activity Database

    Dědek, Jan

    Seňa : Pont, 2009 - (Vojtáš, P.), s. 1-6 ISBN 978-80-970179-2-7. [ITAT 2009. Conference on Theory and Practice of Information Theory. Kráľova studňa (SK), 25.09.2009-29.09.2009] R&D Projects: GA AV ČR 1ET100300517; GA ČR GD201/09/H057 Institutional research plan: CEZ:AV0Z10300504 Keywords : web information extraction * web semantization * semantic web * information systems Subject RIV: IN - Informatics, Computer Science

  13. Advanced Secure Information Retrieval Technology for Multilayer Information Extraction

    Directory of Open Access Journals (Sweden)

    Shoude Chang

    2008-01-01

    Full Text Available Secure information retrieval technology aims at status identification and documentation authentication. Ideally, materials or devices used in these technologies should be hard to find, difficult to counterfeit, and as simple as possible. This manuscript addresses a novel information retrieval technology, with photoluminescent (PL semiconductor quantum dots (QDs synthesized via wet chemistry approaches used as its coding materials. Conceptually, these QDs are designed to exhibit emission at Fraunhofer line positions, namely, black lines in the solar spectrum; thus, the retrieval system can extract useful information under sunshine covering areas. Furthermore, multiphoton excitation (MPE technology enables the retrieval system to be multilayer information extraction, with thin films consisting of QDs applied to various substrates, such as military helmets and vehicle and fingernails. Anticipated applications include security, military, and law enforcement. QD-based security information can be easily destroyed by preset expiration in the presence of timing agents.

  14. Web Information Extraction%Web信息抽取

    Institute of Scientific and Technical Information of China (English)

    李晶; 陈恩红

    2003-01-01

    With the tremendous amount of information available on the Web, the ability to quickly obtain information has become a crucial problem. It is not enough for us to acquire information only with Web information retrieval technology. Therefore more and more people pay attention to Web information extraction technology. This paper first in- troduces some concepts of information extraction technology, then introduces and analyzes several typical Web information extraction methods based on the differences in extraction patterns.

  15. Unsupervised information extraction by text segmentation

    CERN Document Server

    Cortez, Eli

    2013-01-01

    A new unsupervised approach to the problem of Information Extraction by Text Segmentation (IETS) is proposed, implemented and evaluated herein. The authors' approach relies on information available on pre-existing data to learn how to associate segments in the input string with attributes of a given domain relying on a very effective set of content-based features. The effectiveness of the content-based features is also exploited to directly learn from test data structure-based features, with no previous human-driven training, a feature unique to the presented approach. Based on the approach, a

  16. Bio-medical (EMG Signal Analysis and Feature Extraction Using Wavelet Transform

    Directory of Open Access Journals (Sweden)

    Rhutuja Raut

    2015-03-01

    Full Text Available In this paper, the multi-channel electromyogram acquisition system is being developed using programmable system on chip (PSOC microcontroller to obtain the surface of EMG signal. The two pairs of single-channel surface electrodes are utilized to measure the EMG signal obtained from forearm muscles. Then different levels of Wavelet family are used to analyze the EMG signal. Later features in terms of root mean square, logarithm of root mean square, centroid of frequency, as well as standard deviation were used to extract the EMG signal. The proposed method of feature extraction for extracting EMG signal states that root means square feature extraction method gives better performance as compared to the other features. In the near future, this method can be used to control a mechanical arm as well as robotic arm in field of real-time processing.

  17. CONAN : Text Mining in the Biomedical Domain

    NARCIS (Netherlands)

    Malik, R.

    2006-01-01

    This thesis is about Text Mining. Extracting important information from literature. In the last years, the number of biomedical articles and journals is growing exponentially. Scientists might not find the information they want because of the large number of publications. Therefore a system was cons

  18. The caCORE Software Development Kit: Streamlining construction of interoperable biomedical information services

    Directory of Open Access Journals (Sweden)

    Warzel Denise

    2006-01-01

    Full Text Available Abstract Background Robust, programmatically accessible biomedical information services that syntactically and semantically interoperate with other resources are challenging to construct. Such systems require the adoption of common information models, data representations and terminology standards as well as documented application programming interfaces (APIs. The National Cancer Institute (NCI developed the cancer common ontologic representation environment (caCORE to provide the infrastructure necessary to achieve interoperability across the systems it develops or sponsors. The caCORE Software Development Kit (SDK was designed to provide developers both within and outside the NCI with the tools needed to construct such interoperable software systems. Results The caCORE SDK requires a Unified Modeling Language (UML tool to begin the development workflow with the construction of a domain information model in the form of a UML Class Diagram. Models are annotated with concepts and definitions from a description logic terminology source using the Semantic Connector component. The annotated model is registered in the Cancer Data Standards Repository (caDSR using the UML Loader component. System software is automatically generated using the Codegen component, which produces middleware that runs on an application server. The caCORE SDK was initially tested and validated using a seven-class UML model, and has been used to generate the caCORE production system, which includes models with dozens of classes. The deployed system supports access through object-oriented APIs with consistent syntax for retrieval of any type of data object across all classes in the original UML model. The caCORE SDK is currently being used by several development teams, including by participants in the cancer biomedical informatics grid (caBIG program, to create compatible data services. caBIG compatibility standards are based upon caCORE resources, and thus the caCORE SDK has

  19. Web Information Extraction for e-environment

    Czech Academy of Sciences Publication Activity Database

    Dědek, Jan; Vojtáš, Peter

    Brno : Masarykova univerzita, 2009 - (Hřebíček, J.; Hradec, J.; Pelikán, E.; Mírovský, O.; Pillmann, W.; Holoubek, I.; Bandholz, T.), s. 138-143 ISBN 978-80-210-4824-9. [Towards eEnvironment. European Conference of the Czech Presidency of the Council of the EU. Prague (CZ), 25.03.2009-27.03.2009] R&D Projects: GA AV ČR 1ET100300517; GA ČR GD201/09/H057 Institutional research plan: CEZ:AV0Z10300504 Keywords : Web * information extraction * natural language processing Subject RIV: IN - Informatics, Computer Science

  20. Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature

    OpenAIRE

    Ravikumar, Komandur Elayavilli; Wagholikar, Kavishwar B; Li, Dingcheng; Kocher, Jean-Pierre; PhD, Hongfang Liu

    2015-01-01

    Background Advances in the next generation sequencing technology has accelerated the pace of individualized medicine (IM), which aims to incorporate genetic/genomic information into medicine. One immediate need in interpreting sequencing data is the assembly of information about genetic variants and their corresponding associations with other entities (e.g., diseases or medications). Even with dedicated effort to capture such information in biological databases, much of this information remai...

  1. Biomedical Applications of the Information-efficient Spectral Imaging Sensor (ISIS)

    Energy Technology Data Exchange (ETDEWEB)

    Gentry, S.M.; Levenson, R.

    1999-01-21

    The Information-efficient Spectral Imaging Sensor (ISIS) approach to spectral imaging seeks to bridge the gap between tuned multispectral and fixed hyperspectral imaging sensors. By allowing the definition of completely general spectral filter functions, truly optimal measurements can be made for a given task. These optimal measurements significantly improve signal-to-noise ratio (SNR) and speed, minimize data volume and data rate, while preserving classification accuracy. The following paper investigates the application of the ISIS sensing approach in two sample biomedical applications: prostate and colon cancer screening. It is shown that in these applications, two to three optimal measurements are sufficient to capture the majority of classification information for critical sample constituents. In the prostate cancer example, the optimal measurements allow 8% relative improvement in classification accuracy of critical cell constituents over a red, green, blue (RGB) sensor. In the colon cancer example, use of optimal measurements boost the classification accuracy of critical cell constituents by 28% relative to the RGB sensor. In both cases, optimal measurements match the performance achieved by the entire hyperspectral data set. The paper concludes that an ISIS style spectral imager can acquire these optimal spectral images directly, allowing improved classification accuracy over an RGB sensor. Compared to a hyperspectral sensor, the ISIS approach can achieve similar classification accuracy using a significantly lower number of spectral samples, thus minimizing overall sample classification time and cost.

  2. Synonym set extraction from the biomedical literature by lexical pattern discovery

    Science.gov (United States)

    McCrae, John; Collier, Nigel

    2008-01-01

    Background Although there are a large number of thesauri for the biomedical domain many of them lack coverage in terms and their variant forms. Automatic thesaurus construction based on patterns was first suggested by Hearst [1], but it is still not clear how to automatically construct such patterns for different semantic relations and domains. In particular it is not certain which patterns are useful for capturing synonymy. The assumption of extant resources such as parsers is also a limiting factor for many languages, so it is desirable to find patterns that do not use syntactical analysis. Finally to give a more consistent and applicable result it is desirable to use these patterns to form synonym sets in a sound way. Results We present a method that automatically generates regular expression patterns by expanding seed patterns in a heuristic search and then develops a feature vector based on the occurrence of term pairs in each developed pattern. This allows for a binary classifications of term pairs as synonymous or non-synonymous. We then model this result as a probability graph to find synonym sets, which is equivalent to the well-studied problem of finding an optimal set cover. We achieved 73.2% precision and 29.7% recall by our method, out-performing hand-made resources such as MeSH and Wikipedia. Conclusion We conclude that automatic methods can play a practical role in developing new thesauri or expanding on existing ones, and this can be done with only a small amount of training data and no need for resources such as parsers. We also concluded that the accuracy can be improved by grouping into synonym sets. PMID:18366721

  3. Synonym set extraction from the biomedical literature by lexical pattern discovery

    Directory of Open Access Journals (Sweden)

    Collier Nigel

    2008-03-01

    Full Text Available Abstract Background Although there are a large number of thesauri for the biomedical domain many of them lack coverage in terms and their variant forms. Automatic thesaurus construction based on patterns was first suggested by Hearst 1, but it is still not clear how to automatically construct such patterns for different semantic relations and domains. In particular it is not certain which patterns are useful for capturing synonymy. The assumption of extant resources such as parsers is also a limiting factor for many languages, so it is desirable to find patterns that do not use syntactical analysis. Finally to give a more consistent and applicable result it is desirable to use these patterns to form synonym sets in a sound way. Results We present a method that automatically generates regular expression patterns by expanding seed patterns in a heuristic search and then develops a feature vector based on the occurrence of term pairs in each developed pattern. This allows for a binary classifications of term pairs as synonymous or non-synonymous. We then model this result as a probability graph to find synonym sets, which is equivalent to the well-studied problem of finding an optimal set cover. We achieved 73.2% precision and 29.7% recall by our method, out-performing hand-made resources such as MeSH and Wikipedia. Conclusion We conclude that automatic methods can play a practical role in developing new thesauri or expanding on existing ones, and this can be done with only a small amount of training data and no need for resources such as parsers. We also concluded that the accuracy can be improved by grouping into synonym sets.

  4. Extraction of information from unstructured text

    Energy Technology Data Exchange (ETDEWEB)

    Irwin, N.H.; DeLand, S.M.; Crowder, S.V.

    1995-11-01

    Extracting information from unstructured text has become an emphasis in recent years due to the large amount of text now electronically available. This status report describes the findings and work done by the end of the first year of a two-year LDRD. Requirements of the approach included that it model the information in a domain independent way. This means that it would differ from current systems by not relying on previously built domain knowledge and that it would do more than keyword identification. Three areas that are discussed and expected to contribute to a solution include (1) identifying key entities through document level profiling and preprocessing, (2) identifying relationships between entities through sentence level syntax, and (3) combining the first two with semantic knowledge about the terms.

  5. Information sources in biomedical science and medical journalism: methodological approaches and assessment.

    Science.gov (United States)

    Miranda, Giovanna F; Vercellesi, Luisa; Bruno, Flavia

    2004-09-01

    Throughout the world the public is showing increasing interest in medical and scientific subjects and journalists largely spread this information, with an important impact on knowledge and health. Clearly, therefore, the relationship between the journalist and his sources is delicate: freedom and independence of information depend on the independence and truthfulness of the sources. The new "precision journalism" holds that scientific methods should be applied to journalism, so authoritative sources are a common need for journalists and scientists. We therefore compared the individual classifications and methods of assessing of sources in biomedical science and medical journalism to try to extrapolate scientific methods of evaluation to journalism. In journalism and science terms used to classify sources of information show some similarities, but their meanings are different. In science primary and secondary classes of information, for instance, refer to the levels of processing, but in journalism to the official nature of the source itself. Scientists and journalists must both always consult as many sources as possible and check their authoritativeness, reliability, completeness, up-to-dateness and balance. In journalism, however, there are some important differences and limits: too many sources can sometimes diminish the quality of the information. The sources serve a first filter between the event and the journalist, who is not providing the reader with the fact, but with its projection. Journalists have time constraints and lack the objective criteria for searching, the specific background knowledge, and the expertise to fully assess sources. To assist in understanding the wealth of sources of information in journalism, we have prepared a checklist of items and questions. There are at least four fundamental points that a good journalist, like any scientist, should know: how to find the latest information (the sources), how to assess it (the quality and

  6. System architecture and information model for integrated access to distributed biomedical information

    Science.gov (United States)

    Kim, Dongkyu; Alaoui, Adil; Levine, Betty; Leondaridis, Leonidas; Shields, Peter; Byers, Steve; Cleary, Kevin

    2009-02-01

    The current trend towards systems medicine will rely heavily on computational and bioinformatics capabilities to collect, integrate, and analyze massive amounts of data from disparate sources. The objective is to use this information to make medical decisions that improve patient care. At Georgetown University Medical Center, we are developing an informatics capability to integrate several research and clinical databases. Our long term goal is to provide researchers at Georgetown's Lombardi Comprehensive Cancer Center better access to aggregated molecular and clinical information facilitating the investigation of new hypotheses that impact patient care. We also recognize the need for data mining tools and intelligent agents to help researchers in these efforts. This paper describes our initial work to create a flexible platform for researchers and physicians that provides access to information sources including clinical records, medical images, genomic, epigenomic, proteomic and metabolomic data. This paper describes the data sources selected for this pilot project and possible approaches to integrating these databases. We present the different database integration models that we considered. We conclude by outlining the proposed Information Model for the project.

  7. A Biomedical Information System for Retrieval and Manipulation of NHANES Data

    OpenAIRE

    Mukherjee, Sukrit; Martins, David; Norris, Keith C.; Jenders, Robert A

    2013-01-01

    The retrieval and manipulation of data from large public databases like the U.S. National Health and Nutrition Examination Survey (NHANES) may require sophisticated statistical software and significant expertise that may be unavailable in the university setting. In response, we have developed the Data Retrieval And Manipulation System (DReAMS), an automated information system to handle all processes of data extraction and cleaning and then joining different subsets to produce analysis-ready o...

  8. Using Biomedical Technologies to Inform Economic Modeling: Challenges and Opportunities for Improving Analysis of Environmental Policies

    OpenAIRE

    Roe, Brian E.; Haab, Timothy C.

    2009-01-01

    Advances in biomedical technology have irrevocably jarred open the black box of human decision making, offering social scientists the potential to validate, reject, refine and redefine the individual models of resource allocation that form the foundation of modern economics. In this paper we (1) provide a comprehensive overview of the biomedical methods that may be harnessed by economists and other social scientists to better understand the economic decision making process; (2) review researc...

  9. Chaotic spectra: How to extract dynamic information

    International Nuclear Information System (INIS)

    Nonlinear dynamics is applied to chaotic unassignable atomic and molecular spectra with the aim of extracting detailed information about regular dynamic motions that exist over short intervals of time. It is shown how this motion can be extracted from high resolution spectra by doing low resolution studies or by Fourier transforming limited regions of the spectrum. These motions mimic those of periodic orbits (PO) and are inserts into the dominant chaotic motion. Considering these inserts and the PO as a dynamically decoupled region of space, resonant scattering theory and stabilization methods enable us to compute ladders of resonant states which interact with the chaotic quasi-continuum computed in principle from basis sets placed off the PO. The interaction of the resonances with the quasicontinuum explains the low resolution spectra seen in such experiments. It also allows one to associate low resolution features with a particular PO. The motion on the PO thereby supplies the molecular movements whose quantization causes the low resolution spectra. Characteristic properties of the periodic orbit based resonances are discussed. The method is illustrated on the photoabsorption spectrum of the hydrogen atom in a strong magnetic field and on the photodissociation spectrum of H3+. Other molecular systems which are currently under investigation using this formalism are also mentioned. 53 refs., 10 figs., 2 tabs

  10. Chaotic spectra: How to extract dynamic information

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, H.S.; Gomez Llorente, J.M.; Zakrzewski, J.; Kulander, K.C.

    1988-10-01

    Nonlinear dynamics is applied to chaotic unassignable atomic and molecular spectra with the aim of extracting detailed information about regular dynamic motions that exist over short intervals of time. It is shown how this motion can be extracted from high resolution spectra by doing low resolution studies or by Fourier transforming limited regions of the spectrum. These motions mimic those of periodic orbits (PO) and are inserts into the dominant chaotic motion. Considering these inserts and the PO as a dynamically decoupled region of space, resonant scattering theory and stabilization methods enable us to compute ladders of resonant states which interact with the chaotic quasi-continuum computed in principle from basis sets placed off the PO. The interaction of the resonances with the quasicontinuum explains the low resolution spectra seen in such experiments. It also allows one to associate low resolution features with a particular PO. The motion on the PO thereby supplies the molecular movements whose quantization causes the low resolution spectra. Characteristic properties of the periodic orbit based resonances are discussed. The method is illustrated on the photoabsorption spectrum of the hydrogen atom in a strong magnetic field and on the photodissociation spectrum of H/sub 3//sup +/. Other molecular systems which are currently under investigation using this formalism are also mentioned. 53 refs., 10 figs., 2 tabs.

  11. A Novel Feature Selection Strategy for Enhanced Biomedical Event Extraction Using the Turku System

    Directory of Open Access Journals (Sweden)

    Jingbo Xia

    2014-01-01

    Full Text Available Feature selection is of paramount importance for text-mining classifiers with high-dimensional features. The Turku Event Extraction System (TEES is the best performing tool in the GENIA BioNLP 2009/2011 shared tasks, which relies heavily on high-dimensional features. This paper describes research which, based on an implementation of an accumulated effect evaluation (AEE algorithm applying the greedy search strategy, analyses the contribution of every single feature class in TEES with a view to identify important features and modify the feature set accordingly. With an updated feature set, a new system is acquired with enhanced performance which achieves an increased F-score of 53.27% up from 51.21% for Task 1 under strict evaluation criteria and 57.24% according to the approximate span and recursive criterion.

  12. Extraction of quantifiable information from complex systems

    CERN Document Server

    Dahmen, Wolfgang; Griebel, Michael; Hackbusch, Wolfgang; Ritter, Klaus; Schneider, Reinhold; Schwab, Christoph; Yserentant, Harry

    2014-01-01

    In April 2007, the  Deutsche Forschungsgemeinschaft (DFG) approved the  Priority Program 1324 “Mathematical Methods for Extracting Quantifiable Information from Complex Systems.” This volume presents a comprehensive overview of the most important results obtained over the course of the program.   Mathematical models of complex systems provide the foundation for further technological developments in science, engineering and computational finance.  Motivated by the trend toward steadily increasing computer power, ever more realistic models have been developed in recent years. These models have also become increasingly complex, and their numerical treatment poses serious challenges.   Recent developments in mathematics suggest that, in the long run, much more powerful numerical solution strategies could be derived if the interconnections between the different fields of research were systematically exploited at a conceptual level. Accordingly, a deeper understanding of the mathematical foundations as w...

  13. SEMANTIC INFORMATION EXTRACTION IN UNIVERSITY DOMAIN

    Directory of Open Access Journals (Sweden)

    Swathi

    2012-07-01

    Full Text Available Today’s conventional search engines hardly do provide the essential content relevant to the user’s search query. This is because the context and semantics of the request made by the user is not analyzed to the full extent. So here the need for a semantic web search arises. SWS is upcoming in the area of web search which combines Natural Language Processing and Artificial Intelligence. The objective of the work done here is to design, develop and implement a semantic search engine- SIEU(Semantic Information Extraction in University Domain confined to the university domain. SIEU uses ontology as a knowledge base for the information retrieval process. It is not just a mere keyword search. It is one layer above what Google or any other search engines retrieve by analyzing just the keywords. Here the query is analyzed both syntactically and semantically. The developed system retrieves the web results more relevant to the user query through keyword expansion. The results obtained here will be accurate enough to satisfy the request made by the user. The level of accuracy will be enhanced since the query is analyzed semantically. The system will be of great use to the developers and researchers who work on web. The Google results are re-ranked and optimized for providing the relevant links. For ranking an algorithm has been applied which fetches more apt results for the user query.

  14. Enhancing retinal images by extracting structural information

    Science.gov (United States)

    Molodij, G.; Ribak, E. N.; Glanc, M.; Chenegros, G.

    2014-02-01

    High-resolution imaging of the retina has significant importance for science: physics and optics, biology, and medicine. The enhancement of images with poor contrast and the detection of faint structures require objective methods for assessing perceptual image quality. Under the assumption that human visual perception is highly adapted for extracting structural information from a scene, we introduce a framework for quality assessment based on the degradation of structural information. We implemented a new processing technique on a long sequence of retinal images of subjects with normal vision. We were able to perform a precise shift-and-add at the sub-pixel level in order to resolve the structures of the size of single cells in the living human retina. Last, we quantified the restoration reliability of the distorted images using an improved quality assessment. To that purpose, we used the single image restoration method based on the ergodic principle, which has originated in solar astronomy, to deconvolve aberrations after adaptive optics compensation.

  15. Respiratory Information Extraction from Electrocardiogram Signals

    KAUST Repository

    Amin, Gamal El Din Fathy

    2010-12-01

    The Electrocardiogram (ECG) is a tool measuring the electrical activity of the heart, and it is extensively used for diagnosis and monitoring of heart diseases. The ECG signal reflects not only the heart activity but also many other physiological processes. The respiratory activity is a prominent process that affects the ECG signal due to the close proximity of the heart and the lungs. In this thesis, several methods for the extraction of respiratory process information from the ECG signal are presented. These methods allow an estimation of the lung volume and the lung pressure from the ECG signal. The potential benefit of this is to eliminate the corresponding sensors used to measure the respiration activity. A reduction of the number of sensors connected to patients will increase patients’ comfort and reduce the costs associated with healthcare. As a further result, the efficiency of diagnosing respirational disorders will increase since the respiration activity can be monitored with a common, widely available method. The developed methods can also improve the detection of respirational disorders that occur while patients are sleeping. Such disorders are commonly diagnosed in sleeping laboratories where the patients are connected to a number of different sensors. Any reduction of these sensors will result in a more natural sleeping environment for the patients and hence a higher sensitivity of the diagnosis.

  16. Information Extraction on the Web with Credibility Guarantee

    OpenAIRE

    Nguyen, Thanh Tam

    2015-01-01

    The Web became the central medium for valuable sources of information extraction applications. However, such user-generated resources are often plagued by inaccuracies and misinformation due to the inherent openness and uncertainty of the Web. In this work we study the problem of extracting structured information out of Web data with a credibility guarantee. The ultimate goal is that not only the structured information should be extracted as much as possible but also its credibility is high. ...

  17. Early Steps Towards Web Scale Information Extraction with LODIE

    OpenAIRE

    Gentile, Anna Lisa; The University of Sheffield; Zhang, Ziqi; The University of Sheffield; Ciravegna, Fabio; The University of Sheffield

    2015-01-01

    Information extraction (IE) is the technique for transforming unstructured textual data into structured representation that can be understood by machines. The exponential growth of the Web generates an exceptional quantity of data for which automatic knowledge capture is essential. This work describes the methodology for web scale information extraction in the LODIE project (linked open data information extraction) and highlights results from the early experiments carried out in the initial p...

  18. What is biomedical informatics?

    OpenAIRE

    Bernstam, Elmer V.; Smith, Jack W.; Johnson, Todd R

    2009-01-01

    Biomedical informatics lacks a clear and theoretically grounded definition. Many proposed definitions focus on data, information, and knowledge, but do not provide an adequate definition of these terms. Leveraging insights from the philosophy of information, we define informatics as the science of information, where information is data plus meaning. Biomedical informatics is the science of information as applied to or studied in the context of biomedicine. Defining the object of study of info...

  19. [Application of the life sciences platform based on oracle to biomedical informations].

    Science.gov (United States)

    Zhao, Zhi-Yun; Li, Tai-Huan; Yang, Hong-Qiao

    2008-03-01

    The life sciences platform based on Oracle database technology is introduced in this paper. By providing a powerful data access, integrating a variety of data types, and managing vast quantities of data, the software presents a flexible, safe and scalable management platform for biomedical data processing. PMID:18581881

  20. A Study of the Information Literacy of Biomedical Graduate Students: Based on the Thesis Topic Discovery Process in Molecular Biology Research

    Directory of Open Access Journals (Sweden)

    Jhao-Yen Huang

    2014-06-01

    Full Text Available The biomedical information environment is in a state of constant and rapid change due to the increase in research data and rapid technological advances. In Taiwan, few research has investigated the information literacy of biomedical graduate students. This exploratory study examined the information literacy abilities and training of biomedical graduate students in Taiwan. Semi-structured interviews based on the Association of College and Research Libraries Information Literacy Competency Standards for Science and Engineering/Technology were conducted with 20 molecular biological graduate students. The interview inquired about their information-seeking channels and information literacy education. The findings show that the biomedical graduate students developed a workable thesis topic with their advisors. Through various information-seeking channels and retrieval strategies, they obtained and critically evaluated information to address different information needs for their thesis research. Through seminars, annual conferences and papers, the interviewees were informed of current developments in their field. Subsequently, through written or oral communications, they were able to integrate and exchange the information. Most interviewees cared about the social, economic, legal, and ethical issues surrounding the use of information. College courses and labs were the main information literacy education environment for them to learn about research skills and knowledge. The study concludes four areas to address for the information literacy of biomedical graduate students, i.e., using professional information, using the current information, efficiency in assessing the domain information, and utilization of diverse information channels. Currently, the interviewees showed rather low usage of library resources, which is a concern for biomedical educators and libraries. [Article content in Chinese

  1. Turning Informal Thesauri Into Formal Ontologies: A Feasibility Study on Biomedical Knowledge re-Use

    OpenAIRE

    Udo Hahn

    2003-01-01

    This paper reports a large-scale knowledge conversion and curation experiment. Biomedical domain knowledge from a semantically weak and shallow terminological resource, the UMLS, is transformed into a rigorous description logics format. This way, the broad coverage of the UMLS is combined with inference mechanisms for consistency and cycle checking. They are the key to proper cleansing of the knowledge directly imported from the UMLS, as well as subsequent updating, maintenance an...

  2. The Agent of extracting Internet Information with Lead Order

    Science.gov (United States)

    Mo, Zan; Huang, Chuliang; Liu, Aijun

    In order to carry out e-commerce better, advanced technologies to access business information are in need urgently. An agent is described to deal with the problems of extracting internet information that caused by the non-standard and skimble-scamble structure of Chinese websites. The agent designed includes three modules which respond to the process of extracting information separately. A method of HTTP tree and a kind of Lead algorithm is proposed to generate a lead order, with which the required web can be retrieved easily. How to transform the extracted information structuralized with natural language is also discussed.

  3. Research on extraction of aeromagnetic weak information based on GIS

    International Nuclear Information System (INIS)

    This paper introduces the meaning of weak information extraction and discusses the theoretic foundation of aeromagnetic weak information extraction and expounds the principle of selected mathematic-physics methods. A kind of data visualization method--'1/4 standard deviation', which is favorable for displaying weak information, is proposed in the GIS software platform. The validity test of weak information extraction has been completed based on the GIS platform in Dongsheng area. Results indicate that the weak anomaly enhancement technique may effectively restrain the interfering noise, improve the signal-to-noise ratio and further delineate the prospective targets of sandstone uranium deposits

  4. Information Extraction Using Distant Supervision and Semantic Similarities

    Directory of Open Access Journals (Sweden)

    PARK, Y.

    2016-02-01

    Full Text Available Information extraction is one of the main research tasks in natural language processing and text mining that extracts useful information from unstructured sentences. Information extraction techniques include named entity recognition, relation extraction, and co-reference resolution. Among them, relation extraction refers to a task that extracts semantic relations between entities such as personal and geographic names in documents. This is an important research area, which is used in knowledge base construction and question and answering systems. This study presents relation extraction using a distant supervision learning technique among semi-supervised learning methods, which have been spotlighted in recent years to reduce human manual work and costs required for supervised learning. That is, this study proposes a method that can improve relation extraction by improving a distant supervision learning technique by applying a clustering method to create a learning corpus and semantic analysis for relation extraction that is difficult to identify using existing distant supervision. Through comparison experiments of various semantic similarity comparison methods, similarity calculation methods that are useful to relation extraction using distant supervision are searched, and a large number of accurate relation triples can be extracted using the proposed structural advantages and semantic similarity comparison.

  5. Visual Architecture based Web Information Extraction

    OpenAIRE

    S. Oswalt Manoj

    2011-01-01

    The World Wide Web has more online web database which can be searched through their web query interface. Deep Web contents are accessed by queries submitted to Web databases and the returned data records are enwrapped in dynamically generated Web pages. Extracting structured data from deep Web pages is a challenging task due to the underlying complicate structures of such pages. Until now, a large number of techniques have been proposed to address this problem, but all of them have inherent l...

  6. Information Extraction from Unstructured Text for the Biodefense Knowledge Center

    Energy Technology Data Exchange (ETDEWEB)

    Samatova, N F; Park, B; Krishnamurthy, R; Munavalli, R; Symons, C; Buttler, D J; Cottom, T; Critchlow, T J; Slezak, T

    2005-04-29

    The Bio-Encyclopedia at the Biodefense Knowledge Center (BKC) is being constructed to allow an early detection of emerging biological threats to homeland security. It requires highly structured information extracted from variety of data sources. However, the quantity of new and vital information available from every day sources cannot be assimilated by hand, and therefore reliable high-throughput information extraction techniques are much anticipated. In support of the BKC, Lawrence Livermore National Laboratory and Oak Ridge National Laboratory, together with the University of Utah, are developing an information extraction system built around the bioterrorism domain. This paper reports two important pieces of our effort integrated in the system: key phrase extraction and semantic tagging. Whereas two key phrase extraction technologies developed during the course of project help identify relevant texts, our state-of-the-art semantic tagging system can pinpoint phrases related to emerging biological threats. Also we are enhancing and tailoring the Bio-Encyclopedia by augmenting semantic dictionaries and extracting details of important events, such as suspected disease outbreaks. Some of these technologies have already been applied to large corpora of free text sources vital to the BKC mission, including ProMED-mail, PubMed abstracts, and the DHS's Information Analysis and Infrastructure Protection (IAIP) news clippings. In order to address the challenges involved in incorporating such large amounts of unstructured text, the overall system is focused on precise extraction of the most relevant information for inclusion in the BKC.

  7. Rank Based Clustering For Document Retrieval From Biomedical Databases

    Directory of Open Access Journals (Sweden)

    Jayanthi Manicassamy

    2009-09-01

    Full Text Available Now a day's, search engines are been most widely used for extracting information's from various resources throughout the world. Where, majority of searches lies in the field of biomedical for retrieving related documents from various biomedical databases. Currently search engines lacks in document clustering and representing relativeness level of documents extracted from the databases. In order to overcome these pitfalls a text based search engine have been developed for retrieving documents from Medline and PubMed biomedical databases. The search engine has incorporated page ranking bases clustering concept which automatically represents relativeness on clustering bases. Apart from this graph tree construction is made for representing the level of relatedness of the documents that are networked together. This advance functionality incorporation for biomedical document based search engine found to provide better results in reviewing related documents based on relativeness.

  8. Efficient Retrieval of Text for Biomedical Domain using Expectation Maximization Algorithm

    Directory of Open Access Journals (Sweden)

    Sumit Vashishtha

    2011-11-01

    Full Text Available Data mining, a branch of computer science [1], is the process of extracting patterns from large data sets by combining methods from statistics and artificial intelligence with database management. Data mining is seen as an increasingly important tool by modern business to transform data into business intelligence giving an informational advantage. Biomedical text retrieval refers to text retrieval techniques applied to biomedical resources and literature available of the biomedical and molecular biology domain. The volume of published biomedical research, and therefore the underlying biomedical knowledge base, is expanding at an increasing rate. Biomedical text retrieval is a way to aid researchers in coping with information overload. By discovering predictive relationships between different pieces of extracted data, data-mining algorithms can be used to improve the accuracy of information extraction. However, textual variation due to typos, abbreviations, and other sources can prevent the productive discovery and utilization of hard-matching rules. Recent methods of soft clustering can exploit predictive relationships in textual data. This paper presents a technique for using soft clustering data mining algorithm to increase the accuracy of biomedical text extraction. Experimental results demonstrate that this approach improves text extraction more effectively that hard keyword matching rules.

  9. Extracting information from free-text mammography reports

    OpenAIRE

    Esuli, Andrea; Marcheggiani, Diego; Sebastiani, Fabrizio

    2010-01-01

    Researchers from ISTI-CNR, Pisa, aim at effectively and efficiently extracting information from free-text mammography reports, as a step towards the automatic transformation of unstructured medical documentation into structured data.

  10. ONTOGRABBING: Extracting Information from Texts Using Generative Ontologies

    DEFF Research Database (Denmark)

    Nilsson, Jørgen Fischer; Szymczak, Bartlomiej Antoni; Jensen, P.A.

    2009-01-01

    We describe principles for extracting information from texts using a so-called generative ontology in combination with syntactic analysis. Generative ontologies are introduced as semantic domains for natural language phrases. Generative ontologies extend ordinary finite ontologies with rules for...

  11. Moving Target Information Extraction Based on Single Satellite Image

    Directory of Open Access Journals (Sweden)

    ZHAO Shihu

    2015-03-01

    Full Text Available The spatial and time variant effects in high resolution satellite push broom imaging are analyzed. A spatial and time variant imaging model is established. A moving target information extraction method is proposed based on a single satellite remote sensing image. The experiment computes two airplanes' flying speed using ZY-3 multispectral image and proves the validity of spatial and time variant model and moving information extracting method.

  12. Mining knowledge from text repositories using information extraction: A review

    Indian Academy of Sciences (India)

    Sandeep R Sirsat; Dr Vinay Chavan; Dr Shrinivas P Deshpande

    2014-02-01

    There are two approaches to mining text form online repositories. First, when the knowledge to be discovered is expressed directly in the documents to be mined, Information Extraction (IE) alone can serve as an effective tool for such text mining. Second, when the documents contain concrete data in unstructured form rather than abstract knowledge, Information Extraction (IE) can be used to first transform the unstructured data in the document corpus into a structured database, and then use some state-of-the-art data mining algorithms/tools to identify abstract patterns in this extracted data. This paper presents the review of several methods related to these two approaches.

  13. Extracting medication information from clinical text.

    Science.gov (United States)

    Uzuner, Ozlem; Solti, Imre; Cadag, Eithon

    2010-01-01

    The Third i2b2 Workshop on Natural Language Processing Challenges for Clinical Records focused on the identification of medications, their dosages, modes (routes) of administration, frequencies, durations, and reasons for administration in discharge summaries. This challenge is referred to as the medication challenge. For the medication challenge, i2b2 released detailed annotation guidelines along with a set of annotated discharge summaries. Twenty teams representing 23 organizations and nine countries participated in the medication challenge. The teams produced rule-based, machine learning, and hybrid systems targeted to the task. Although rule-based systems dominated the top 10, the best performing system was a hybrid. Of all medication-related fields, durations and reasons were the most difficult for all systems to detect. While medications themselves were identified with better than 0.75 F-measure by all of the top 10 systems, the best F-measure for durations and reasons were 0.525 and 0.459, respectively. State-of-the-art natural language processing systems go a long way toward extracting medication names, dosages, modes, and frequencies. However, they are limited in recognizing duration and reason fields and would benefit from future research. PMID:20819854

  14. Fine-grained information extraction from German transthoracic echocardiography reports

    OpenAIRE

    Toepfer, Martin; Corovic, Hamo; Fette, Georg; Klügl, Peter; Störk, Stefan; Puppe, Frank

    2015-01-01

    Background Information extraction techniques that get structured representations out of unstructured data make a large amount of clinically relevant information about patients accessible for semantic applications. These methods typically rely on standardized terminologies that guide this process. Many languages and clinical domains, however, lack appropriate resources and tools, as well as evaluations of their applications, especially if detailed conceptualizations of the domain are required....

  15. The study of the extraction of 3-D informations

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Min Ki [Korea Univ., Seoul (Korea); Kim, Jin Hun; Kim, Hui Yung; Lee, Gi Sik; Lee, Yung Shin [Sokyung Univ., Seoul (Korea)

    1998-04-01

    To extract three dimensional information in 3 dimensional real world two methods are applied (stereo image method, virtual reality environment method). 1. Stereo image method. From the paris of stereo image matching methods are applied to find the corresponding points in the two images. To solve the problem various methods are applied 2. Virtual reality environment method. As an alternate method to extract 3-D information, virtual reality environment is use. It is very useful to fine 6 DOF for a some given target points in 3-D space. We considered the accuracies and reliability of the 3-D informations. 34 figs., 4 tabs. (Author)

  16. Addressing Information Proliferation: Applications of Information Extraction and Text Mining

    Science.gov (United States)

    Li, Jingjing

    2013-01-01

    The advent of the Internet and the ever-increasing capacity of storage media have made it easy to store, deliver, and share enormous volumes of data, leading to a proliferation of information on the Web, in online libraries, on news wires, and almost everywhere in our daily lives. Since our ability to process and absorb this information remains…

  17. Application of four-layer neural network on information extraction.

    Science.gov (United States)

    Han, Min; Cheng, Lei; Meng, Hua

    2003-01-01

    This paper applies neural network to extract marsh information. An adaptive back-propagation algorithm based on a robust error function is introduced to build a four-layer neural network, and it is used to classify Thematic Mapper (TM) image of Zhalong Wetland in China and then extract marsh information. Comparing marsh information extraction results of the four-layer neural network with three-layer neural network and the maximum likelihood classifier, conclusion can be drawn as follows: the structure of the four-layer neural network and the adaptive back-propagation algorithm based on the robust error function is effective to extract marsh information. The four-layer neural network adopted in this paper succeeded in building the complex model of TM image, and it avoided the problem of great storage of remotely sensed data, and the adaptive back-propagation algorithm speeded up the descending of error. Above all, the four-layer neural network is superior to the three-layer neural network and the maximum likelihood classifier in the accuracy of the total classification and marsh information extraction. PMID:12850006

  18. Extracting and summarizing information from large data repositories

    OpenAIRE

    Albanese, Massimiliano

    2006-01-01

    Information retrieval from large data repositories has become an important area of computer science. Research in this field is highly encouraged by the ever-increasing rate with which today's society is able to produce digital data. Unfortunately most of such data (e.g. video recordings, plain text documents) are unstructured. Two major issues thus arise in this scenario: i) extracting structured data -- information -- from unstructured data; ii) summarizing information, i.e. reducing large v...

  19. Linguistic information extraction for job ads (SIRE project)

    OpenAIRE

    Loth, Romain; Battistelli, Delphine; Chaumartin, François-Régis; De Mazancourt, Hugues; Minel, Jean-Luc; Vinckx, Axelle

    2010-01-01

    International audience As a text, each job advertisement expresses rich information about the occupation at hand, such as competence needs (i.e. required degrees, field knowledge, task expertise or technical skills). To facilitate the access to this information, the SIRE project conducted a corpus based study of how to articulate HR expert ontologies with modern semi-supervised information extraction techniques. An adaptive semantic labeling framework is developed through a parallel work o...

  20. Automated extraction of change information from multispectral satellite imagery

    International Nuclear Information System (INIS)

    Seeing the expected technical improvements as to the spatial and spectral resolution, satellite imagery could more and more provide a basis for complex information systems for recognizing and monitoring even small-scale and short-term structural features of interests within nuclear facilities, for instance construction of buildings, plant expansion, changes of the operational status, underground activities etc. The analysis of large volumes of multi sensor satellite data will then definitely require a high degree of automation for (pre-) processing, analysis and interpretation in order to extract the features of interest. Against this background, the present paper focuses on the automated extraction of change information from multispectral satellite imagery

  1. The CRISP system: an untapped resource for biomedical research project information.

    OpenAIRE

    Collins, K. A.

    1989-01-01

    CRISP (Computer Retrieval of Information on Scientific Projects) is a large database maintained and operated by the National Institutes of Health (NIH). It contains comprehensive scientific and selected administrative data on research carried out by the U.S. Public Health Service (PHS) or supported by PHS grants and contracts. Developed originally to meet the needs of NIH, it is an excellent, largely untapped resource for health information professionals at large, revealing new trends, method...

  2. Ethics Review Committee approval and informed consent: an analysis of biomedical publications originating from Sri Lanka

    OpenAIRE

    Siriwardhana Chesmal; Athukorale Manjula; Lekamwattage Manura; Hewege Suwin; Siribaddana Sisira; Sumathipala Athula; Murray Joanna; Prince Martin

    2008-01-01

    Abstract Background International guidelines on research have focused on protecting research participants. Ethical Research Committee (ERC) approval and informed consent are the cornerstones. Externally sponsored research requires approval through ethical review in both the host and the sponsoring country. This study aimed to determine to what extent ERC approval and informed consent procedures are documented in locally and internationally published human subject research carried out in Sri L...

  3. Why not just Google it? An assessment of information literacy skills in a biomedical science curriculum

    Directory of Open Access Journals (Sweden)

    Stewart Tanis

    2011-04-01

    Full Text Available Abstract Background Few issues in higher education are as fundamental as the ability to search for, evaluate, and synthesize information. The need to develop information literacy, the process of finding, retrieving, organizing, and evaluating the ever-expanding collection of online information, has precipitated the need for training in skill-based competencies in higher education, as well as medical and dental education. Methods The current study evaluated the information literacy skills of first-year dental students, consisting of two, consecutive dental student cohorts (n = 160. An assignment designed to evaluate information literacy skills was conducted. In addition, a survey of student online search engine or database preferences was conducted to identify any significant associations. Subsequently, an intervention was developed, based upon the results of the assessment and survey, to address any deficiencies in information literacy. Results Nearly half of students (n = 70/160 or 43% missed one or more question components that required finding an evidence-based citation. Analysis of the survey revealed a significantly higher percentage of students who provided incorrect responses (n = 53/70 or 75.7% reported using Google as their preferred online search method (p Conclusions This study confirmed that information literacy among this student population was lacking and that integration of modules within the curriculum can help students to filter and establish the quality of online information, a critical component in the training of new health care professionals. Furthermore, incorporation of these modules early in the curriculum may be of significant value to other dental, medical, health care, and professional schools with similar goals of incorporating the evidence base into teaching and learning activities.

  4. Improving information extraction using a probability-based approach

    DEFF Research Database (Denmark)

    Kim, S.; Ahmed, Saeema; Wallace, K.

    2007-01-01

    Information plays a crucial role during the entire life-cycle of a product. It has been shown that engineers frequently consult colleagues to obtain the information they require to solve problems. However, the industrial world is now more transient and key personnel move to other companies or...... retire. It is becoming essential to retrieve vital information from archived product documents, if it is available. There is, therefore, great interest in ways of extracting relevant and sharable information from documents. A keyword-based search is commonly used, but studies have shown that these...

  5. Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task.

    Science.gov (United States)

    Wei, Chih-Hsuan; Peng, Yifan; Leaman, Robert; Davis, Allan Peter; Mattingly, Carolyn J; Li, Jiao; Wiegers, Thomas C; Lu, Zhiyong

    2016-01-01

    Manually curating chemicals, diseases and their relationships is significantly important to biomedical research, but it is plagued by its high cost and the rapid growth of the biomedical literature. In recent years, there has been a growing interest in developing computational approaches for automatic chemical-disease relation (CDR) extraction. Despite these attempts, the lack of a comprehensive benchmarking dataset has limited the comparison of different techniques in order to assess and advance the current state-of-the-art. To this end, we organized a challenge task through BioCreative V to automatically extract CDRs from the literature. We designed two challenge tasks: disease named entity recognition (DNER) and chemical-induced disease (CID) relation extraction. To assist system development and assessment, we created a large annotated text corpus that consisted of human annotations of chemicals, diseases and their interactions from 1500 PubMed articles. 34 teams worldwide participated in the CDR task: 16 (DNER) and 18 (CID). The best systems achieved an F-score of 86.46% for the DNER task--a result that approaches the human inter-annotator agreement (0.8875)--and an F-score of 57.03% for the CID task, the highest results ever reported for such tasks. When combining team results via machine learning, the ensemble system was able to further improve over the best team results by achieving 88.89% and 62.80% in F-score for the DNER and CID task, respectively. Additionally, another novel aspect of our evaluation is to test each participating system's ability to return real-time results: the average response time for each team's DNER and CID web service systems were 5.6 and 9.3 s, respectively. Most teams used hybrid systems for their submissions based on machining learning. Given the level of participation and results, we found our task to be successful in engaging the text-mining research community, producing a large annotated corpus and improving the results of

  6. THE METHODS OF EXTRACTING WATER INFORMATION FROM SPOT IMAGE

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Some techniques and methods for deriving water information from SPOT -4 (XI) image were investigatedand discussed in this paper. An algorithm of decision-tree (DT) classification which includes several classifiers based onthe spectral responding characteristics of water bodies and other objects, was developed and put forward to delineate wa-ter bodies. Another algorithm of decision-tree classification based on both spectral characteristics and auxiliary informa-tion of DEM and slope (DTDS) was also designed for water bodies extraction. In addition, supervised classificationmethod of maximum-likelyhood classification (MLC), and unsupervised method of interactive self-organizing dada analy-sis technique (ISODATA) were used to extract waterbodies for comparison purpose. An index was designed and used toassess the accuracy of different methods adopted in the research. Results have shown that water extraction accuracy wasvariable with respect to the various techniques applied. It was low using ISODATA, very high using DT algorithm andmuch higher using both DTDS and MLC.

  7. A Lip Extraction Algorithm by Using Color Information Considering Obscurity

    Science.gov (United States)

    Shirasawa, Yoichi; Nishida, Makoto

    This paper proposes a method for extracting lip shape and its location from sequential facial images by using color information. The proposed method has no need of extra information on a position nor a form in advance. It is also carried out without special conditions such as lipstick or lighting. Psychometric quantities of a metric hue angle, a metric hue difference and a rectangular coordinates, which are defined in CIE 1976 L*a*b* color space, are used for the extraction. The method employs fuzzy reasoning in order to consider obscurity in image data such as shade on the face. The experimental result indicate the effectiveness of the proposed method; 100 percent of facial images data was estimated a lip’s position, and about 94 percent of facial images data was extracted its shape.

  8. Ontology Learning and Information Extraction for the Semantic Web

    OpenAIRE

    Kavalec, Martin

    2006-01-01

    The work gives overview of its three main topics: semantic web, information extraction and ontology learning. A method for identification relevant information on web pages is described and experimentally tested on pages of companies offering products and services. The method is based on analysis of a sample web pages and their position in the Open Directory catalogue. Furthermore, a modfication of association rules mining algorithm is proposed and experimentally tested. In addition to an iden...

  9. Ethics Review Committee approval and informed consent: an analysis of biomedical publications originating from Sri Lanka

    Directory of Open Access Journals (Sweden)

    Siriwardhana Chesmal

    2008-02-01

    Full Text Available Abstract Background International guidelines on research have focused on protecting research participants. Ethical Research Committee (ERC approval and informed consent are the cornerstones. Externally sponsored research requires approval through ethical review in both the host and the sponsoring country. This study aimed to determine to what extent ERC approval and informed consent procedures are documented in locally and internationally published human subject research carried out in Sri Lanka. Methods We obtained ERC approval in Sri Lanka and the United Kingdom. Theses from 1985 to 2005 available at the Postgraduate Institute of Medicine (PGIM library affiliated to the University of Colombo were scrutinised using checklists agreed in consultation with senior research collaborators. A Medline search was carried out with MeSH major and minor heading 'Sri Lanka' as the search term for international publications originating in Sri Lanka during 1999 to 2004. All research publications from CMJ during 1999 to 2005 were also scrutinized. Results Of 291 theses, 34% documented ERC approvals and 61% documented obtaining consent. From the international journal survey, 250 publications originated from Sri Lanka of which only 79 full text original research publications could be accessed electronically. Of these 38% documented ERC approval and 39% documented obtaining consent. In the Ceylon Medical Journal 36% documented ERC approval and 37% documented obtaining consent. Conclusion Only one third of the publications scrutinized recorded ERC approval and procurement of informed consent. However, there is a positive trend in documenting these ethical requirements in local postgraduate research and in the local medical journal.

  10. Extracting Semantic Information from Visual Data: A Survey

    Directory of Open Access Journals (Sweden)

    Qiang Liu

    2016-03-01

    Full Text Available The traditional environment maps built by mobile robots include both metric ones and topological ones. These maps are navigation-oriented and not adequate for service robots to interact with or serve human users who normally rely on the conceptual knowledge or semantic contents of the environment. Therefore, the construction of semantic maps becomes necessary for building an effective human-robot interface for service robots. This paper reviews recent research and development in the field of visual-based semantic mapping. The main focus is placed on how to extract semantic information from visual data in terms of feature extraction, object/place recognition and semantic representation methods.

  11. A semi-supervised approach to extract pharmacogenomics-specific drug-gene pairs from biomedical literature for personalized medicine.

    Science.gov (United States)

    Xu, Rong; Wang, Quanqiu

    2013-08-01

    Personalized medicine is to deliver the right drug to the right patient in the right dose. Pharmacogenomics (PGx) is to identify genetic variants that may affect drug efficacy and toxicity. The availability of a comprehensive and accurate PGx-specific drug-gene relationship knowledge base is important for personalized medicine. However, building a large-scale PGx-specific drug-gene knowledge base is a difficult task. In this study, we developed a bootstrapping, semi-supervised learning approach to iteratively extract and rank drug-gene pairs according to their relevance to drug pharmacogenomics. Starting with a single PGx-specific seed pair and 20 million MEDLINE abstracts, the extraction algorithm achieved a precision of 0.219, recall of 0.368 and F1 of 0.274 after two iterations, a significant improvement over the results of using non-PGx-specific seeds (precision: 0.011, recall: 0.018, and F1: 0.014) or co-occurrence (precision: 0.015, recall: 1.000, and F1: 0.030). After the extraction step, the ranking algorithm further improved the precision from 0.219 to 0.561 for top ranked pairs. By comparing to a dictionary-based approach with PGx-specific gene lexicon as input, we showed that the bootstrapping approach has better performance in terms of both precision and F1 (precision: 0.251 vs. 0.152, recall: 0.396 vs. 0.856 and F1: 0.292 vs. 0.254). By integrative analysis using a large drug adverse event database, we have shown that the extracted drug-gene pairs strongly correlate with drug adverse events. In conclusion, we developed a novel semi-supervised bootstrapping approach for effective PGx-specific drug-gene pair extraction from large number of MEDLINE articles with minimal human input. PMID:23570835

  12. Biomedical photonics handbook biomedical diagnostics

    CERN Document Server

    Vo-Dinh, Tuan

    2014-01-01

    Shaped by Quantum Theory, Technology, and the Genomics RevolutionThe integration of photonics, electronics, biomaterials, and nanotechnology holds great promise for the future of medicine. This topic has recently experienced an explosive growth due to the noninvasive or minimally invasive nature and the cost-effectiveness of photonic modalities in medical diagnostics and therapy. The second edition of the Biomedical Photonics Handbook presents fundamental developments as well as important applications of biomedical photonics of interest to scientists, engineers, manufacturers, teachers, studen

  13. Advanced applications of natural language processing for performing information extraction

    CERN Document Server

    Rodrigues, Mário

    2015-01-01

    This book explains how can be created information extraction (IE) applications that are able to tap the vast amount of relevant information available in natural language sources: Internet pages, official documents such as laws and regulations, books and newspapers, and social web. Readers are introduced to the problem of IE and its current challenges and limitations, supported with examples. The book discusses the need to fill the gap between documents, data, and people, and provides a broad overview of the technology supporting IE. The authors present a generic architecture for developing systems that are able to learn how to extract relevant information from natural language documents, and illustrate how to implement working systems using state-of-the-art and freely available software tools. The book also discusses concrete applications illustrating IE uses.   ·         Provides an overview of state-of-the-art technology in information extraction (IE), discussing achievements and limitations for t...

  14. Extracting Depth Information Using a Correlation Matching Algorithm

    OpenAIRE

    Mohammed Omar; Jeffery Beers; Mahmoud Abdelhamid

    2012-01-01

    This manuscript presents a modified algorithm to extract depth information from stereo-vision acquisitions using a correlation based approaches. The main implementation of the proposed method is in the area of autonomous Pick & Place, using a robotic manipulator. Current vision-guided robotics is still based on a priori training and teaching steps, and still suffers from long response time. This study uses a stereo triangulation setup where two Charged Coupled Devices CCDs are arranged to...

  15. Sensor data analysis and information extraction for structural health monitoring

    OpenAIRE

    Yan, Linjun

    2006-01-01

    Recently, advances in sensing techniques, internet technologies, and wireless communications are increasingly facilitating and allowing practical deployment of large and dense sensor networks for structural health monitoring. Thus, it is vital to develop efficient techniques to process and analyze the massive amount of sensor data in order to extract essential information on the monitored structures. The efforts in this dissertation are mainly dedicated to this direction, including studies on...

  16. Information extraction for enhanced access to disease outbreak reports.

    Science.gov (United States)

    Grishman, Ralph; Huttunen, Silja; Yangarber, Roman

    2002-08-01

    Document search is generally based on individual terms in the document. However, for collections within limited domains it is possible to provide more powerful access tools. This paper describes a system designed for collections of reports of infectious disease outbreaks. The system, Proteus-BIO, automatically creates a table of outbreaks, with each table entry linked to the document describing that outbreak; this makes it possible to use database operations such as selection and sorting to find relevant documents. Proteus-BIO consists of a Web crawler which gathers relevant documents; an information extraction engine which converts the individual outbreak events to a tabular database; and a database browser which provides access to the events and, through them, to the documents. The information extraction engine uses sets of patterns and word classes to extract the information about each event. Preparing these patterns and word classes has been a time-consuming manual operation in the past, but automated discovery tools now make this task significantly easier. A small study comparing the effectiveness of the tabular index with conventional Web search tools demonstrated that users can find substantially more documents in a given time period with Proteus-BIO. PMID:12755518

  17. Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature

    OpenAIRE

    Chen, Guocai; Zhao, Jieyi; Cohen, Trevor; Tao, Cui; Sun, Jingchun; Xu, Hua; Bernstam, Elmer V.; Lawson, Andrew; Zeng, Jia; Johnson, Amber M.; Holla, Vijaykumar; Bailey, Ann M.; Lara-Guerra, Humberto; Litzenburger, Beate; Meric-Bernstam, Funda

    2015-01-01

    Ambiguous gene names in the biomedical literature are a barrier to accurate information extraction. To overcome this hurdle, we generated Ontology Fingerprints for selected genes that are relevant for personalized cancer therapy. These Ontology Fingerprints were used to evaluate the association between genes and biomedical literature to disambiguate gene names. We obtained 93.6% precision for the test gene set and 80.4% for the area under a receiver-operating characteristics curve for gene an...

  18. Model-Based Information Extraction From Synthetic Aperture Radar Signals

    Science.gov (United States)

    Matzner, Shari A.

    2011-07-01

    Synthetic aperture radar (SAR) is a remote sensing technology for imaging areas of the earth's surface. SAR has been successfully used for monitoring characteristics of the natural environment such as land cover type and tree density. With the advent of higher resolution sensors, it is now theoretically possible to extract information about individual structures such as buildings from SAR imagery. This information could be used for disaster response and security-related intelligence. SAR has an advantage over other remote sensing technologies for these applications because SAR data can be collected during the night and in rainy or cloudy conditions. This research presents a model-based method for extracting information about a building -- its height and roof slope -- from a single SAR image. Other methods require multiple images or ancillary data from specialized sensors, making them less practical. The model-based method uses simulation to match a hypothesized building to an observed SAR image. The degree to which a simulation matches the observed data is measured by mutual information. The success of this method depends on the accuracy of the simulation and on the reliability of the mutual information similarity measure. Electromagnetic theory was applied to relate a building's physical characteristics to the features present in a SAR image. This understanding was used to quantify the precision of building information contained in SAR data, and to identify the inputs needed for accurate simulation. A new SAR simulation technique was developed to meet the accuracy and efficiency requirements of model-based information extraction. Mutual information, a concept from information theory, has become a standard for measuring the similarity between medical images. Its performance in the context of matching a simulation image to a SAR image was evaluated in this research, and it was found to perform well under certain conditions. The factors that affect its performance

  19. miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature

    Directory of Open Access Journals (Sweden)

    Zimmer Ralf

    2010-03-01

    Full Text Available Abstract Background MicroRNAs have been discovered as important regulators of gene expression. To identify the target genes of microRNAs, several databases and prediction algorithms have been developed. Only few experimentally confirmed microRNA targets are available in databases. Many of the microRNA targets stored in databases were derived from large-scale experiments that are considered not very reliable. We propose to use text mining of publication abstracts for extracting microRNA-gene associations including microRNA-target relations to complement current repositories. Results The microRNA-gene association database miRSel combines text-mining results with existing databases and computational predictions. Text mining enables the reliable extraction of microRNA, gene and protein occurrences as well as their relationships from texts. Thereby, we increased the number of human, mouse and rat miRNA-gene associations by at least three-fold as compared to e.g. TarBase, a resource for miRNA-gene associations. Conclusions Our database miRSel offers the currently largest collection of literature derived miRNA-gene associations. Comprehensive collections of miRNA-gene associations are important for the development of miRNA target prediction tools and the analysis of regulatory networks. miRSel is updated daily and can be queried using a web-based interface via microRNA identifiers, gene and protein names, PubMed queries as well as gene ontology (GO terms. miRSel is freely available online at http://services.bio.ifi.lmu.de/mirsel.

  20. Biomedical Engineering

    CERN Document Server

    Suh, Sang C; Tanik, Murat M

    2011-01-01

    Biomedical Engineering: Health Care Systems, Technology and Techniques is an edited volume with contributions from world experts. It provides readers with unique contributions related to current research and future healthcare systems. Practitioners and researchers focused on computer science, bioinformatics, engineering and medicine will find this book a valuable reference.

  1. Extraction of spatial information for low-bandwidth telerehabilitation applications

    Directory of Open Access Journals (Sweden)

    Kok Kiong Tan, PhD

    2014-09-01

    Full Text Available Telemedicine applications, based on two-dimensional (2D video conferencing technology, have been around for the past 15 to 20 yr. They have been demonstrated to be acceptable for face-to-face consultations and useful for visual examination of wounds and abrasions. However, certain telerehabilitation assessments need the use of spatial information in order to accurately assess the patient’s condition and sending three-dimensional video data over low-bandwidth networks is extremely challenging. This article proposes an innovative way of extracting the key spatial information from the patient’s movement during telerehabilitation assessment based on 2D video and then presenting the extracted data by using graph plots alongside the video to help physicians in assessments with minimum burden on existing video data transfer. Some common rehabilitation scenarios are chosen for illustrations, and experiments are conducted based on skeletal tracking and color detection algorithms using the Microsoft Kinect sensor. Extracted data are analyzed in detail and their usability discussed.

  2. THE METHODS OF EXTRACTING WATER INFORMATION FROM SPOT IMAGE

    Institute of Scientific and Technical Information of China (English)

    DUJin-kang; FENGXue-zhi; 等

    2002-01-01

    Some techniques and methods for deriving water information from SPOT-4(XI) image were investigated and discussed in this paper.An algorithmoif decision-tree(DT) classification which includes several classifiers based on the spectral responding characteristics of water bodies and other objects,was developed and put forward to delineate water bodies.Another algorithm of decision-tree classification based on both spectral characteristics and auxiliary information of DEM and slope(DTDS) was also designed for water bodies extraction.In addition,supervised classification method of maximum-likelyhood classification(MLC),and unsupervised method of interactive self -organizing dada analysis technique(ISODATA) were used to extract waterbodies for comparison purpose.An index was designed and used to assess the accuracy of different methods abopted in the research.Results have shown that water extraction accuracy was variable with respect to the various techniques applied.It was low using ISODATA,very high using DT algorithm and much higher using both DTDS and MLC.

  3. Transliteration normalization for Information Extraction and Machine Translation

    Directory of Open Access Journals (Sweden)

    Yuval Marton

    2014-12-01

    Full Text Available Foreign name transliterations typically include multiple spelling variants. These variants cause data sparseness and inconsistency problems, increase the Out-of-Vocabulary (OOV rate, and present challenges for Machine Translation, Information Extraction and other natural language processing (NLP tasks. This work aims to identify and cluster name spelling variants using a Statistical Machine Translation method: word alignment. The variants are identified by being aligned to the same “pivot” name in another language (the source-language in Machine Translation settings. Based on word-to-word translation and transliteration probabilities, as well as the string edit distance metric, names with similar spellings in the target language are clustered and then normalized to a canonical form. With this approach, tens of thousands of high-precision name transliteration spelling variants are extracted from sentence-aligned bilingual corpora in Arabic and English (in both languages. When these normalized name spelling variants are applied to Information Extraction tasks, improvements over strong baseline systems are observed. When applied to Machine Translation tasks, a large improvement potential is shown.

  4. Knowledge discovery: Extracting usable information from large amounts of data

    International Nuclear Information System (INIS)

    The threat of nuclear weapons proliferation is a problem of world wide concern. Safeguards are the key to nuclear nonproliferation and data is the key to safeguards. The safeguards community has access to a huge and steadily growing volume of data. The advantages of this data rich environment are obvious, there is a great deal of information which can be utilized. The challenge is to effectively apply proven and developing technologies to find and extract usable information from that data. That information must then be assessed and evaluated to produce the knowledge needed for crucial decision making. Efficient and effective analysis of safeguards data will depend on utilizing technologies to interpret the large, heterogeneous data sets that are available from diverse sources. With an order-of-magnitude increase in the amount of data from a wide variety of technical, textual, and historical sources there is a vital need to apply advanced computer technologies to support all-source analysis. There are techniques of data warehousing, data mining, and data analysis that can provide analysts with tools that will expedite their extracting useable information from the huge amounts of data to which they have access. Computerized tools can aid analysts by integrating heterogeneous data, evaluating diverse data streams, automating retrieval of database information, prioritizing inputs, reconciling conflicting data, doing preliminary interpretations, discovering patterns or trends in data, and automating some of the simpler prescreening tasks that are time consuming and tedious. Thus knowledge discovery technologies can provide a foundation of support for the analyst. Rather than spending time sifting through often irrelevant information, analysts could use their specialized skills in a focused, productive fashion. This would allow them to make their analytical judgments with more confidence and spend more of their time doing what they do best

  5. Recognition techniques for extracting information from semistructured documents

    Science.gov (United States)

    Della Ventura, Anna; Gagliardi, Isabella; Zonta, Bruna

    2000-12-01

    Archives of optical documents are more and more massively employed, the demand driven also by the new norms sanctioning the legal value of digital documents, provided they are stored on supports that are physically unalterable. On the supply side there is now a vast and technologically advanced market, where optical memories have solved the problem of the duration and permanence of data at costs comparable to those for magnetic memories. The remaining bottleneck in these systems is the indexing. The indexing of documents with a variable structure, while still not completely automated, can be machine supported to a large degree with evident advantages both in the organization of the work, and in extracting information, providing data that is much more detailed and potentially significant for the user. We present here a system for the automatic registration of correspondence to and from a public office. The system is based on a general methodology for the extraction, indexing, archiving, and retrieval of significant information from semi-structured documents. This information, in our prototype application, is distributed among the database fields of sender, addressee, subject, date, and body of the document.

  6. Evolutionary computation for information extraction from remotely sensed imagery

    Science.gov (United States)

    Momm, Henrique Garcia

    Automated and semi-automated techniques have been researched as an alternative way to reduce human interaction and thus improve the information extraction process from imagery. This research developed an innovative methodology by integrating machine learning algorithms with image processing and remote sensing procedures to form the evolutionary framework. In this biologically-inspired methodology, non-linear solutions are developed by iteratively updating a set of candidate solutions through operations such as: reproduction, competition, and selection. Uncertainty analysis is conducted to quantitatively assess the system's variability due to the random generation of the initial set of candidate solutions, from which the algorithm begins. A new convergence approach is proposed and results indicate that it not only reduces the overall variability of the system but also the number of iterations needed to obtain the optimal solution. Additionally, the evolutionary framework is evaluated in solving different remote sensing problems, such as: non-linear inverse modeling, integration of image texture with spectral information, and multitemporal feature extraction. The investigations in this research revealed that the use of evolutionary computation to solve remote sensing problems is feasible. Results also indicate that, the evolutionary framework reduces the overall dimensionality of the data by removing redundant information while generating robust solutions regardless of the variations in the statistics and the distribution of the data. Thus, signifying that the proposed framework is capable of mathematically incorporating the non-linear relationship between features into the final solution.

  7. Audio enabled information extraction system for cricket and hockey domains

    CERN Document Server

    Saraswathi, S; B., Sai Vamsi Krishna; S, Suresh Reddy

    2010-01-01

    The proposed system aims at the retrieval of the summarized information from the documents collected from web based search engine as per the user query related to cricket and hockey domain. The system is designed in a manner that it takes the voice commands as keywords for search. The parts of speech in the query are extracted using the natural language extractor for English. Based on the keywords the search is categorized into 2 types: - 1.Concept wise - information retrieved to the query is retrieved based on the keywords and the concept words related to it. The retrieved information is summarized using the probabilistic approach and weighted means algorithm.2.Keyword search - extracts the result relevant to the query from the highly ranked document retrieved from the search by the search engine. The relevant search results are retrieved and then keywords are used for summarizing part. During summarization it follows the weighted and probabilistic approaches in order to identify the data comparable to the k...

  8. [Study on Information Extraction of Clinic Expert Information from Hospital Portals].

    Science.gov (United States)

    Zhang, Yuanpeng; Dong, Jiancheng; Qian, Danmin; Geng, Xingyun; Wu, Huiqun; Wang, Li

    2015-12-01

    Clinic expert information provides important references for residents in need of hospital care. Usually, such information is hidden in the deep web and cannot be directly indexed by search engines. To extract clinic expert information from the deep web, the first challenge is to make a judgment on forms. This paper proposes a novel method based on a domain model, which is a tree structure constructed by the attributes of search interfaces. With this model, search interfaces can be classified to a domain and filled in with domain keywords. Another challenge is to extract information from the returned web pages indexed by search interfaces. To filter the noise information on a web page, a block importance model is proposed. The experiment results indicated that the domain model yielded a precision 10.83% higher than that of the rule-based method, whereas the block importance model yielded an F₁ measure 10.5% higher than that of the XPath method. PMID:27079096

  9. A High Accuracy Method for Semi-supervised Information Extraction

    Energy Technology Data Exchange (ETDEWEB)

    Tratz, Stephen C.; Sanfilippo, Antonio P.

    2007-04-22

    Customization to specific domains of dis-course and/or user requirements is one of the greatest challenges for today’s Information Extraction (IE) systems. While demonstrably effective, both rule-based and supervised machine learning approaches to IE customization pose too high a burden on the user. Semi-supervised learning approaches may in principle offer a more resource effective solution but are still insufficiently accurate to grant realistic application. We demonstrate that this limitation can be overcome by integrating fully-supervised learning techniques within a semi-supervised IE approach, without increasing resource requirements.

  10. Using XBRL Technology to Extract Competitive Information from Financial Statements

    Directory of Open Access Journals (Sweden)

    Dominik Ditter

    2011-12-01

    Full Text Available The eXtensible Business Reporting Language, or XBRL, is a reporting format for the automatic and electronic exchange of business and financial data. In XBRL every single reported fact is marked with a unique tag, enabling a full computer-based readout of financial data. It has the potential to improve the collection and analysis of financial data for Competitive Intelligence (e.g., the profiling of publicly available financial statements. The article describes how easily information from XBRL reports can be extracted.

  11. Biomedical Materials

    Institute of Scientific and Technical Information of China (English)

    CHANG Jiang; ZHOU Yanling

    2011-01-01

    @@ Biomedical materials, biomaterials for short, is regarded as "any substance or combination of substances, synthetic or natural in origin, which can be used for any period of time, as a whole or as part of a system which treats, augments, or replaces any tissue, organ or function of the body" (Vonrecum & Laberge, 1995).Biomaterials can save lives, relieve suffering and enhance the quality of life for human being.

  12. An Italian Biomedical Publications Database

    OpenAIRE

    De Robbio, Antonella; Mozzati, Paola; Lazzari, Luigina; Maguolo, Dario; Dolfino, Manuela; Gradito, Paola

    2002-01-01

    Periodical scientific literature is one of the most important information sources for the scientific community and particularly for biomedicine. As regards Italian publications today, a part from very few laudable exceptions, there is a lack of the instruments necessary for accessing the information that they contain. With over 700 Italian biomedical texts, only 25% are mentioned in the more important biomedical data banks, such as Medline, Embase, Pascal, CAB, with unfortunately a great deal...

  13. Computational intelligence in biomedical imaging

    CERN Document Server

    2014-01-01

    This book provides a comprehensive overview of the state-of-the-art computational intelligence research and technologies in biomedical images with emphasis on biomedical decision making. Biomedical imaging offers useful information on patients’ medical conditions and clues to causes of their symptoms and diseases. Biomedical images, however, provide a large number of images which physicians must interpret. Therefore, computer aids are demanded and become indispensable in physicians’ decision making. This book discusses major technical advancements and research findings in the field of computational intelligence in biomedical imaging, for example, computational intelligence in computer-aided diagnosis for breast cancer, prostate cancer, and brain disease, in lung function analysis, and in radiation therapy. The book examines technologies and studies that have reached the practical level, and those technologies that are becoming available in clinical practices in hospitals rapidly such as computational inte...

  14. Automated extraction of chemical structure information from digital raster images

    Directory of Open Access Journals (Sweden)

    Shedden Kerby A

    2009-02-01

    Full Text Available Abstract Background To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader – a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links

  15. Text mining patents for biomedical knowledge.

    Science.gov (United States)

    Rodriguez-Esteban, Raul; Bundschus, Markus

    2016-06-01

    Biomedical text mining of scientific knowledge bases, such as Medline, has received much attention in recent years. Given that text mining is able to automatically extract biomedical facts that revolve around entities such as genes, proteins, and drugs, from unstructured text sources, it is seen as a major enabler to foster biomedical research and drug discovery. In contrast to the biomedical literature, research into the mining of biomedical patents has not reached the same level of maturity. Here, we review existing work and highlight the associated technical challenges that emerge from automatically extracting facts from patents. We conclude by outlining potential future directions in this domain that could help drive biomedical research and drug discovery. PMID:27179985

  16. Secure Transmission and Recovery of Embedded Patient Information from Biomedical Images of Different Modalities through a Combination of Cryptography and Watermarking

    Directory of Open Access Journals (Sweden)

    Subhajit Koley

    2014-03-01

    Full Text Available In this paper a new type of information hiding skill in biomedical images is proposed through a combination of cryptography and digital watermarking to achieve the enhancement in confidential and authenticated data storage and secured transmission. Here patient's name and doctor's name are considered as patient's information which is encrypted using cryptography and embedded in the scan image of that patient through watermarking. RSA algorithm is used for encryption and higher order bit LSB replacement technique is used for embedding the information. The private keys are also embedded in the cover image to have better security and accurate recovery of the hidden information. The outcome of the proposed methodology shows that the hidden information doesn't affect the cover image and it can be recovered efficiently even from several noisy images. The strength of the proposed embedding scheme is also supported by several image quality matrices.

  17. Event extraction for DNA methylation

    OpenAIRE

    Ohta Tomoko; Pyysalo Sampo; Miwa Makoto; Tsujii Jun’ichi

    2011-01-01

    Abstract Background We consider the task of automatically extracting DNA methylation events from the biomedical domain literature. DNA methylation is a key mechanism of epigenetic control of gene expression and implicated in many cancers, but there has been little study of automatic information extraction for DNA methylation. Results We present an annotation scheme for DNA methylation following the representation of the BioNLP shared task on event extraction, select a set of 200 abstracts inc...

  18. Searching Biomedical Text: Towards Maximum Relevant Results

    OpenAIRE

    Galde, Ola; Sevaldsen, John Harald

    2006-01-01

    The amount of biomedical information available to users today is large and increasing. The ability to precisely retrieve desired information is vital in order to utilize available knowledge. In this work we investigated how to improve the relevance of biomedical search results. Using the Lucene Java API we applied a series of information retrieval techniques to search in biomedical data. The techniques ranged from basic stemming and stop-word removal to more advanced methods like user relevan...

  19. Research of information classification and strategy intelligence extract algorithm based on military strategy hall

    Science.gov (United States)

    Chen, Lei; Li, Dehua; Yang, Jie

    2007-12-01

    Constructing virtual international strategy environment needs many kinds of information, such as economy, politic, military, diploma, culture, science, etc. So it is very important to build an information auto-extract, classification, recombination and analysis management system with high efficiency as the foundation and component of military strategy hall. This paper firstly use improved Boost algorithm to classify obtained initial information, then use a strategy intelligence extract algorithm to extract strategy intelligence from initial information to help strategist to analysis information.

  20. An Extraction Method of an Informative DOM Node from a Web Page by Using Layout Information

    Science.gov (United States)

    Tsuruta, Masanobu; Masuyama, Shigeru

    We propose an informative DOM node extraction method from a Web page for preprocessing of Web content mining. Our proposed method LM uses layout data of DOM nodes generated by a generic Web browser, and the learning set consists of hundreds of Web pages and the annotations of informative DOM nodes of those Web pages. Our method does not require large scale crawling of the whole Web site to which the target Web page belongs. We design LM so that it uses the information of the learning set more efficiently in comparison to the existing method that uses the same learning set. By experiments, we evaluate the methods obtained by combining one that consists of the method for extracting the informative DOM node both the proposed method and the existing methods, and the existing noise elimination methods: Heur removes advertisements and link-lists by some heuristics and CE removes the DOM nodes existing in the Web pages in the same Web site to which the target Web page belongs. Experimental results show that 1) LM outperforms other methods for extracting the informative DOM node, 2) the combination method (LM, {CE(10), Heur}) based on LM (precision: 0.755, recall: 0.826, F-measure: 0.746) outperforms other combination methods.

  1. Holography In Biomedical Sciences

    Science.gov (United States)

    von Bally, G.

    1988-01-01

    Today not only physicists and engineers but also biological and medical scientists are exploring the potentials of holographic methods in their special field of work. Most of the underlying physical principles such as coherence, interference, diffraction and polarization as well as general features of holography e.g. storage and retrieval of amplitude and phase of a wavefront, 3-d-imaging, large field of depth, redundant storage of information, spatial filtering, high-resolving, non-contactive, 3-d form and motion analysis are explained in detail in other contributions to this book. Therefore, this article is confined to the applications of holography in biomedical sciences. Because of the great number of contributions and the variety of applications [1,2,3,4,5,6,7,8] in this review the investigations can only be mentioned briefly and the survey has to be confined to some examples. As in all fields of optics and laser metrology, a review of biomedical applications of holography would be incomplete if military developments and their utilization are not mentioned. As will be demonstrated by selected examples the increasing interlacing of science with the military does not stop at domains that traditionally are regarded as exclusively oriented to human welfare like biomedical research [9]. This fact is actually characterized and stressed by the expression "Star Wars Medicine", which becomes increasingly common as popular description for laser applications (including holography) in medicine [10]. Thus, the consequence - even in such highly specialized fields like biomedical applications of holography - have to be discussed.

  2. Spectra in the chaotic region: Methods for extracting dynamic information

    Energy Technology Data Exchange (ETDEWEB)

    Gomez Llorente, J.M.; Zakrzewski, J.; Taylor, H.S.; Kulander, K.C.

    1989-02-01

    Nonlinear dynamics is applied to chaotic unassignable atomic and molecular spectra with the aim of extracting detailed information about regular dynamic motions that exist over short intervals of time. It is shown how this motion can be extracted from high resolution spectra by doing low resolution studies or by Fourier transforming limited regions of the spectrum. These motions mimic those of periodic orbits (PO) and are inserts into the dominant chaotic motion. Considering these inserts and the PO as a dynamically decoupled region of space, resonant scattering theory and stabilization methods enable us to compute ladders of resonant states which interact with the chaotic quasicontinuum computed in principle from basis sets placed off the PO. The interaction of the resonances with the quasicontinuum explains the low resolution spectra seen in such experiments. It also allows one to associate low resolution features with a particular PO. The motion on the PO thereby supplies the molecular movements whose quantization causes the low resolution spectra. Characteristic properties of the periodic orbit based resonances are discussed. The method is illustrated on the photoabsorption spectrum of the hydrogen atom in a strong magnetic field and on the photodissociation spectrum of H/sup +//sub 3/ . Other molecular systems which are currently under investigation using this formalism are also mentioned.

  3. Domain-independent information extraction in unstructured text

    Energy Technology Data Exchange (ETDEWEB)

    Irwin, N.H. [Sandia National Labs., Albuquerque, NM (United States). Software Surety Dept.

    1996-09-01

    Extracting information from unstructured text has become an important research area in recent years due to the large amount of text now electronically available. This status report describes the findings and work done during the second year of a two-year Laboratory Directed Research and Development Project. Building on the first-year`s work of identifying important entities, this report details techniques used to group words into semantic categories and to output templates containing selective document content. Using word profiles and category clustering derived during a training run, the time-consuming knowledge-building task can be avoided. Though the output still lacks in completeness when compared to systems with domain-specific knowledge bases, the results do look promising. The two approaches are compatible and could complement each other within the same system. Domain-independent approaches retain appeal as a system that adapts and learns will soon outpace a system with any amount of a priori knowledge.

  4. Extracting kinetic information from literature with KineticRE.

    Science.gov (United States)

    Freitas, Ana Alão; Costa, Hugo; Rocha, Miguel; Rocha, Isabel

    2015-01-01

    To better understand the dynamic behavior of metabolic networks in a wide variety of conditions, the field of Systems Biology has increased its interest in the use of kinetic models. The different databases, available these days, do not contain enough data regarding this topic. Given that a significant part of the relevant information for the development of such models is still wide spread in the literature, it becomes essential to develop specific and powerful text mining tools to collect these data. In this context, this work has as main objective the development of a text mining tool to extract, from scientific literature, kinetic parameters, their respective values and their relations with enzymes and metabolites. The approach proposed integrates the development of a novel plug-in over the text mining framework @Note2. In the end, the pipeline developed was validated with a case study on Kluyveromyces lactis, spanning the analysis and results of 20 full text documents. PMID:26673933

  5. ONTOGRABBING: Extracting Information from Texts Using Generative Ontologies

    DEFF Research Database (Denmark)

    Nilsson, Jørgen Fischer; Szymczak, Bartlomiej Antoni; Jensen, P.A.

    2009-01-01

    We describe principles for extracting information from texts using a so-called generative ontology in combination with syntactic analysis. Generative ontologies are introduced as semantic domains for natural language phrases. Generative ontologies extend ordinary finite ontologies with rules for...... producing recursively shaped terms representing the ontological content (ontological semantics) of NL noun phrases and other phrases. We focus here on achieving a robust, often only partial, ontology-driven parsing of and ascription of semantics to a sentence in the text corpus. The aim of the ontological...... analysis is primarily to identify paraphrases, thereby achieving a search functionality beyond mere keyword search with synsets. We further envisage use of the generative ontology as a phrase-based rather than word-based browser into text corpora....

  6. Querying and Extracting Timeline Information from Road Traffic Sensor Data.

    Science.gov (United States)

    Imawan, Ardi; Indikawati, Fitri Indra; Kwon, Joonho; Rao, Praveen

    2016-01-01

    The escalation of traffic congestion in urban cities has urged many countries to use intelligent transportation system (ITS) centers to collect historical traffic sensor data from multiple heterogeneous sources. By analyzing historical traffic data, we can obtain valuable insights into traffic behavior. Many existing applications have been proposed with limited analysis results because of the inability to cope with several types of analytical queries. In this paper, we propose the QET (querying and extracting timeline information) system-a novel analytical query processing method based on a timeline model for road traffic sensor data. To address query performance, we build a TQ-index (timeline query-index) that exploits spatio-temporal features of timeline modeling. We also propose an intuitive timeline visualization method to display congestion events obtained from specified query parameters. In addition, we demonstrate the benefit of our system through a performance evaluation using a Busan ITS dataset and a Seattle freeway dataset. PMID:27563900

  7. Multi-Filter String Matching and Human-Centric Entity Matching for Information Extraction

    Science.gov (United States)

    Sun, Chong

    2012-01-01

    More and more information is being generated in text documents, such as Web pages, emails and blogs. To effectively manage this unstructured information, one broadly used approach includes locating relevant content in documents, extracting structured information and integrating the extracted information for querying, mining or further analysis. In…

  8. Multilingual Biomedical Dictionary

    OpenAIRE

    Daumke, Philipp; Markó, Kornél; Poprat, Michael; Schulz, Stefan

    2005-01-01

    We present a unique technique to create a multilingual biomedical dictionary, based on a methodology called Morpho-Semantic indexing. Our approach closes a gap caused by the absence of free available multilingual medical dictionaries and the lack of accuracy of non-medical electronic translation tools. We first explain the underlying technology followed by a description of the dictionary interface, which makes use of a multilingual subword thesaurus and of statistical inform...

  9. Applying an information transmission approach to extract valence electron information from reconstructed exit waves

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Qiang, E-mail: q.xu@tudelft.nl [EMAT, University of Antwerp, 2020 Antwerp Groenenborgerlaan, 171, U316 (Belgium); National Centre for HREM, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Lorentzweg 1, Delft (Netherlands); Zandbergen, Henny W. [National Centre for HREM, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Lorentzweg 1, Delft (Netherlands); Van Dyck, Dirk [EMAT, University of Antwerp, 2020 Antwerp Groenenborgerlaan, 171, U316 (Belgium); Vison Vision Lab, University of Antwerp, 2020 Antwerp Groenenborgerlaan, 171, U316 (Belgium)

    2011-06-15

    The knowledge of the valence electron distribution is essential for understanding the properties of materials. However this information is difficult to obtain from HREM images because it is easily obscured by the large scattering contribution of core electrons and by the strong dynamical scattering process. In order to develop a sensitive method to extract the information of valence electrons, we have used an information transmission approach to describe the electron interaction with the object. The scattered electron wave is decomposed in a set of basic functions, which are the eigen functions of the Hamiltonian of the projected electrostatic object potential. Each basic function behaves as a communication channel that transfers the information of the object with its own transmission characteristic. By properly combining the components of the different channels, it is possible to design a scheme to extract the information of valence electron distribution from a series of exit waves. The method is described theoretically and demonstrated by means of computer simulations. -- Research highlights: {yields} Dynamic scattering and image formation processes limit interpretation of HREM images. {yields} Electron distribution (ED) can be obtained by solving two inverse problems. {yields} These two are: Exit wave reconstruction and retrieval of ED from exit waves. {yields} The two inverse problems are inherently same in view of information transmission. {yields} The method to solve one of the problems can also be used for the other.

  10. Automated Information Extraction of Key Trial Design Elements from Clinical Trial Publications

    OpenAIRE

    de Bruijn, Berry; Carini, Simona; Kiritchenko, Svetlana; Martin, Joel; Sim, Ida

    2008-01-01

    Clinical trials are one of the most valuable sources of scientific evidence for improving the practice of medicine. The Trial Bank project aims to improve structured access to trial findings by including formalized trial information into a knowledge base. Manually extracting trial information from published articles is costly, but automated information extraction techniques can assist. The current study highlights a single architecture to extract a wide array of information elements from full...

  11. Network fingerprint: a knowledge-based characterization of biomedical networks

    Science.gov (United States)

    Cui, Xiuliang; He, Haochen; He, Fuchu; Wang, Shengqi; Li, Fei; Bo, Xiaochen

    2015-01-01

    It can be difficult for biomedical researchers to understand complex molecular networks due to their unfamiliarity with the mathematical concepts employed. To represent molecular networks with clear meanings and familiar forms for biomedical researchers, we introduce a knowledge-based computational framework to decipher biomedical networks by making systematic comparisons to well-studied “basic networks”. A biomedical network is characterized as a spectrum-like vector called “network fingerprint”, which contains similarities to basic networks. This knowledge-based multidimensional characterization provides a more intuitive way to decipher molecular networks, especially for large-scale network comparisons and clustering analyses. As an example, we extracted network fingerprints of 44 disease networks in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The comparisons among the network fingerprints of disease networks revealed informative disease-disease and disease-signaling pathway associations, illustrating that the network fingerprinting framework will lead to new approaches for better understanding of biomedical networks. PMID:26307246

  12. ANALYSIS OF INTELLIGENT DATA MINING FOR INFORMATION EXTRACTION USING JAVA AGENT DEVELOPMENT ENVIRONMENT PLATFORM

    Directory of Open Access Journals (Sweden)

    M. Vinoth Kumar

    2013-01-01

    Full Text Available In this study, the problem of unstructured information extraction has been analyzed and the need for a new Information Extraction algorithm is justified. We propose an Intelligent Information Extraction using Java Agent Development Environment (JADE to be an optimal solution for intelligent information extraction. This proposed algorithm first assigns intelligent agents to gathering data, which they then classify, match and organize to construct sequential information for a user query. It improves the efficiency and performance for retrieving a proper information results as a sequence that satisfy user’s needs. It gives the user needed documents based on similarity between query matching and relevant document mechanism. The results obtained from the Intelligent Information Extraction are optimal.

  13. a Probability-Based Statistical Method to Extract Water Body of TM Images with Missing Information

    Science.gov (United States)

    Lian, Shizhong; Chen, Jiangping; Luo, Minghai

    2016-06-01

    Water information cannot be accurately extracted using TM images because true information is lost in some images because of blocking clouds and missing data stripes, thereby water information cannot be accurately extracted. Water is continuously distributed in natural conditions; thus, this paper proposed a new method of water body extraction based on probability statistics to improve the accuracy of water information extraction of TM images with missing information. Different disturbing information of clouds and missing data stripes are simulated. Water information is extracted using global histogram matching, local histogram matching, and the probability-based statistical method in the simulated images. Experiments show that smaller Areal Error and higher Boundary Recall can be obtained using this method compared with the conventional methods.

  14. Biomedical engineering and nanotechnology

    International Nuclear Information System (INIS)

    This book is predominantly a compilation of papers presented in the conference which is focused on the development in biomedical materials, biomedical devises and instrumentation, biomedical effects of electromagnetic radiation, electrotherapy, radiotherapy, biosensors, biotechnology, bioengineering, tissue engineering, clinical engineering and surgical planning, medical imaging, hospital system management, biomedical education, biomedical industry and society, bioinformatics, structured nanomaterial for biomedical application, nano-composites, nano-medicine, synthesis of nanomaterial, nano science and technology development. The papers presented herein contain the scientific substance to suffice the academic directivity of the researchers from the field of biomedicine, biomedical engineering, material science and nanotechnology. Papers relevant to INIS are indexed separately

  15. Information Extraction from Hypertext Mark-Up Language Web Pages

    OpenAIRE

    Mahmoud Shaker; Hamidah Ibrahim; Aida Mustapha; Lili N. Abdullah

    2009-01-01

    Problems statement: Nowadays, many users use web search engines to find and gather information. User faces an increasing amount of various HTML information sources. The issue of correlating, integrating and presenting related information to users becomes important. When a user uses a search engine such as Yahoo and Google to seek specific information, the results are not only information about the availability of the desired information, but also information about other pages on which the des...

  16. Automatic Data Extraction from Websites for Generating Aquatic Product Market Information

    Institute of Scientific and Technical Information of China (English)

    YUAN Hong-chun; CHEN Ying; SUN Yue-fu

    2006-01-01

    The massive web-based information resources have led to an increasing demand for effective automatic retrieval of target information for web applications. This paper introduces a web-based data extraction tool that deploys various algorithms to locate, extract and filter tabular data from HTML pages and to transform them into new web-based representations. The tool has been applied in an aquaculture web application platform for extracting and generating aquatic product market information.Results prove that this tool is very effective in extracting the required data from web pages.

  17. News Discourse and Strategic Monitoring of Events Textometry and Information Extraction for Text Mining

    OpenAIRE

    Erin, Macmurray

    2012-01-01

    This research demonstrates two methods of text mining for strategic monitoring purposes: information extraction and Textometry. In strategic monitoring, text mining is used to automatically obtain information on the activities of corporations. For this objective, information extraction identifies and labels units of information, named entities (companies, places, people), which then constitute entry points for the analysis of economic activities or events. These include mergers, bankruptcies,...

  18. News Discourse and Strategic Monitoring of Events. Textometry and Information Extraction for Text Mining

    OpenAIRE

    MacMurray, Erin

    2012-01-01

    This research demonstrates two methods of text mining for strategic monitoring purposes: information extraction and Textometry. In strategic monitoring, text mining is used to automatically obtain information on the activities of corporations. For this objective, information extraction identifies and labels units of information, named entities (companies, places, people), which then constitute entry points for the analysis of economic activities or events. These include mergers, bankruptcies,...

  19. Medicaid Analytic eXtract (MAX) General Information

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Medicaid Analytic eXtract (MAX) data is a set of person-level data files on Medicaid eligibility, service utilization, and payments. The MAX data are created to...

  20. Tagline: Information Extraction for Semi-Structured Text Elements in Medical Progress Notes

    Science.gov (United States)

    Finch, Dezon Kile

    2012-01-01

    Text analysis has become an important research activity in the Department of Veterans Affairs (VA). Statistical text mining and natural language processing have been shown to be very effective for extracting useful information from medical documents. However, neither of these techniques is effective at extracting the information stored in…

  1. Population information extraction in Chaohu watershed based on RS and GIS

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    It is always difficult to extract population information of small watershed during the region environment assessment. The report adopted compound areal interpolation to study the population in Chaohu watershed with the GIS technique and landuse interpretation data from remote sensing. The result indicated that the method is effective to extract population information of small watershed.

  2. A Framework For Extracting Information From Web Using VTD-XML‘s XPath

    OpenAIRE

    C. Subhashini; Dr.Arti Arya

    2012-01-01

    The exponential growth of WWW (World Wide Web) is the cause for vast pool of information as well as several challenges posed by it, such as extracting potentially useful and unknown information from WWW. Many websites are built with HTML, because of its unstructured layout, it is difficult to obtain effective and precise data from web using HTML. The advent of XML (Extensible Markup Language) proposes a better solution to extract useful knowledge from WWW. Web Data Extraction based on XML Tec...

  3. Extracting the symmetry energy information with heavy ion collisions

    International Nuclear Information System (INIS)

    Nuclear symmetry energy plays an important role in the properties of nuclei and neutron stars. Since theoretical predictions of the density dependence of symmetry energy S(ρ) from microscopic nucleon-nucleon interactions show large uncertainties, especially in the region of suprasaturation density, constraining the density dependence of symmetry energy has become one of the main goals in nuclear physics and has stimulated many theoretical and experimental studies. In this paper, we have reviewed the ImQMD05 code and its description on charge distribution, collective flow and nuclear-nuclear stopping. By comparing ImQMD05 prediction with data, the isoscalar part of nucleonic mean field, the energy and density dependence of in-medium NN cross sectoin in the ImQMD05 were determined. In order to extracting the symmetry energy information by comparing the ImQMD05 calculations with the data for 112,124Sn +112,124 Sn at Ebeam=50 MeV/u, the influence of symmetry potential and in-medium NN cross section on the isospin sensitive observables of intermediate-energy heavy-ion collisions was investigated. Focusing on the region above the Fermi energy, our results show that the symmetry potential plays a more important role in the experimental observables, such as double neutron to proton ratio and the isospin transport ratio Ri, than that the in-medium nucleon-nucleon cross section does. Since the copious production of intermediate mass fragments is a distinguishing feature of intermediate-energy heavy-ion collisions, we also examined the influence of cluster emission on the isospin transport ratio using different isospin tracers. The values of the isospin transport ratios with the tracer defined by the isospin asymmetry of the heaviest fragments with Z≥20 in the projectile region is greater than those obtained from projectile residues (emitting source). This phenomenon can be tested experimentally. By comparing the ImQMD05 predictions with the data for three observables, the

  4. Telemedicine optoelectronic biomedical data processing system

    Science.gov (United States)

    Prosolovska, Vita V.

    2010-08-01

    The telemedicine optoelectronic biomedical data processing system is created to share medical information for the control of health rights and timely and rapid response to crisis. The system includes the main blocks: bioprocessor, analog-digital converter biomedical images, optoelectronic module for image processing, optoelectronic module for parallel recording and storage of biomedical imaging and matrix screen display of biomedical images. Rated temporal characteristics of the blocks defined by a particular triggering optoelectronic couple in analog-digital converters and time imaging for matrix screen. The element base for hardware implementation of the developed matrix screen is integrated optoelectronic couples produced by selective epitaxy.

  5. Towards Effective Biomedical Knowledge Discovery through Subject-Centric Semantic Integration of the Life-Science Information Space

    OpenAIRE

    Nenova, Karamfilka Krasimirova

    2009-01-01

    Within the last two decades, a vast knowledge gap has emerged between the generated volume of information and discovered novel knowledge in life-science. Accordingly to bridge this crucial gap, biological information has to be integrated and provided not only in a homogenous way, but also in the right context, which represents still a demanding knowledge management task. The objective of this thesis was the development of an integrative approach applicable for the life-science information spa...

  6. Extraction of spatio-temporal information of earthquake event based on semantic technology

    Science.gov (United States)

    Fan, Hong; Guo, Dan; Li, Huaiyuan

    2015-12-01

    In this paper a web information extraction method is presented which identifies a variety of thematic events utilizing the event knowledge framework derived from text training, and then further uses the syntactic analysis to extract the event key information. The method which combines the text semantic information and domain knowledge of the event makes the extraction of information people interested more accurate. In this paper, web based earthquake news extraction is taken as an example. The paper firstly briefs the overall approaches, and then details the key algorithm and experiments of seismic events extraction. Finally, this paper conducts accuracy analysis and evaluation experiments which demonstrate that the proposed method is a promising way of hot events mining.

  7. Fast object tracking based on template matching and region information fusion extraction

    Science.gov (United States)

    Liu, Liman; Chen, Yun; Liu, Haihua

    2015-12-01

    In this paper, a fast object tracking algorithm based on template matching and region information fusion extraction is proposed. In the prediction framework, the data connection task is achieved by object template and object information extraction. And then the object is tracked accurately by using the object motion information. We handle the tracking shift by using the confidence estimation strategy. The experiments show that the proposed algorithm has robust performance.

  8. Extraction of Protein Sequence Motif Information using PSO K-Means

    OpenAIRE

    Gowri, R.; Rathipriya, R.

    2015-01-01

    The main objective of the paper is to find the motif information.The functionalities of the proteins are ideally found from their motif information which is extracted using various techniques like clustering with k-means, hybrid k-means, self-organising maps, etc., in the literature. In this work protein sequence information is extracted using optimised k-means algorithm. The particle swarm optimisation technique is one of the frequently used optimisation method. In the current work the PSO k...

  9. Semantic information extracting system for classification of radiological reports in radiology information system (RIS)

    Science.gov (United States)

    Shi, Liehang; Ling, Tonghui; Zhang, Jianguo

    2016-03-01

    Radiologists currently use a variety of terminologies and standards in most hospitals in China, and even there are multiple terminologies being used for different sections in one department. In this presentation, we introduce a medical semantic comprehension system (MedSCS) to extract semantic information about clinical findings and conclusion from free text radiology reports so that the reports can be classified correctly based on medical terms indexing standards such as Radlex or SONMED-CT. Our system (MedSCS) is based on both rule-based methods and statistics-based methods which improve the performance and the scalability of MedSCS. In order to evaluate the over all of the system and measure the accuracy of the outcomes, we developed computation methods to calculate the parameters of precision rate, recall rate, F-score and exact confidence interval.

  10. BIG: a Grid Portal for Biomedical Data and Images

    Directory of Open Access Journals (Sweden)

    Giovanni Aloisio

    2004-06-01

    Full Text Available Modern management of biomedical systems involves the use of many distributed resources, such as high performance computational resources to analyze biomedical data, mass storage systems to store them, medical instruments (microscopes, tomographs, etc., advanced visualization and rendering tools. Grids offer the computational power, security and availability needed by such novel applications. This paper presents BIG (Biomedical Imaging Grid, a Web-based Grid portal for management of biomedical information (data and images in a distributed environment. BIG is an interactive environment that deals with complex user's requests, regarding the acquisition of biomedical data, the "processing" and "delivering" of biomedical images, using the power and security of Computational Grids.

  11. Using rule-based natural language processing to improve disease normalization in biomedical text

    OpenAIRE

    2013-01-01

    Background and objective In order for computers to extract useful information from unstructured text, a concept normalization system is needed to link relevant concepts in a text to sources that contain further information about the concept. Popular concept normalization tools in the biomedical field are dictionary-based. In this study we investigate the usefulness of natural language processing (NLP) as an adjunct to dictionary-based concept normalization. Methods We compared the performance...

  12. Using rule-based natural language processing to improve disease normalization in biomedical text

    OpenAIRE

    Kang, Ning; Singh, Bharat; Afzal, Zubair; Mulligen, Erik; Kors, Jan

    2013-01-01

    textabstractBackground and objective: In order for computers to extract useful information from unstructured text, a concept normalization system is needed to link relevant concepts in a text to sources that contain further information about the concept. Popular concept normalization tools in the biomedical field are dictionarybased. In this study we investigate the usefulness of natural language processing (NLP) as an adjunct to dictionary-based concept normalization. Methods: We compared th...

  13. Biomedical applications of X-ray absorption and vibrational spectroscopic microscopies in obtaining structural information from complex systems

    Energy Technology Data Exchange (ETDEWEB)

    Aitken, Jade B.; Carter, Elizabeth A. [School of Chemistry, University of Sydney, NSW 2006 (Australia); Eastgate, Harold [Eastmac Pty Ltd, 8 Cassinia Close, Knoxfield, Vic 3180 (Australia); Hackett, Mark J.; Harris, Hugh H.; Levina, Aviva [School of Chemistry, University of Sydney, NSW 2006 (Australia); Lee, Y.-C.; Chen, C.-I. [National Synchrotron Radiation Research Centre, No. 101 Hsin-Ann Road, Hsinchu 30076, Taiwan (China); Lai, Barry; Vogt, Stefan [X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439 (United States); Lay, Peter A., E-mail: p.lay@chem.usyd.edu.a [School of Chemistry, University of Sydney, NSW 2006 (Australia)

    2010-02-15

    Protein crystallography and NMR spectroscopy took decades to emerge as routine techniques in structural biology. X-ray absorption spectroscopy now has reached a similar stage of maturity for obtaining complementary local structural information around metals in metalloproteins. However, the relatively recent emergence of X-ray and vibrational spectroscopic microprobes that build on these techniques has enabled the structural information obtained from the 'mature' techniques on isolated biomolecules to be translated into in situ structural information from inhomogeneous complex systems, such as whole cells and tissues.

  14. Environmental/Biomedical Terminology Index

    Energy Technology Data Exchange (ETDEWEB)

    Huffstetler, J.K.; Dailey, N.S.; Rickert, L.W.; Chilton, B.D.

    1976-12-01

    The Information Center Complex (ICC), a centrally administered group of information centers, provides information support to environmental and biomedical research groups and others within and outside Oak Ridge National Laboratory. In-house data base building and development of specialized document collections are important elements of the ongoing activities of these centers. ICC groups must be concerned with language which will adequately classify and insure retrievability of document records. Language control problems are compounded when the complexity of modern scientific problem solving demands an interdisciplinary approach. Although there are several word lists, indexes, and thesauri specific to various scientific disciplines usually grouped as Environmental Sciences, no single generally recognized authority can be used as a guide to the terminology of all environmental science. If biomedical terminology for the description of research on environmental effects is also needed, the problem becomes even more complex. The building of a word list which can be used as a general guide to the environmental/biomedical sciences has been a continuing activity of the Information Center Complex. This activity resulted in the publication of the Environmental Biomedical Terminology Index (EBTI).

  15. Environmental/Biomedical Terminology Index

    International Nuclear Information System (INIS)

    The Information Center Complex (ICC), a centrally administered group of information centers, provides information support to environmental and biomedical research groups and others within and outside Oak Ridge National Laboratory. In-house data base building and development of specialized document collections are important elements of the ongoing activities of these centers. ICC groups must be concerned with language which will adequately classify and insure retrievability of document records. Language control problems are compounded when the complexity of modern scientific problem solving demands an interdisciplinary approach. Although there are several word lists, indexes, and thesauri specific to various scientific disciplines usually grouped as Environmental Sciences, no single generally recognized authority can be used as a guide to the terminology of all environmental science. If biomedical terminology for the description of research on environmental effects is also needed, the problem becomes even more complex. The building of a word list which can be used as a general guide to the environmental/biomedical sciences has been a continuing activity of the Information Center Complex. This activity resulted in the publication of the Environmental Biomedical Terminology Index

  16. Biomedical image understanding methods and applications

    CERN Document Server

    Lim, Joo-Hwee; Xiong, Wei

    2015-01-01

    A comprehensive guide to understanding and interpreting digital images in medical and functional applications Biomedical Image Understanding focuses on image understanding and semantic interpretation, with clear introductions to related concepts, in-depth theoretical analysis, and detailed descriptions of important biomedical applications. It covers image processing, image filtering, enhancement, de-noising, restoration, and reconstruction; image segmentation and feature extraction; registration; clustering, pattern classification, and data fusion. With contributions from ex

  17. Biomedical Imaging Principles and Applications

    CERN Document Server

    Salzer, Reiner

    2012-01-01

    This book presents and describes imaging technologies that can be used to study chemical processes and structural interactions in dynamic systems, principally in biomedical systems. The imaging technologies, largely biomedical imaging technologies such as MRT, Fluorescence mapping, raman mapping, nanoESCA, and CARS microscopy, have been selected according to their application range and to the chemical information content of their data. These technologies allow for the analysis and evaluation of delicate biological samples, which must not be disturbed during the profess. Ultimately, this may me

  18. Biomedical engineering fundamentals

    CERN Document Server

    Bronzino, Joseph D

    2014-01-01

    Known as the bible of biomedical engineering, The Biomedical Engineering Handbook, Fourth Edition, sets the standard against which all other references of this nature are measured. As such, it has served as a major resource for both skilled professionals and novices to biomedical engineering.Biomedical Engineering Fundamentals, the first volume of the handbook, presents material from respected scientists with diverse backgrounds in physiological systems, biomechanics, biomaterials, bioelectric phenomena, and neuroengineering. More than three dozen specific topics are examined, including cardia

  19. PPInterFinder—a mining tool for extracting causal relations on human proteins from literature

    OpenAIRE

    Raja, Kalpana; Subramani, Suresh; Natarajan, Jeyakumar

    2013-01-01

    One of the most common and challenging problem in biomedical text mining is to mine protein–protein interactions (PPIs) from MEDLINE abstracts and full-text research articles because PPIs play a major role in understanding the various biological processes and the impact of proteins in diseases. We implemented, PPInterFinder—a web-based text mining tool to extract human PPIs from biomedical literature. PPInterFinder uses relation keyword co-occurrences with protein names to extract information...

  20. Study on methods and techniques of aeroradiometric weak information extraction for sandstone-hosted uranium deposits based on GIS

    International Nuclear Information System (INIS)

    The weak information extraction is one of the important research contents in the current sandstone-type uranium prospecting in China. This paper introduces the connotation of aeroradiometric weak information extraction, and discusses the formation theories of aeroradiometric weak information extraction, and discusses the formation theories of aeroradiometric weak information and establishes some effective mathematic models for weak information extraction. Models for weak information extraction are realized based on GIS software platform. Application tests of weak information extraction are realized based on GIS software platform. Application tests of weak information extraction are completed in known uranium mineralized areas. Research results prove that the prospective areas of sandstone-type uranium deposits can be rapidly delineated by extracting aeroradiometric weak information. (authors)

  1. Using Clustering to extract Personality Information from socio economic data

    OpenAIRE

    Ladas, Alexandros; Aickelin, Uwe; Garibaldi, Jonathan M.; Ferguson, Eamonn

    2013-01-01

    It has become apparent that models that have been applied widely in economics, including Machine Learning techniques and Data Mining methods, should take into consideration principles that derive from the theories of Personality Psychology in order to discover more comprehensive knowledge regarding complicated economic behaviours. In this work, we present a method to extract Behavioural Groups by using simple clustering techniques that can potentially reveal aspects of the Personalities for t...

  2. Vision Based Extraction of Nutrition Information from Skewed Nutrition Labels

    OpenAIRE

    Zaman, Tanwir

    2016-01-01

    An important component of a healthy diet is the comprehension and retention of nutritional information and understanding of how different food items and nutritional constituents affect our bodies. In the U.S. and many other countries, nutritional information is primarily conveyed to consumers through nutrition labels (NLs) which can be found in all packaged food products. However, sometimes it becomes really challenging to utilize all this information available in these NLs even for consumers...

  3. Extracting local information from crowds through betting markets

    Science.gov (United States)

    Weijs, Steven

    2015-04-01

    In this research, a set-up is considered in which users can bet against a forecasting agency to challenge their probabilistic forecasts. From an information theory standpoint, a reward structure is considered that either provides the forecasting agency with better information, paying the successful providers of information for their winning bets, or funds excellent forecasting agencies through users that think they know better. Especially for local forecasts, the approach may help to diagnose model biases and to identify local predictive information that can be incorporated in the models. The challenges and opportunities for implementing such a system in practice are also discussed.

  4. The Extraction Model of Paddy Rice Information Based on GF-1 Satellite WFV Images.

    Science.gov (United States)

    Yang, Yan-jun; Huang, Yan; Tian, Qing-jiu; Wang, Lei; Geng, Jun; Yang, Ran-ran

    2015-11-01

    In the present, using the characteristics of paddy rice at different phenophase to identify it by remote sensing images is an efficient way in the information extraction. According to the remarkably properties of paddy rice different from other vegetation, which the surface of paddy fields is with a large number of water in the early stage, NDWI (normalized difference water index) which is used to extract water information can reasonably be applied in the extraction of paddy rice at the early stage of the growth. And using NDWI ratio of two phenophase can expand the difference between paddy rice and other surface features, which is an important part for the extraction of paddy rice with high accuracy. Then using the variation of NDVI (normalized differential vegetation index) in different phenophase can further enhance accuracy of paddy rice information extraction. This study finds that making full advantage of the particularity of paddy rice in different phenophase and combining two indices (NDWI and NDVI) associated with paddy rice can establish a reasonable, accurate and effective extraction model of paddy rice. This is also the main way to improve the accuracy of paddy rice extraction. The present paper takes Lai'an in Anhui Province as the research area, and rice as the research object. It constructs the extraction model of paddy rice information using NDVI and NDWI between tillering stage and heading stage. Then the model was applied to GF1-WFV remote sensing image on July 12, 2013 and August 30, 2013. And it effectively extracted out of paddy rice distribution in Lai'an and carried on the mapping. At last, the result of extraction was verified and evaluated combined with field investigation data in the study area. The result shows that using the extraction model can quickly and accurately obtain the distribution of rice information, and it has the very good universality. PMID:26978945

  5. Constructing a semantic predication gold standard from the biomedical literature

    Directory of Open Access Journals (Sweden)

    Kilicoglu Halil

    2011-12-01

    Full Text Available Abstract Background Semantic relations increasingly underpin biomedical text mining and knowledge discovery applications. The success of such practical applications crucially depends on the quality of extracted relations, which can be assessed against a gold standard reference. Most such references in biomedical text mining focus on narrow subdomains and adopt different semantic representations, rendering them difficult to use for benchmarking independently developed relation extraction systems. In this article, we present a multi-phase gold standard annotation study, in which we annotated 500 sentences randomly selected from MEDLINE abstracts on a wide range of biomedical topics with 1371 semantic predications. The UMLS Metathesaurus served as the main source for conceptual information and the UMLS Semantic Network for relational information. We measured interannotator agreement and analyzed the annotations closely to identify some of the challenges in annotating biomedical text with relations based on an ontology or a terminology. Results We obtain fair to moderate interannotator agreement in the practice phase (0.378-0.475. With improved guidelines and additional semantic equivalence criteria, the agreement increases by 12% (0.415 to 0.536 in the main annotation phase. In addition, we find that agreement increases to 0.688 when the agreement calculation is limited to those predications that are based only on the explicitly provided UMLS concepts and relations. Conclusions While interannotator agreement in the practice phase confirms that conceptual annotation is a challenging task, the increasing agreement in the main annotation phase points out that an acceptable level of agreement can be achieved in multiple iterations, by setting stricter guidelines and establishing semantic equivalence criteria. Mapping text to ontological concepts emerges as the main challenge in conceptual annotation. Annotating predications involving biomolecular

  6. Spoken Language Understanding Systems for Extracting Semantic Information from Speech

    CERN Document Server

    Tur, Gokhan

    2011-01-01

    Spoken language understanding (SLU) is an emerging field in between speech and language processing, investigating human/ machine and human/ human communication by leveraging technologies from signal processing, pattern recognition, machine learning and artificial intelligence. SLU systems are designed to extract the meaning from speech utterances and its applications are vast, from voice search in mobile devices to meeting summarization, attracting interest from both commercial and academic sectors. Both human/machine and human/human communications can benefit from the application of SLU, usin

  7. Extracting short distance information from b -> s l+ l- effectively

    OpenAIRE

    Lee, Keith S. M.; Ligeti, Zoltan; Stewart, Iain W.; Tackmann, Frank J.

    2006-01-01

    We point out that in inclusive B -> Xs l+ l- decay an angular decomposition provides a third (q^2 dependent) observable sensitive to a different combination of Wilson coefficients than the rate and the forward-backward asymmetry. Since a precise measurement of q^2 dependence requires large data sets, it is important to consider the data integrated over regions of q^2. We develop a strategy to extract all measurable Wilson coefficients in B -> Xs l+ l- from a few simple integrated rates in the...

  8. Advanced remote sensing terrestrial information extraction and applications

    CERN Document Server

    Liang, Shunlin; Wang, Jindi

    2012-01-01

    Advanced Remote Sensing is an application-based reference that provides a single source of mathematical concepts necessary for remote sensing data gathering and assimilation. It presents state-of-the-art techniques for estimating land surface variables from a variety of data types, including optical sensors such as RADAR and LIDAR. Scientists in a number of different fields including geography, geology, atmospheric science, environmental science, planetary science and ecology will have access to critically-important data extraction techniques and their virtually unlimited application

  9. Analysis of space-borne data for coastal zone information extraction of Goa Coast, India

    Digital Repository Service at National Institute of Oceanography (India)

    Kunte, P.D.; Wagle, B.G.

    Space-borne data covering the coastal zone of Goa State were processed using digital and visual image-processing techniques to extract information about the coastal zone. Digital image processing of thematic data included principal component...

  10. Extraction of information about periodic orbits from scattering functions

    OpenAIRE

    Bütikofer, Thomas; Jung, Christof; Seligman, Thomas H.

    1999-01-01

    As a contribution to the inverse scattering problem for classical chaotic systems, we show that one can select sequences of intervals of continuity, each of which yields the information about period, eigenvalue and symmetry of one unstable periodic orbit.

  11. Semantic relations extraction from unstructured information for domain ontologies enrichment

    OpenAIRE

    Paiva, Luis Miguel Sintra Salvo

    2015-01-01

    Based in internet growth, through semantic web, together with communication speed improvement and fast development of storage device sizes, data and information volume rises considerably every day. Because of this, in the last few years there has been a growing interest in structures for formal representation with suitable characteristics, such as the possibility to organize data and information, as well as the reuse of its contents aimed for the generation of new knowledge. Controlled ...

  12. Parallelization in Extracting Fresh Information from Online Social Network

    OpenAIRE

    Guo, Rui; Wang, Hongzhi; Chen, Mengwen; Li, Jianzhong; Gao, Hong

    2013-01-01

    Online Social Network (OSN) is one of the most hottest services in the past years. It preserves the life of users and provides great potential for journalists, sociologists and business analysts. Crawling data from social network is a basic step for social network information analysis and processing. As the network becomes huge and information on the network updates faster than web pages, crawling is more difficult because of the limitations of band-width, politeness etiquette and computation...

  13. An Information Extraction Framework for Cohort Identification Using Electronic Health Records

    OpenAIRE

    Liu, Hongfang; Bielinski, Suzette J.; Sohn, Sunghwan; Murphy, Sean; WAGHOLIKAR, KAVISHWAR B.; Jonnalagadda, Siddhartha R.; Ravikumar, K.E. (Komandur Elayavilli); Wu, Stephen T; Kullo, Iftikhar J.; Chute, Christopher G

    2013-01-01

    Information extraction (IE), a natural language processing (NLP) task that automatically extracts structured or semi-structured information from free text, has become popular in the clinical domain for supporting automated systems at point-of-care and enabling secondary use of electronic health records (EHRs) for clinical and translational research. However, a high performance IE system can be very challenging to construct due to the complexity and dynamic nature of human language. In this pa...

  14. Information extraction from FN plots of tungsten microemitters

    International Nuclear Information System (INIS)

    Tungsten based microemitter tips have been prepared both clean and coated with dielectric materials. For clean tungsten tips, apex radii have been varied ranging from 25 to 500 nm. These tips were manufactured by electrochemical etching a 0.1 mm diameter high purity (99.95%) tungsten wire at the meniscus of two molar NaOH solution. Composite micro-emitters considered here are consisting of a tungsten core coated with different dielectric materials—such as magnesium oxide (MgO), sodium hydroxide (NaOH), tetracyanoethylene (TCNE), and zinc oxide (ZnO). It is worthwhile noting here, that the rather unconventional NaOH coating has shown several interesting properties. Various properties of these emitters were measured including current–voltage (IV) characteristics and the physical shape of the tips. A conventional field emission microscope (FEM) with a tip (cathode)–screen (anode) separation standardized at 10 mm was used to electrically characterize the electron emitters. The system was evacuated down to a base pressure of ∼10−8mbar when baked at up to ∼180°C overnight. This allowed measurements of typical field electron emission (FE) characteristics, namely the IV characteristics and the emission images on a conductive phosphorus screen (the anode). Mechanical characterization has been performed through a FEI scanning electron microscope (SEM). Within this work, the mentioned experimental results are connected to the theory for analyzing Fowler Nordheim (FN) plots. We compared and evaluated the data extracted from clean tungsten tips of different radii and determined deviations between the results of different extraction methods applied. In particular, we derived the apex radii of several clean and coated tungsten tips by both SEM imaging and analyzing FN plots. The aim of this analysis is to support the ongoing discussion on recently developed improvements of the theory for analyzing FN plots related to metal field electron emitters, which in particular

  15. TIGER5---Extraction of geographic information from the TIGER system

    Energy Technology Data Exchange (ETDEWEB)

    Gryder, R.K.

    1992-03-01

    The need for geographic information in digital form is becoming apparent in many areas, including Emergency Response Planning and Management. The Bureau of Census recognized this need and developed an automated geographic data base, known as Topologically Integrated Geographic Encoding and Referencing (TIGER) System, to produce the geographic products for the 1990 census. The Bureau makes the information available to the public on CD-ROM disks. As distributed, the geographic information is not directly visible, and a program is needed to display the information in a graphic form. MapInfo is a commercially available program that has the capability to display maps and allows the user to perform certain geographic analyses. MapInfo runs on a variety of low-cost platforms that may be found in an average office environment, as well as on high-performance work stations. The TIGER5 program developed by the Emergency Management Information Systems (EMIS) project at Oak Ridge National Laboratory reads files directly from the Census Bureau TIGER/Line CD-ROM and creates MapInfo Exchange Format Files that can be directly imported into MapInfo. The standard default values for scaling parameters are used, and the resulting map is in the same coordinate system as the world and state maps distributed with MapInfo.

  16. Extracting short distance information from b -> s l+ l- effectively

    CERN Document Server

    Lee, K S M; Stewart, I W; Tackmann, F J; Lee, Keith S. M.; Ligeti, Zoltan; Stewart, Iain W.; Tackmann, Frank J.

    2007-01-01

    We point out that in inclusive B -> Xs l+ l- decay an angular decomposition provides a third (q^2-dependent) observable, in addition to the rate and the forward-backward asymmetry, which is sensitive to a different combination of Wilson coefficients. Since a precise measurement of q^2 dependence requires large data sets, it is important to consider the data integrated over regions of q^2. We develop a strategy to extract all measurable Wilson coefficients in B -> Xs l+ l- from a few simple integrated rates in the low q^2 region. A similar decomposition in B -> K* l+ l-, together with the B -> K* \\gamma rate, also provides a model independent determination of the Wilson coefficients, without reliance on form factor models and without having to measure the zero of the forward-backward asymmetry.

  17. Advanced Extraction of Spatial Information from High Resolution Satellite Data

    Science.gov (United States)

    Pour, T.; Burian, J.; Miřijovský, J.

    2016-06-01

    In this paper authors processed five satellite image of five different Middle-European cities taken by five different sensors. The aim of the paper was to find methods and approaches leading to evaluation and spatial data extraction from areas of interest. For this reason, data were firstly pre-processed using image fusion, mosaicking and segmentation processes. Results going into the next step were two polygon layers; first one representing single objects and the second one representing city blocks. In the second step, polygon layers were classified and exported into Esri shapefile format. Classification was partly hierarchical expert based and partly based on the tool SEaTH used for separability distinction and thresholding. Final results along with visual previews were attached to the original thesis. Results are evaluated visually and statistically in the last part of the paper. In the discussion author described difficulties of working with data of large size, taken by different sensors and different also thematically.

  18. Visualization and classification in biomedical terahertz pulsed imaging

    International Nuclear Information System (INIS)

    'Visualization' in imaging is the process of extracting useful information from raw data in such a way that meaningful physical contrasts are developed. 'Classification' is the subsequent process of defining parameter ranges which allow us to identify elements of images such as different tissues or different objects. In this paper, we explore techniques for visualization and classification in terahertz pulsed imaging (TPI) for biomedical applications. For archived (formalin-fixed, alcohol-dehydrated and paraffin-mounted) test samples, we investigate both time- and frequency-domain methods based on bright- and dark-field TPI. Successful tissue classification is demonstrated

  19. Applications of computational intelligence in biomedical technology

    CERN Document Server

    Majernik, Jaroslav; Pancerz, Krzysztof; Zaitseva, Elena

    2016-01-01

    This book presents latest results and selected applications of Computational Intelligence in Biomedical Technologies. Most of contributions deal with problems of Biomedical and Medical Informatics, ranging from theoretical considerations to practical applications. Various aspects of development methods and algorithms in Biomedical and Medical Informatics as well as Algorithms for medical image processing, modeling methods are discussed. Individual contributions also cover medical decision making support, estimation of risks of treatments, reliability of medical systems, problems of practical clinical applications and many other topics  This book is intended for scientists interested in problems of Biomedical Technologies, for researchers and academic staff, for all dealing with Biomedical and Medical Informatics, as well as PhD students. Useful information is offered also to IT companies, developers of equipment and/or software for medicine and medical professionals.  .

  20. Source-specific Informative Prior for i-Vector Extraction

    DEFF Research Database (Denmark)

    Shepstone, Sven Ewan; Lee, Kong Aik; Li, Haizhou; Tan, Zheng-Hua; Jensen, Søren Holdt

    An i-vector is a low-dimensional fixed-length representation of a variable-length speech utterance, and is defined as the posterior mean of a latent variable conditioned on the observed feature sequence of an utterance. The assumption is that the prior for the latent variable is non-informative, ...

  1. On Depth Information Extraction from Metal Detector Signals

    NARCIS (Netherlands)

    Schoolderman, A.J.; Wolf, F.J. de; Merlat, L.

    2003-01-01

    Information on the depth of objects detected with the help of a metal detector is useful for safe excavation of these objects in demining operations. Apart from that, depth informatíon may be used in advanced sensor fusion algorithms for a detection system where a metal detector is combíned with eg.

  2. Extraction of quadrature phase information from multiple pulse NMR signals

    Science.gov (United States)

    Rhim, W.-K.; Burum, D. P.; Vaughan, R. W.

    1976-01-01

    A multiple pulse sequence (8-pulse sequence) used for high-resolution solid state NMR is analyzed with regard to the information available from each of the four wide sampling windows. It is demonstrated that full quadrature phase information can be obtained using only a single phase detector and that, for the commonly encountered situation where the spectral width is much less than the folding frequency, the signals from the various windows can be combined easily using standard complex Fourier transform software. An improvement in the signal-to-noise ratio equal to the square root of 3 is obtained over either standard single or quadrature phase detection schemes. Procedures for correcting spectral distortions are presented.

  3. Question Processing and Clustering in INDOC: A Biomedical Question Answering System

    Directory of Open Access Journals (Sweden)

    Ankush Mittal

    2007-12-01

    Full Text Available The exponential growth in the volume of publications in the biomedical domain has made it impossible for an individual to keep pace with the advances. Even though evidence-based medicine has gained wide acceptance, the physicians are unable to access the relevant information in the required time, leaving most of the questions unanswered. This accentuates the need for fast and accurate biomedical question answering systems. In this paper we introduce INDOC—a biomedical question answering system based on novel ideas of indexing and extracting the answer to the questions posed. INDOC displays the results in clusters to help the user arrive the most relevant set of documents quickly. Evaluation was done against the standard OHSUMED test collection. Our system achieves high accuracy and minimizes user effort.

  4. Question Processing and Clustering in INDOC: A Biomedical Question Answering System

    Directory of Open Access Journals (Sweden)

    Sondhi Parikshit

    2007-01-01

    Full Text Available The exponential growth in the volume of publications in the biomedical domain has made it impossible for an individual to keep pace with the advances. Even though evidence-based medicine has gained wide acceptance, the physicians are unable to access the relevant information in the required time, leaving most of the questions unanswered. This accentuates the need for fast and accurate biomedical question answering systems. In this paper we introduce INDOC—a biomedical question answering system based on novel ideas of indexing and extracting the answer to the questions posed. INDOC displays the results in clusters to help the user arrive the most relevant set of documents quickly. Evaluation was done against the standard OHSUMED test collection. Our system achieves high accuracy and minimizes user effort.

  5. Using XBRL Technology to Extract Competitive Information from Financial Statements

    OpenAIRE

    Dominik Ditter; Klaus Henselmann; Elisabeth Scherr

    2011-01-01

    The eXtensible Business Reporting Language, or XBRL, is a reporting format for the automatic and electronic exchange of business and financial data. In XBRL every single reported fact is marked with a unique tag, enabling a full computer-based readout of financial data. It has the potential to improve the collection and analysis of financial data for Competitive Intelligence (e.g., the profiling of publicly available financial statements). The article describes how easily information from XBR...

  6. Textural Properties of Hybrid Biomedical Materials Made from Extracts of Tournefortia hirsutissima L. Imbibed and Deposited on Mesoporous and Microporous Materials

    Directory of Open Access Journals (Sweden)

    Miguel Ángel Hernández

    2016-01-01

    Full Text Available Our research group has developed a group of hybrid biomedical materials potentially useful in the healing of diabetic foot ulcerations. The organic part of this type of hybrid materials consists of nanometric deposits, proceeding from the Mexican medicinal plant Tournefortia hirsutissima L., while the inorganic part is composed of a zeolite mixture that includes LTA, ZSM-5, clinoptilolite, and montmorillonite (PZX as well as a composite material, made of CaCO3 and montmorillonite (NABE. The organic part has been analyzed by GC-MS to detect the most abundant components present therein. In turn, the inorganic supports were characterized by XRD, SEM, and High Resolution Adsorption (HRADS of N2 at 76 K. Through this latter methodology, the external surface area of the hybrid materials was evaluated; besides, the most representative textural properties of each substrate such as total pore volume, pore size distribution, and, in some cases, the volume of micropores were calculated. The formation and stabilization of nanodeposits on the inorganic segments of the hybrid supports led to a partial blockage of the microporosity of the LTA and ZSM5 zeolites; this same effect occurred with the NABE and PZX substrates.

  7. Drug name recognition in biomedical texts: a machine-learning-based method.

    Science.gov (United States)

    He, Linna; Yang, Zhihao; Lin, Hongfei; Li, Yanpeng

    2014-05-01

    Currently, there is an urgent need to develop a technology for extracting drug information automatically from biomedical texts, and drug name recognition is an essential prerequisite for extracting drug information. This article presents a machine-learning-based approach to recognize drug names in biomedical texts. In this approach, a drug name dictionary is first constructed with the external resource of DrugBank and PubMed. Then a semi-supervised learning method, feature coupling generalization, is used to filter this dictionary. Finally, the dictionary look-up and the condition random field method are combined to recognize drug names. Experimental results show that our approach achieves an F-score of 92.54% on the test set of DDIExtraction2011. PMID:24140287

  8. Data-Driven Information Extraction from Chinese Electronic Medical Records.

    Directory of Open Access Journals (Sweden)

    Dong Xu

    Full Text Available This study aims to propose a data-driven framework that takes unstructured free text narratives in Chinese Electronic Medical Records (EMRs as input and converts them into structured time-event-description triples, where the description is either an elaboration or an outcome of the medical event.Our framework uses a hybrid approach. It consists of constructing cross-domain core medical lexica, an unsupervised, iterative algorithm to accrue more accurate terms into the lexica, rules to address Chinese writing conventions and temporal descriptors, and a Support Vector Machine (SVM algorithm that innovatively utilizes Normalized Google Distance (NGD to estimate the correlation between medical events and their descriptions.The effectiveness of the framework was demonstrated with a dataset of 24,817 de-identified Chinese EMRs. The cross-domain medical lexica were capable of recognizing terms with an F1-score of 0.896. 98.5% of recorded medical events were linked to temporal descriptors. The NGD SVM description-event matching achieved an F1-score of 0.874. The end-to-end time-event-description extraction of our framework achieved an F1-score of 0.846.In terms of named entity recognition, the proposed framework outperforms state-of-the-art supervised learning algorithms (F1-score: 0.896 vs. 0.886. In event-description association, the NGD SVM is superior to SVM using only local context and semantic features (F1-score: 0.874 vs. 0.838.The framework is data-driven, weakly supervised, and robust against the variations and noises that tend to occur in a large corpus. It addresses Chinese medical writing conventions and variations in writing styles through patterns used for discovering new terms and rules for updating the lexica.

  9. Post-processing of Deep Web Information Extraction Based on Domain Ontology

    Directory of Open Access Journals (Sweden)

    PENG, T.

    2013-11-01

    Full Text Available Many methods are utilized to extract and process query results in deep Web, which rely on the different structures of Web pages and various designing modes of databases. However, some semantic meanings and relations are ignored. So, in this paper, we present an approach for post-processing deep Web query results based on domain ontology which can utilize the semantic meanings and relations. A block identification model (BIM based on node similarity is defined to extract data blocks that are relevant to specific domain after reducing noisy nodes. Feature vector of domain books is obtained by result set extraction model (RSEM based on vector space model (VSM. RSEM, in combination with BIM, builds the domain ontology on books which can not only remove the limit of Web page structures when extracting data information, but also make use of semantic meanings of domain ontology. After extracting basic information of Web pages, a ranking algorithm is adopted to offer an ordered list of data records to users. Experimental results show that BIM and RSEM extract data blocks and build domain ontology accurately. In addition, relevant data records and basic information are extracted and ranked. The performances precision and recall show that our proposed method is feasible and efficient.

  10. Omnidirectional vision systems calibration, feature extraction and 3D information

    CERN Document Server

    Puig, Luis

    2013-01-01

    This work focuses on central catadioptric systems, from the early step of calibration to high-level tasks such as 3D information retrieval. The book opens with a thorough introduction to the sphere camera model, along with an analysis of the relation between this model and actual central catadioptric systems. Then, a new approach to calibrate any single-viewpoint catadioptric camera is described.  This is followed by an analysis of existing methods for calibrating central omnivision systems, and a detailed examination of hybrid two-view relations that combine images acquired with uncalibrated

  11. MIDAS: an information-extraction approach to medical text classification

    OpenAIRE

    Sotelsek Margalef, Anastasia; Villena Román, Julio

    2008-01-01

    Este artículo realiza una descripción de MIDAS (Medical Diagnosis Assistant), un sistema experto avanzado capaz de proporcionar un diagnóstico médico a partir de los informes radiológicos/patológicos del paciente, basado en extracción de información y aprendizaje automático a partir de historias clínicas de pacientes diagnosticados anteriormente. MIDAS fue diseñado para participar en la competición Medical Natural Language Processing Challenge 2007. Específicamente, el sistema ...

  12. Analysis of Automated Modern Web Crawling and Testing Tools and Their Possible Employment for Information Extraction

    Directory of Open Access Journals (Sweden)

    Tomas Grigalis

    2012-04-01

    Full Text Available World Wide Web has become an enormously big repository of data. Extracting, integrating and reusing this kind of data has a wide range of applications, including meta-searching, comparison shopping, business intelligence tools and security analysis of information in websites. However, reaching information in modern WEB 2.0 web pages, where HTML tree is often dynamically modified by various JavaScript codes, new data are added by asynchronous requests to the web server and elements are positioned with the help of cascading style sheets, is a difficult task. The article reviews automated web testing tools for information extraction tasks.Article in Lithuanian

  13. Introduction to biomedical engineering

    CERN Document Server

    Enderle, John

    2011-01-01

    Introduction to Biomedical Engineering is a comprehensive survey text for biomedical engineering courses. It is the most widely adopted text across the BME course spectrum, valued by instructors and students alike for its authority, clarity and encyclopedic coverage in a single volume. Biomedical engineers need to understand the wide range of topics that are covered in this text, including basic mathematical modeling; anatomy and physiology; electrical engineering, signal processing and instrumentation; biomechanics; biomaterials science and tissue engineering; and medical and engineering e

  14. Biomedical optical imaging

    CERN Document Server

    Fujimoto, James G

    2009-01-01

    Biomedical optical imaging is a rapidly emerging research area with widespread fundamental research and clinical applications. This book gives an overview of biomedical optical imaging with contributions from leading international research groups who have pioneered many of these techniques and applications. A unique research field spanning the microscopic to the macroscopic, biomedical optical imaging allows both structural and functional imaging. Techniques such as confocal and multiphoton microscopy provide cellular level resolution imaging in biological systems. The integration of this tech

  15. Surface tailoring of inorganic materials for biomedical applications

    CERN Document Server

    Rimondini, Lia; Vernè, Enrica

    2012-01-01

    This e-book provides comprehensive information on technologies for development and characterization of successful functionalized materials for biomedical applications relevant to surface modification.

  16. Biomedical engineering principles

    CERN Document Server

    Ritter, Arthur B; Valdevit, Antonio; Ascione, Alfred N

    2011-01-01

    Introduction: Modeling of Physiological ProcessesCell Physiology and TransportPrinciples and Biomedical Applications of HemodynamicsA Systems Approach to PhysiologyThe Cardiovascular SystemBiomedical Signal ProcessingSignal Acquisition and ProcessingTechniques for Physiological Signal ProcessingExamples of Physiological Signal ProcessingPrinciples of BiomechanicsPractical Applications of BiomechanicsBiomaterialsPrinciples of Biomedical Capstone DesignUnmet Clinical NeedsEntrepreneurship: Reasons why Most Good Designs Never Get to MarketAn Engineering Solution in Search of a Biomedical Problem

  17. Fundamental of biomedical engineering

    CERN Document Server

    Sawhney, GS

    2007-01-01

    About the Book: A well set out textbook explains the fundamentals of biomedical engineering in the areas of biomechanics, biofluid flow, biomaterials, bioinstrumentation and use of computing in biomedical engineering. All these subjects form a basic part of an engineer''s education. The text is admirably suited to meet the needs of the students of mechanical engineering, opting for the elective of Biomedical Engineering. Coverage of bioinstrumentation, biomaterials and computing for biomedical engineers can meet the needs of the students of Electronic & Communication, Electronic & Instrumenta

  18. Abstract Information Extraction From Consumer's Comments On Internet Media

    Directory of Open Access Journals (Sweden)

    Kadriye Ergün

    2013-01-01

    Full Text Available In this study, a system developed to summarize by automatically evaluating comments about product with using text mining techniques will be described. The data has been primarily went through morphological analysis process, because they are texts written in natural language. Words and adjectives meaning positive or negative are determined. They show product features in texts. The tree structure is established according to Turkish grammar rules as subordinate and modified words are designated. The software which uses the depth-first search algorithm on the tree structure is developed. Data from result of software is stored in the SQL database. When any inquiry is made from these data depending on any property of product, numerical information which indicates the degree of satisfaction about this property is obtained.

  19. Unsupervised Biomedical Named Entity Recognition: Experiments with Clinical and Biological Texts

    OpenAIRE

    Zhang, Shaodian; Elhadad, Nóemie

    2013-01-01

    Named entity recognition is a crucial component of biomedical natural language processing, enabling information extraction and ultimately reasoning over and knowledge discovery from text. Much progress has been made in the design of rule-based and supervised tools, but they are often genre and task dependent. As such, adapting them to different genres of text or identifying new types of entities requires major effort in re-annotation or rule development. In this paper, we propose an unsupervi...

  20. Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery

    OpenAIRE

    Gonzalez, Graciela H.; Tahsin, Tasnia; Britton C Goodale; Greene, Anna C.; Greene, Casey S

    2015-01-01

    Precision medicine will revolutionize the way we treat and prevent disease. A major barrier to the implementation of precision medicine that clinicians and translational scientists face is understanding the underlying mechanisms of disease. We are starting to address this challenge through automatic approaches for information extraction, representation and analysis. Recent advances in text and data mining have been applied to a broad spectrum of key biomedical questions in genomics, pharmacog...

  1. International symposium on Biomedical Data Infrastructure (BDI 2013)

    CERN Document Server

    Dhillon, Sarinder; Advances in biomedical infrastructure 2013

    2013-01-01

    Current Biomedical Databases are independently administered in geographically distinct locations, lending them almost ideally to adoption of intelligent data management approaches. This book focuses on research issues, problems and opportunities in Biomedical Data Infrastructure identifying new issues and directions for future research in Biomedical Data and Information Retrieval, Semantics in Biomedicine, and Biomedical Data Modeling and Analysis. The book will be a useful guide for researchers, practitioners, and graduate-level students interested in learning state-of-the-art development in biomedical data management.

  2. What do professional forecasters' stock market expectations tell us about herding, information extraction and beauty contests?

    DEFF Research Database (Denmark)

    Rangvid, Jesper; Schmeling, M.; Schrimpf, A.

    2013-01-01

    We study how professional forecasters form equity market expectations based on a new micro-level dataset which includes rich cross-sectional information about individual characteristics. We focus on testing whether agents rely on the beliefs of others, i.e., consensus expectations, when forming t...... indicate that neither information extraction to incorporate dispersed private information, nor herding for reputational reasons can fully explain these results, leaving Keynes' beauty contest argument as a potential candidate for explaining forecaster behavior....

  3. Context-specific Consistencies in Information Extraction: Rule-based and Probabilistic Approaches

    OpenAIRE

    Klügl, Peter

    2015-01-01

    Large amounts of communication, documentation as well as knowledge and information are stored in textual documents. Most often, these texts like webpages, books, tweets or reports are only available in an unstructured representation since they are created and interpreted by humans. In order to take advantage of this huge amount of concealed information and to include it in analytic processes, it needs to be transformed into a structured representation. Information extraction considers exactly...

  4. A Multithreaded Java Framework for Information Extraction in the Context of Enterprise Application Integration

    OpenAIRE

    Stefan Kuhlins; Axel Korthaus

    2004-01-01

    In this paper, we present a new multithreaded framework for information extraction with Java in heterogeneous enterprise application environments, which frees the developer from having to deal with the error-prone task of low-level thread programming. The power of this framework is demonstrated by an example of extracting product prices from web sites, but the framework is useful for numerous other purposes, too. Strong points of the framework are its performance, continuous feedback, and adh...

  5. Extracting information from the data flood of new solar telescopes. Brainstorming

    CERN Document Server

    Ramos, A Asensio

    2012-01-01

    Extracting magnetic and thermodynamic information from spectropolarimetric observations is a difficult and time consuming task. The amount of science-ready data that will be generated by the new family of large solar telescopes is so large that we will be forced to modify the present approach to inference. In this contribution, I propose several possible ways that might be useful for extracting the thermodynamic and magnetic properties of solar plasmas from such observations quickly.

  6. A cascade of classifiers for extracting medication information from discharge summaries

    OpenAIRE

    Halgrim Scott; Xia Fei; Solti Imre; Cadag Eithon; Uzuner Özlem

    2011-01-01

    Abstract Background Extracting medication information from clinical records has many potential applications, and recently published research, systems, and competitions reflect an interest therein. Much of the early extraction work involved rules and lexicons, but more recently machine learning has been applied to the task. Methods We present a hybrid system consisting of two parts. The first part, field detection, uses a cascade of statistical classifiers to identify medication-related named ...

  7. Biomedical signal and image processing

    CERN Document Server

    Najarian, Kayvan

    2012-01-01

    INTRODUCTION TO DIGITAL SIGNAL AND IMAGE PROCESSINGSignals and Biomedical Signal ProcessingIntroduction and OverviewWhat is a ""Signal""?Analog, Discrete, and Digital SignalsProcessing and Transformation of SignalsSignal Processing for Feature ExtractionSome Characteristics of Digital ImagesSummaryProblemsFourier TransformIntroduction and OverviewOne-Dimensional Continuous Fourier TransformSampling and NYQUIST RateOne-Dimensional Discrete Fourier TransformTwo-Dimensional Discrete Fourier TransformFilter DesignSummaryProblemsImage Filtering, Enhancement, and RestorationIntroduction and Overview

  8. An automatic abrupt information extraction method based on singular value decomposition and higher-order statistics

    International Nuclear Information System (INIS)

    One key aspect of local fault diagnosis is how to effectively extract abrupt features from the vibration signals. This paper proposes a method to automatically extract abrupt information based on singular value decomposition and higher-order statistics. In order to observe the distribution law of singular values, a numerical analysis to simulate the noise, periodic signal, abrupt signal and singular value distribution is conducted. Based on higher-order statistics and spectrum analysis, a method to automatically choose the upper and lower borders of the singular value interval reflecting the abrupt information is built. And the selected singular values derived from this method are used to reconstruct abrupt signals. It is proven that the method is able to obtain accurate results by processing the rub-impact fault signal measured from the experiments. The analytical and experimental results indicate that the proposed method is feasible for automatically extracting abrupt information caused by faults like the rotor–stator rub-impact. (paper)

  9. Real-time traffic information extraction based on compressed video with interframe motion vector

    Institute of Scientific and Technical Information of China (English)

    黄庆明; 王聪

    2003-01-01

    Extraction of traffic information from image or video sequence is a hot research topic in intelligenttransportation system and computer vision. A real-time traffic information extraction method based on com-pressed video with interframe motion vectors for speed, density and flow detection, has been proposed for ex-traction of traffic information under fixed camera setting and well-defined environment. The motion vectors arefirst separated from the compressed video streams, and then filtered to eliminate incorrect and noisy vectors u-sing the well-defined environmental knowledge. By applying the projective transform and using the filtered mo-tion vectors, speed can be calculated from motion vector statistics, density can be estimated using the motionvector occupancy, and flow can be detected using the combination of speed and density. The embodiment of aprototype system for sky camera traffic monitoring using the MPEG video has been implemented, and experi-mental results proved the effectiveness of the method proposed.

  10. UMLS knowledge for biomedical language processing.

    OpenAIRE

    McCray, A T; Aronson, A. R.; Browne, A. C.; Rindflesch, T. C.; A razi; Srinivasan, S

    1993-01-01

    This paper describes efforts to provide access to the free text in biomedical databases. The focus of the effort is the development of SPECIALIST, an experimental natural language processing system for the biomedical domain. The system includes a broad coverage parser supported by a large lexicon, modules that provide access to the extensive Unified Medical Language System (UMLS) Knowledge Sources, and a retrieval module that permits experiments in information retrieval. The UMLS Metathesauru...

  11. Science gateways for biomedical big data analysis

    OpenAIRE

    Kampen, van, PJW; Olabarriaga, S.D.; Shahand, S.

    2015-01-01

    Biomedical researchers are facing data deluge challenges such as dealing with large volume of complex heterogeneous data and complex and computationally demanding data processing methods. Such scale and complexity of biomedical research requires multi-disciplinary collaboration between scientists from different organizations. Data-driven or e-Science methods are defined as a combination of Information Technology (IT) and science that enables scientists to tackle the data deluge challenges. Th...

  12. Statistics and Biomedical Informatics in Forensic Sciences

    Czech Academy of Sciences Publication Activity Database

    Zvárová, Jana

    2009-01-01

    Roč. 20, č. 6 (2009), s. 743-750. ISSN 1180-4009. [TIES 2007. Annual Meeting of the International Environmental Society /18./. Mikulov, 16.08.2007-20.08.2007] Institutional research plan: CEZ:AV0Z10300504 Keywords : biomedical informatics * biomedical statistics * genetic information * forensic dentistry Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 1.000, year: 2009

  13. Learning the Structure of Biomedical Relationships from Unstructured Text.

    Directory of Open Access Journals (Sweden)

    Bethany Percha

    2015-07-01

    Full Text Available The published biomedical research literature encompasses most of our understanding of how drugs interact with gene products to produce physiological responses (phenotypes. Unfortunately, this information is distributed throughout the unstructured text of over 23 million articles. The creation of structured resources that catalog the relationships between drugs and genes would accelerate the translation of basic molecular knowledge into discoveries of genomic biomarkers for drug response and prediction of unexpected drug-drug interactions. Extracting these relationships from natural language sentences on such a large scale, however, requires text mining algorithms that can recognize when different-looking statements are expressing similar ideas. Here we describe a novel algorithm, Ensemble Biclustering for Classification (EBC, that learns the structure of biomedical relationships automatically from text, overcoming differences in word choice and sentence structure. We validate EBC's performance against manually-curated sets of (1 pharmacogenomic relationships from PharmGKB and (2 drug-target relationships from DrugBank, and use it to discover new drug-gene relationships for both knowledge bases. We then apply EBC to map the complete universe of drug-gene relationships based on their descriptions in Medline, revealing unexpected structure that challenges current notions about how these relationships are expressed in text. For instance, we learn that newer experimental findings are described in consistently different ways than established knowledge, and that seemingly pure classes of relationships can exhibit interesting chimeric structure. The EBC algorithm is flexible and adaptable to a wide range of problems in biomedical text mining.

  14. Learning the Structure of Biomedical Relationships from Unstructured Text.

    Science.gov (United States)

    Percha, Bethany; Altman, Russ B

    2015-07-01

    The published biomedical research literature encompasses most of our understanding of how drugs interact with gene products to produce physiological responses (phenotypes). Unfortunately, this information is distributed throughout the unstructured text of over 23 million articles. The creation of structured resources that catalog the relationships between drugs and genes would accelerate the translation of basic molecular knowledge into discoveries of genomic biomarkers for drug response and prediction of unexpected drug-drug interactions. Extracting these relationships from natural language sentences on such a large scale, however, requires text mining algorithms that can recognize when different-looking statements are expressing similar ideas. Here we describe a novel algorithm, Ensemble Biclustering for Classification (EBC), that learns the structure of biomedical relationships automatically from text, overcoming differences in word choice and sentence structure. We validate EBC's performance against manually-curated sets of (1) pharmacogenomic relationships from PharmGKB and (2) drug-target relationships from DrugBank, and use it to discover new drug-gene relationships for both knowledge bases. We then apply EBC to map the complete universe of drug-gene relationships based on their descriptions in Medline, revealing unexpected structure that challenges current notions about how these relationships are expressed in text. For instance, we learn that newer experimental findings are described in consistently different ways than established knowledge, and that seemingly pure classes of relationships can exhibit interesting chimeric structure. The EBC algorithm is flexible and adaptable to a wide range of problems in biomedical text mining. PMID:26219079

  15. The Ontology for Biomedical Investigations.

    Directory of Open Access Journals (Sweden)

    Anita Bandrowski

    Full Text Available The Ontology for Biomedical Investigations (OBI is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI and Phenotype Attribute and Trait Ontology (PATO without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT. The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org providing details on the people, policies, and issues being

  16. The Ontology for Biomedical Investigations

    Science.gov (United States)

    Bandrowski, Anita; Brinkman, Ryan; Brochhausen, Mathias; Brush, Matthew H.; Chibucos, Marcus C.; Clancy, Kevin; Courtot, Mélanie; Derom, Dirk; Dumontier, Michel; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Gibson, Frank; Gonzalez-Beltran, Alejandra; Haendel, Melissa A.; He, Yongqun; Heiskanen, Mervi; Hernandez-Boussard, Tina; Jensen, Mark; Lin, Yu; Lister, Allyson L.; Lord, Phillip; Malone, James; Manduchi, Elisabetta; McGee, Monnie; Morrison, Norman; Overton, James A.; Parkinson, Helen; Peters, Bjoern; Rocca-Serra, Philippe; Ruttenberg, Alan; Sansone, Susanna-Assunta; Scheuermann, Richard H.; Schober, Daniel; Smith, Barry; Soldatova, Larisa N.; Stoeckert, Christian J.; Taylor, Chris F.; Torniai, Carlo; Turner, Jessica A.; Vita, Randi; Whetzel, Patricia L.; Zheng, Jie

    2016-01-01

    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed

  17. The Ontology for Biomedical Investigations.

    Science.gov (United States)

    Bandrowski, Anita; Brinkman, Ryan; Brochhausen, Mathias; Brush, Matthew H; Bug, Bill; Chibucos, Marcus C; Clancy, Kevin; Courtot, Mélanie; Derom, Dirk; Dumontier, Michel; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Gibson, Frank; Gonzalez-Beltran, Alejandra; Haendel, Melissa A; He, Yongqun; Heiskanen, Mervi; Hernandez-Boussard, Tina; Jensen, Mark; Lin, Yu; Lister, Allyson L; Lord, Phillip; Malone, James; Manduchi, Elisabetta; McGee, Monnie; Morrison, Norman; Overton, James A; Parkinson, Helen; Peters, Bjoern; Rocca-Serra, Philippe; Ruttenberg, Alan; Sansone, Susanna-Assunta; Scheuermann, Richard H; Schober, Daniel; Smith, Barry; Soldatova, Larisa N; Stoeckert, Christian J; Taylor, Chris F; Torniai, Carlo; Turner, Jessica A; Vita, Randi; Whetzel, Patricia L; Zheng, Jie

    2016-01-01

    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed

  18. Extraction of Informative Blocks from Deep Web Page Using Similar Layout Feature

    OpenAIRE

    Zeng, Jun; Flanagan, Brendan; Hirokawa, Sachio

    2013-01-01

    Due to the explosive growth and popularity of the deep web, information extraction from deep web page has gained more and more attention. However, the HTML structure of web page has become more complicated, making it difficult to recognize target content by only analyzing the HTML source code. In this paper, we propose a method to extract the informative blocks from a deep web using the layout feature. We consider the visual rectangular region of an HTML element as a visual block in web page....

  19. Ultrasonic Signal Processing Algorithm for Crack Information Extraction on the Keyway of Turbine Rotor Disk

    International Nuclear Information System (INIS)

    An ultrasonic signal processing algorithm was developed for extracting the information of cracks generated around the keyway of a turbine rotor disk. B-scan images were obtained by using keyway specimens and an ultrasonic scan system with x-y position controller. The B-scan images were used as input images for 2-Dimensional signal processing, and the algorithm was constructed with four processing stages of pre-processing, crack candidate region detection, crack region classification and crack information extraction. It is confirmed by experiments that the developed algorithm is effective for the quantitative evaluation of cracks generated around the keyway of turbine rotor disk

  20. Ultrasonic Signal Processing Algorithm for Crack Information Extraction on the Keyway of Turbine Rotor Disk

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Hong Kyu; Seo, Won Chan; Park, Chan [Pukyong National University, Busan (Korea, Republic of); Lee, Jong O; Son, Young Ho [KIMM, Daejeon (Korea, Republic of)

    2009-10-15

    An ultrasonic signal processing algorithm was developed for extracting the information of cracks generated around the keyway of a turbine rotor disk. B-scan images were obtained by using keyway specimens and an ultrasonic scan system with x-y position controller. The B-scan images were used as input images for 2-Dimensional signal processing, and the algorithm was constructed with four processing stages of pre-processing, crack candidate region detection, crack region classification and crack information extraction. It is confirmed by experiments that the developed algorithm is effective for the quantitative evaluation of cracks generated around the keyway of turbine rotor disk

  1. Information Extraction of High-Resolution Remotely Sensed Image Based on Multiresolution Segmentation

    Directory of Open Access Journals (Sweden)

    Peng Shao

    2014-08-01

    Full Text Available The principle of multiresolution segmentation was represented in detail in this study, and the canny algorithm was applied for edge-detection of a remotely sensed image based on this principle. The target image was divided into regions based on object-oriented multiresolution segmentation and edge-detection. Furthermore, object hierarchy was created, and a series of features (water bodies, vegetation, roads, residential areas, bare land and other information were extracted by the spectral and geometrical features. The results indicate that the edge-detection has a positive effect on multiresolution segmentation, and overall accuracy of information extraction reaches to 94.6% by the confusion matrix.

  2. Services for annotation of biomedical text

    OpenAIRE

    Hakenberg, Jörg

    2008-01-01

    Motivation: Text mining in the biomedical domain in recent years has focused on the development of tools for recognizing named entities and extracting relations. Such research resulted from the need for such tools as basic components for more advanced solutions. Named entity recognition, entity mention normalization, and relationship extraction now have reached a stage where they perform comparably to human annotators (considering inter--annotator agreement, measured in many studies to be aro...

  3. Extraction Method for Earthquake-Collapsed Building Information Based on High-Resolution Remote Sensing

    International Nuclear Information System (INIS)

    At present, the extraction of earthquake disaster information from remote sensing data relies on visual interpretation. However, this technique cannot effectively and quickly obtain precise and efficient information for earthquake relief and emergency management. Collapsed buildings in the town of Zipingpu after the Wenchuan earthquake were used as a case study to validate two kinds of rapid extraction methods for earthquake-collapsed building information based on pixel-oriented and object-oriented theories. The pixel-oriented method is based on multi-layer regional segments that embody the core layers and segments of the object-oriented method. The key idea is to mask layer by layer all image information, including that on the collapsed buildings. Compared with traditional techniques, the pixel-oriented method is innovative because it allows considerably rapid computer processing. As for the object-oriented method, a multi-scale segment algorithm was applied to build a three-layer hierarchy. By analyzing the spectrum, texture, shape, location, and context of individual object classes in different layers, the fuzzy determined rule system was established for the extraction of earthquake-collapsed building information. We compared the two sets of results using three variables: precision assessment, visual effect, and principle. Both methods can extract earthquake-collapsed building information quickly and accurately. The object-oriented method successfully overcomes the pepper salt noise caused by the spectral diversity of high-resolution remote sensing data and solves the problem of same object, different spectrums and that of same spectrum, different objects. With an overall accuracy of 90.38%, the method achieves more scientific and accurate results compared with the pixel-oriented method (76.84%). The object-oriented image analysis method can be extensively applied in the extraction of earthquake disaster information based on high-resolution remote sensing

  4. Terrain Extraction by Integrating Terrestrial Laser Scanner Data and Spectral Information

    Science.gov (United States)

    Lau, C. L.; Halim, S.; Zulkepli, M.; Azwan, A. M.; Tang, W. L.; Chong, A. K.

    2015-10-01

    The extraction of true terrain points from unstructured laser point cloud data is an important process in order to produce an accurate digital terrain model (DTM). However, most of these spatial filtering methods just utilizing the geometrical data to discriminate the terrain points from nonterrain points. The point cloud filtering method also can be improved by using the spectral information available with some scanners. Therefore, the objective of this study is to investigate the effectiveness of using the three-channel (red, green and blue) of the colour image captured from built-in digital camera which is available in some Terrestrial Laser Scanner (TLS) for terrain extraction. In this study, the data acquisition was conducted at a mini replica landscape in Universiti Teknologi Malaysia (UTM), Skudai campus using Leica ScanStation C10. The spectral information of the coloured point clouds from selected sample classes are extracted for spectral analysis. The coloured point clouds which within the corresponding preset spectral threshold are identified as that specific feature point from the dataset. This process of terrain extraction is done through using developed Matlab coding. Result demonstrates that a higher spectral resolution passive image is required in order to improve the output. This is because low quality of the colour images captured by the sensor contributes to the low separability in spectral reflectance. In conclusion, this study shows that, spectral information is capable to be used as a parameter for terrain extraction.

  5. A method of building information extraction based on mathematical morphology and multiscale

    Science.gov (United States)

    Li, Jing-wen; Wang, Ke; Zhang, Zi-ping; Xue, Long-li; Yin, Shou-qiang; Zhou, Song

    2015-12-01

    In view of monitoring the changes of buildings on Earth's surface ,by analyzing the distribution characteristics of building in remote sensing image, combined with multi-scale in image segmentation and the advantages of mathematical morphology, this paper proposes a multi-scale combined with mathematical morphology of high resolution remote sensing image segmentation method, and uses the multiple fuzzy classification method and the shadow of auxiliary method to extract information building, With the comparison of k-means classification, and the traditional maximum likelihood classification method, the results of experiment object based on multi-scale combined with mathematical morphology of image segmentation and extraction method, can accurately extract the structure of the information is more clear classification data, provide the basis for the intelligent monitoring of earth data and theoretical support.

  6. [Advances in researches on hyperspectral remote sensing forestry information-extracting technology].

    Science.gov (United States)

    Wu, Jian; Peng, Dao-Li

    2011-09-01

    The hyperspectral remote sensing technology has become one of the leading technologies in forestry remote sensing domain. In the present review paper, the advances in researches on hyperspectral remote sensing technology in forestry information extraction both at home and abroad were reviewed, and the five main research aspects including the hyperspectral classification and recognition of forest tree species, the hyperspectral inversion and extraction of forest ecological physical parameters, the hyperspectral monitoring and diagnosis of forest nutrient element, the forest crown density information extraction and the hyperspectral monitoring of forest disasters were summarized. The unresolved problems of hyperspectral technology in the forestry remote sensing applications were pointed out and the possible ways to solve these problems were expounded. Finally, the application prospect of hyperspectral remote sensing technology in forestry was analyzed. PMID:22097816

  7. Methods to extract information on the atomic and molecular states from scientific abstracts

    International Nuclear Information System (INIS)

    We propose a new application of information technology to recognize and extract expressions of atomic and molecular states from electrical forms of scientific abstracts. Present results will help scientists to understand atomic states as well as the physics discussed in the articles. Combining with the internet search engines, it will make one possible to collect not only atomic and molecular data but broader scientific information over a wide range of research fields. (author)

  8. Application of high spatial resolution airborne hyperspectral remote sensing data in thematic information extraction

    Science.gov (United States)

    Xu, Hong-gen; Ma, Hong-chao; Li, De-ren; Song, Yan

    2006-10-01

    The airborne hyperspectral remote sensing data, such as PHI, OMIS, has the virtues of high spatial and spectral resolution. Hence, from the view of target classification we can consider that it can provide the ability of discriminating targets more detailedly than other data. So it's important to extract thematic information and update database using this kind of data. Whereas, the hyperspectral data has abundant bands and high between-band correlation, the traditional classification methods such as maximum likelihood classifier (MLC) and spectral angle mapper (SAM) have performed poorly in thematic information extraction. For this reason, we present a new method for thematic information extraction with hyperspectral remote sensing data. We perform classification by means of combining the self-organizing map (SOM) neural network which is considered as full-pixel technique with linear spectral mixture analysis (LSMA) which is considered as mixed-pixel technique. The SOM neural network is improved from some aspects to classify the pure data and find the mixed data. And then the mixed data are unmixed and classified by LSMA. The result of experiment shows that we can have the better performance in thematic information extraction with PHI by this means.

  9. An Information Extraction Core System for Real World German Text Processing

    CERN Document Server

    Neumann, G; Baur, J; Becker, M; Braun, C

    1997-01-01

    This paper describes SMES, an information extraction core system for real world German text processing. The basic design criterion of the system is of providing a set of basic powerful, robust, and efficient natural language components and generic linguistic knowledge sources which can easily be customized for processing different tasks in a flexible manner.

  10. Handbook of biomedical optics

    CERN Document Server

    Boas, David A

    2011-01-01

    Biomedical optics holds tremendous promise to deliver effective, safe, non- or minimally invasive diagnostics and targeted, customizable therapeutics. Handbook of Biomedical Optics provides an in-depth treatment of the field, including coverage of applications for biomedical research, diagnosis, and therapy. It introduces the theory and fundamentals of each subject, ensuring accessibility to a wide multidisciplinary readership. It also offers a view of the state of the art and discusses advantages and disadvantages of various techniques.Organized into six sections, this handbook: Contains intr

  11. Biomedical applications of polymers

    CERN Document Server

    Gebelein, C G

    1991-01-01

    The biomedical applications of polymers span an extremely wide spectrum of uses, including artificial organs, skin and soft tissue replacements, orthopaedic applications, dental applications, and controlled release of medications. No single, short review can possibly cover all these items in detail, and dozens of books andhundreds of reviews exist on biomedical polymers. Only a few relatively recent examples will be cited here;additional reviews are listed under most of the major topics in this book. We will consider each of the majorclassifications of biomedical polymers to some extent, inclu

  12. Powering biomedical devices

    CERN Document Server

    Romero, Edwar

    2013-01-01

    From exoskeletons to neural implants, biomedical devices are no less than life-changing. Compact and constant power sources are necessary to keep these devices running efficiently. Edwar Romero's Powering Biomedical Devices reviews the background, current technologies, and possible future developments of these power sources, examining not only the types of biomedical power sources available (macro, mini, MEMS, and nano), but also what they power (such as prostheses, insulin pumps, and muscular and neural stimulators), and how they work (covering batteries, biofluids, kinetic and ther

  13. Biomedical Engineering Desk Reference

    CERN Document Server

    Ratner, Buddy D; Schoen, Frederick J; Lemons, Jack E; Dyro, Joseph; Martinsen, Orjan G; Kyle, Richard; Preim, Bernhard; Bartz, Dirk; Grimnes, Sverre; Vallero, Daniel; Semmlow, John; Murray, W Bosseau; Perez, Reinaldo; Bankman, Isaac; Dunn, Stanley; Ikada, Yoshito; Moghe, Prabhas V; Constantinides, Alkis

    2009-01-01

    A one-stop Desk Reference, for Biomedical Engineers involved in the ever expanding and very fast moving area; this is a book that will not gather dust on the shelf. It brings together the essential professional reference content from leading international contributors in the biomedical engineering field. Material covers a broad range of topics including: Biomechanics and Biomaterials; Tissue Engineering; and Biosignal Processing* A hard-working desk reference providing all the essential material needed by biomedical and clinical engineers on a day-to-day basis * Fundamentals, key techniques,

  14. Biomedical engineering fundamentals

    CERN Document Server

    Bronzino, Joseph D; Bronzino, Joseph D

    2006-01-01

    Over the last century,medicine has come out of the "black bag" and emerged as one of the most dynamic and advanced fields of development in science and technology. Today, biomedical engineering plays a critical role in patient diagnosis, care, and rehabilitation. As such, the field encompasses a wide range of disciplines, from biology and physiology to informatics and signal processing. Reflecting the enormous growth and change in biomedical engineering during the infancy of the 21st century, The Biomedical Engineering Handbook enters its third edition as a set of three carefully focused and

  15. Semi-automatic building extraction in informal settlements from high-resolution satellite imagery

    Science.gov (United States)

    Mayunga, Selassie David

    The extraction of man-made features from digital remotely sensed images is considered as an important step underpinning management of human settlements in any country. Man-made features and buildings in particular are required for varieties of applications such as urban planning, creation of geographical information systems (GIS) databases and Urban City models. The traditional man-made feature extraction methods are very expensive in terms of equipment, labour intensive, need well-trained personnel and cannot cope with changing environments, particularly in dense urban settlement areas. This research presents an approach for extracting buildings in dense informal settlement areas using high-resolution satellite imagery. The proposed system uses a novel strategy of extracting building by measuring a single point at the approximate centre of the building. The fine measurement of the building outlines is then effected using a modified snake model. The original snake model on which this framework is based, incorporates an external constraint energy term which is tailored to preserving the convergence properties of the snake model; its use to unstructured objects will negatively affect their actual shapes. The external constrained energy term was removed from the original snake model formulation, thereby, giving ability to cope with high variability of building shapes in informal settlement areas. The proposed building extraction system was tested on two areas, which have different situations. The first area was Tungi in Dar Es Salaam, Tanzania where three sites were tested. This area is characterized by informal settlements, which are illegally formulated within the city boundaries. The second area was Oromocto in New Brunswick, Canada where two sites were tested. Oromocto area is mostly flat and the buildings are constructed using similar materials. Qualitative and quantitative measures were employed to evaluate the accuracy of the results as well as the performance

  16. PALM-IST: Pathway Assembly from Literature Mining - an Information Search Tool

    OpenAIRE

    Mandloi, Sapan; Chakrabarti, Saikat

    2015-01-01

    Manual curation of biomedical literature has become extremely tedious process due to its exponential growth in recent years. To extract meaningful information from such large and unstructured text, newer and more efficient mining tool is required. Here, we introduce PALM-IST, a computational platform that not only allows users to explore biomedical abstracts using keyword based text mining but also extracts biological entity (e.g., gene/protein, drug, disease, biological processes, cellular c...

  17. EXTRACT

    DEFF Research Database (Denmark)

    Pafilis, Evangelos; Buttigieg, Pier Luigi; Ferrell, Barbra;

    2016-01-01

    The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation is a highly labor intensive process and requires familiarity with the terminologies used. We have the...... and text-mining-assisted curation revealed that EXTRACT speeds up annotation by 15-25% and helps curators to detect terms that would otherwise have been missed.Database URL: https://extract.hcmr.gr/......., organism, tissue and disease terms. The evaluators in the BioCreative V Interactive Annotation Task found the system to be intuitive, useful, well documented and sufficiently accurate to be helpful in spotting relevant text passages and extracting organism and environment terms. Comparison of fully manual...

  18. Studies on methods and techniques of weak information extraction and integrated evaluation for sandstone-type uranium deposits

    International Nuclear Information System (INIS)

    Weak information extraction and integrated evaluation for sandstone-type uranium deposits are currently one of the important research contents in uranium exploration. Through several years researches, the authors put forward the meaning of aeromagnetic and aeroradioactive weak information extraction, study the formation theories of aeromagnetic and aeroradioactive weak information and establish effective mathematic models for weak information extraction. Based on GIS software, models of weak information extraction are actualized and the expert-grading model for integrated evaluation is developed. The trial of aeromagnetic and aeroradioactive weak information and integrated evaluation of uranium resources are completed by using GIS software in the study area. The researchful results prove that techniques of weak information extraction and integrated evaluation may further delineate the prospective areas of sandstone-type uranium deposits rapidly and improve the predicitive precision. (authors)

  19. A Framework For Extracting Information From Web Using VTD-XML‘s XPath

    Directory of Open Access Journals (Sweden)

    C. Subhashini

    2012-03-01

    Full Text Available The exponential growth of WWW (World Wide Web is the cause for vast pool of information as well as several challenges posed by it, such as extracting potentially useful and unknown information from WWW. Many websites are built with HTML, because of its unstructured layout, it is difficult to obtain effective and precise data from web using HTML. The advent of XML (Extensible Markup Language proposes a better solution to extract useful knowledge from WWW. Web Data Extraction based on XML Technology solves this problem because XML is a general purpose specification for exchanging data over the Web. In this paper, a framework is suggested to extract the data from the web.Here the semi-structured data in the web page is transformed into well-structured data using standard XML technologies and the new parsing technique called extended VTD-XML (Virtual Token Descriptorfor XML along with Xpath implementation has been used to extract data from the well-structured XML document.

  20. Information Extraction for System-Software Safety Analysis: Calendar Year 2008 Year-End Report

    Science.gov (United States)

    Malin, Jane T.

    2009-01-01

    This annual report describes work to integrate a set of tools to support early model-based analysis of failures and hazards due to system-software interactions. The tools perform and assist analysts in the following tasks: 1) extract model parts from text for architecture and safety/hazard models; 2) combine the parts with library information to develop the models for visualization and analysis; 3) perform graph analysis and simulation to identify and evaluate possible paths from hazard sources to vulnerable entities and functions, in nominal and anomalous system-software configurations and scenarios; and 4) identify resulting candidate scenarios for software integration testing. There has been significant technical progress in model extraction from Orion program text sources, architecture model derivation (components and connections) and documentation of extraction sources. Models have been derived from Internal Interface Requirements Documents (IIRDs) and FMEA documents. Linguistic text processing is used to extract model parts and relationships, and the Aerospace Ontology also aids automated model development from the extracted information. Visualizations of these models assist analysts in requirements overview and in checking consistency and completeness.

  1. Automatic Extraction of Spatio-Temporal Information from Arabic Text Documents

    Directory of Open Access Journals (Sweden)

    Abdelkoui Feriel

    2015-10-01

    Full Text Available Unstructured Arabic text documents are an important source of geographical and temporal information. The possibility of automatically tracking spatio-temporal information, capturing changes relating to events from text documents, is a new challenge in the fields of geographic information retrieval (GIR, temporal information retrieval (TIR and natural language processing (NLP. There was a lot of work on the extraction of information in other languages that use Latin alphabet, such as English,, French, or Spanish, by against the Arabic language is still not well supported in GIR and TIR and it needs to conduct more researches. In this paper, we present an approach that support automated exploration and extraction of spatio-temporal information from Arabic text documents in order to capture and model such information before it can be utilized in search and exploration tasks. The system has been successfully tested on 50 documents that include a mixture of types of Spatial/temporal information. The result achieved 91.01% of recall and of 80% precision. This illustrates that our approach is effective and its performance is satisfactory.

  2. Sensors for biomedical applications

    NARCIS (Netherlands)

    Bergveld, Piet

    1986-01-01

    This paper considers the impact during the last decade of modern IC technology, microelectronics, thin- and thick-film technology, fibre optic technology, etc. on the development of sensors for biomedical applications.

  3. Framework for automatic information extraction from research papers on nanocrystal devices

    Directory of Open Access Journals (Sweden)

    Thaer M. Dieb

    2015-09-01

    Full Text Available To support nanocrystal device development, we have been working on a computational framework to utilize information in research papers on nanocrystal devices. We developed an annotated corpus called “ NaDev” (Nanocrystal Device Development for this purpose. We also proposed an automatic information extraction system called “NaDevEx” (Nanocrystal Device Automatic Information Extraction Framework. NaDevEx aims at extracting information from research papers on nanocrystal devices using the NaDev corpus and machine-learning techniques. However, the characteristics of NaDevEx were not examined in detail. In this paper, we conduct system evaluation experiments for NaDevEx using the NaDev corpus. We discuss three main issues: system performance, compared with human annotators; the effect of paper type (synthesis or characterization on system performance; and the effects of domain knowledge features (e.g., a chemical named entity recognition system and list of names of physical quantities on system performance. We found that overall system performance was 89% in precision and 69% in recall. If we consider identification of terms that intersect with correct terms for the same information category as the correct identification, i.e., loose agreement (in many cases, we can find that appropriate head nouns such as temperature or pressure loosely match between two terms, the overall performance is 95% in precision and 74% in recall. The system performance is almost comparable with results of human annotators for information categories with rich domain knowledge information (source material. However, for other information categories, given the relatively large number of terms that exist only in one paper, recall of individual information categories is not high (39–73%; however, precision is better (75–97%. The average performance for synthesis papers is better than that for characterization papers because of the lack of training examples for

  4. Clinic expert information extraction based on domain model and block importance model.

    Science.gov (United States)

    Zhang, Yuanpeng; Wang, Li; Qian, Danmin; Geng, Xingyun; Yao, Dengfu; Dong, Jiancheng

    2015-11-01

    To extract expert clinic information from the Deep Web, there are two challenges to face. The first one is to make a judgment on forms. A novel method based on a domain model, which is a tree structure constructed by the attributes of query interfaces is proposed. With this model, query interfaces can be classified to a domain and filled in with domain keywords. Another challenge is to extract information from response Web pages indexed by query interfaces. To filter the noisy information on a Web page, a block importance model is proposed, both content and spatial features are taken into account in this model. The experimental results indicate that the domain model yields a precision 4.89% higher than that of the rule-based method, whereas the block importance model yields an F1 measure 10.5% higher than that of the XPath method. PMID:26231612

  5. Sharing big biomedical data

    OpenAIRE

    Toga, Arthur W.; Dinov, Ivo D.

    2015-01-01

    Background The promise of Big Biomedical Data may be offset by the enormous challenges in handling, analyzing, and sharing it. In this paper, we provide a framework for developing practical and reasonable data sharing policies that incorporate the sociological, financial, technical and scientific requirements of a sustainable Big Data dependent scientific community. Findings Many biomedical and healthcare studies may be significantly impacted by using large, heterogeneous and incongruent data...

  6. Biomedical signal processing

    CERN Document Server

    Akay, Metin

    1994-01-01

    Sophisticated techniques for signal processing are now available to the biomedical specialist! Written in an easy-to-read, straightforward style, Biomedical Signal Processing presents techniques to eliminate background noise, enhance signal detection, and analyze computer data, making results easy to comprehend and apply. In addition to examining techniques for electrical signal analysis, filtering, and transforms, the author supplies an extensive appendix with several computer programs that demonstrate techniques presented in the text.

  7. Biomedical signal analysis

    CERN Document Server

    Rangayyan, Rangaraj M

    2015-01-01

    The book will help assist a reader in the development of techniques for analysis of biomedical signals and computer aided diagnoses with a pedagogical examination of basic and advanced topics accompanied by over 350 figures and illustrations. Wide range of filtering techniques presented to address various applications. 800 mathematical expressions and equations. Practical questions, problems and laboratory exercises. Includes fractals and chaos theory with biomedical applications.

  8. Pattern-Based Extraction of Argumentation from the Scientific Literature

    Science.gov (United States)

    White, Elizabeth K.

    2010-01-01

    As the number of publications in the biomedical field continues its exponential increase, techniques for automatically summarizing information from this body of literature have become more diverse. In addition, the targets of summarization have become more subtle; initial work focused on extracting the factual assertions from full-text papers,…

  9. Extraction of Hidden Social Networks from Wiki-Environment Involved in Information Conflict

    Directory of Open Access Journals (Sweden)

    Rasim M. Alguliyev

    2016-03-01

    Full Text Available Social network analysis is a widely used technique to analyze relationships among wiki-users in Wikipedia. In this paper the method to identify hidden social networks participating in information conflicts in wiki-environment is proposed. In particular, we describe how text clustering techniques can be used for extraction of hidden social networks of wiki-users caused information conflict. By clustering unstructured text articles caused information conflict we create social network of wiki-users. For clustering of the conflict articles a hybrid weighted fuzzy-c-means method is proposed.

  10. DWDE-IR: An Efficient Deep Web Data Extraction for Information Retrieval on Web Mining

    OpenAIRE

    Aysha Banu; Chitra, M.

    2014-01-01

    Deep Web is a widely unexplored data source, is becoming an important research topic. Retrieving structured data from deep web pages is the challenging problem due to their complex structure. In this paper, Information extracts on the Deep Web pages based on the Deep Web Data Extraction technique (DWDR-IR). Search engines usually return a large number of pages in response to the user queries. To help the users to navigate in the result list, ranking methods are activated on the search results...

  11. Extracting directed information flow networks: an application to genetics and semantics

    CERN Document Server

    Masucci, A P; Hernández-García, E; Kalampokis, A

    2010-01-01

    We introduce a general method to infer the directional information flow between populations whose elements are described by n-dimensional vectors of symbolic attributes. The method is based on the Jensen-Shannon divergence and on the Shannon entropy and has a wide range of application. We show here the results of two applications: first extracting the network of genetic flow between the meadows of the seagrass Poseidonia Oceanica, where the meadow elements are specified by sets of microsatellite markers, then we extract the semantic flow network from a set of Wikipedia pages, showing the semantic channels between different areas of knowledge.

  12. Computer-Aided Design Data Extraction Approach to Identify Product Information

    Directory of Open Access Journals (Sweden)

    Mohamad F.A. Jabal

    2009-01-01

    Full Text Available Problem statement: Many approaches have been proposed in previous such as AUTOFEAT algorithm, feature recognition, Intelligent Feature Recognition Methodology (IFRM, a part recognition algorithm and graph theory-based approach in order to solve the integration issue between CAD and CAM. However, there is no direct connection from CAD database and machine database. Therefore, comparison among the approaches has been conducted because to recognize the suitable approach is the importance tasks before this research can be proceed for the next stage. Approach: This study focused on CAD data extraction approach to identify product information. CAD data referred as Computer-Aided Design (CAD data extracted from the CAD drawing which contained the drawing of product that be produce by manufacturing. CAD data consisted of geometric and non-geometric data. Geometric data contained lines, curves and vertex. While non-geometric data include texts, colors and layers. The extracted CAD data were needed to generate the product information which is useful information for the machine in production field to produce the product for the manufacturing same as depicted in the CAD drawing. Basically, the product information consisted of product details such as length, thickness, wideness and radius of the product, processes information for the machine to process the product such as taper, cutting, drilling and punching. In addition, product information also contained type of materials for the product. Results: As a result, feature recognition is the most suitable approach can be applied for this research. Thus, the approach was selected to precede the next stage. Conclusion: Conclusion from the comparison among the approaches is in term of accuracy of extracted data is not accurate when the drawing is incomplete drawing or contains the noise such as unwanted lines or any shapes cross the object in the drawing.

  13. Using Local Grammar for Entity Extraction from Clinical Reports

    Directory of Open Access Journals (Sweden)

    Aicha Ghoulam

    2015-06-01

    Full Text Available Information Extraction (IE is a natural language processing (NLP task whose aim is to analyze texts written in natural language to extract structured and useful information such as named entities and semantic relations linking these entities. Information extraction is an important task for many applications such as bio-medical literature mining, customer care, community websites, and personal information management. The increasing information available in patient clinical reports is difficult to access. As it is often in an unstructured text form, doctors need tools to enable them access to this information and the ability to search it. Hence, a system for extracting this information in a structured form can benefits healthcare professionals. The work presented in this paper uses a local grammar approach to extract medical named entities from French patient clinical reports. Experimental results show that the proposed approach achieved an F-Measure of 90. 06%.

  14. Semantic preview benefit in English: Individual differences in the extraction and use of parafoveal semantic information.

    Science.gov (United States)

    Veldre, Aaron; Andrews, Sally

    2016-06-01

    Although there is robust evidence that skilled readers of English extract and use orthographic and phonological information from the parafovea to facilitate word identification, semantic preview benefits have been elusive. We sought to establish whether individual differences in the extraction and/or use of parafoveal semantic information could account for this discrepancy. Ninety-nine adult readers who were assessed on measures of reading and spelling ability read sentences while their eye movements were recorded. The gaze-contingent boundary paradigm was used to manipulate the availability of relevant semantic and orthographic information in the parafovea. On average, readers showed a benefit from previews high in semantic feature overlap with the target. However, reading and spelling ability yielded opposite effects on semantic preview benefit. High reading ability was associated with a semantic preview benefit that was equivalent to an identical preview on first-pass reading. High spelling ability was associated with a reduced semantic preview benefit despite an overall higher rate of skipping. These results suggest that differences in the magnitude of semantic preview benefits in English reflect constraints on extracting semantic information from the parafovea and competition between the orthographic features of the preview and the target. (PsycINFO Database Record PMID:26595070

  15. The feasibility of using natural language processing to extract clinical information from breast pathology reports

    Directory of Open Access Journals (Sweden)

    Julliette M Buckley

    2012-01-01

    Full Text Available Objective: The opportunity to integrate clinical decision support systems into clinical practice is limited due to the lack of structured, machine readable data in the current format of the electronic health record. Natural language processing has been designed to convert free text into machine readable data. The aim of the current study was to ascertain the feasibility of using natural language processing to extract clinical information from >76,000 breast pathology reports. Approach and Procedure: Breast pathology reports from three institutions were analyzed using natural language processing software (Clearforest, Waltham, MA to extract information on a variety of pathologic diagnoses of interest. Data tables were created from the extracted information according to date of surgery, side of surgery, and medical record number. The variety of ways in which each diagnosis could be represented was recorded, as a means of demonstrating the complexity of machine interpretation of free text. Results: There was widespread variation in how pathologists reported common pathologic diagnoses. We report, for example, 124 ways of saying invasive ductal carcinoma and 95 ways of saying invasive lobular carcinoma. There were >4000 ways of saying invasive ductal carcinoma was not present. Natural language processor sensitivity and specificity were 99.1% and 96.5% when compared to expert human coders. Conclusion: We have demonstrated how a large body of free text medical information such as seen in breast pathology reports, can be converted to a machine readable format using natural language processing, and described the inherent complexities of the task.

  16. Comparison of edge detection techniques for the automatic information extraction of Lidar data

    Science.gov (United States)

    Li, H.; di, L.; Huang, X.; Li, D.

    2008-05-01

    In recent years, there has been much interest in information extraction from Lidar point cloud data. Many automatic edge detection algorithms have been applied to extracting information from Lidar data. Generally they can be divided as three major categories: early vision gradient operators, optimal detectors and operators using parametric fitting models. Lidar point cloud includes the intensity information and the geographic information. Thus, traditional edge detectors used in remote sensed images can take advantage with the coordination information provided by point data. However, derivation of complex terrain features from Lidar data points depends on the intensity properties and topographic relief of each scene. Take road for example, in some urban area, road has the alike intensity as buildings, but the topographic relationship of road is distinct. The edge detector for road in urban area is different from the detector for buildings. Therefore, in Lidar extraction, each kind of scene has its own suitable edge detector. This paper compares application of the different edge detectors from the previous paragraph to various terrain areas, in order to figure out the proper algorithm for respective terrain type. The Canny, EDISON and SUSAN algorithms were applied to data points with the intensity character and topographic relationship of Lidar data. The Lidar data for test are over different terrain areas, such as an urban area with a mass of buildings, a rural area with vegetation, an area with slope, or an area with a bridge, etc. Results using these edge detectors are compared to determine which algorithm is suitable for a specific terrain area. Key words: Edge detector, Extraction, Lidar, Point data

  17. Unsupervised biomedical named entity recognition: experiments with clinical and biological texts.

    Science.gov (United States)

    Zhang, Shaodian; Elhadad, Noémie

    2013-12-01

    Named entity recognition is a crucial component of biomedical natural language processing, enabling information extraction and ultimately reasoning over and knowledge discovery from text. Much progress has been made in the design of rule-based and supervised tools, but they are often genre and task dependent. As such, adapting them to different genres of text or identifying new types of entities requires major effort in re-annotation or rule development. In this paper, we propose an unsupervised approach to extracting named entities from biomedical text. We describe a stepwise solution to tackle the challenges of entity boundary detection and entity type classification without relying on any handcrafted rules, heuristics, or annotated data. A noun phrase chunker followed by a filter based on inverse document frequency extracts candidate entities from free text. Classification of candidate entities into categories of interest is carried out by leveraging principles from distributional semantics. Experiments show that our system, especially the entity classification step, yields competitive results on two popular biomedical datasets of clinical notes and biological literature, and outperforms a baseline dictionary match approach. Detailed error analysis provides a road map for future work. PMID:23954592

  18. A Study on Lip Extraction due to Fuzzy Reasoning by Using Color Information

    Science.gov (United States)

    Shirasawa, Yoichi; Nishida, Makoto; Nishi, Kenji

    This paper proposes a method for extracting the lip shape from the region around the lip. It is carried out without limited conditions such as the lipstick or lighting. The proposed method uses color information for the lip shape extraction. They are psychometric quantities of a metric hue angle (hab), a rectangular coordinates(a*) , which are defined in CIE 1976 L*a*b* color space. The method employs fuzzy reasoning was employed in order to consider obscurity in image data such as shade on the face. The membership function of condition part for characteristics in each class was defined by the triangular membership function was used for the fuzzy reasoning. In order to reduce the effect of the data acquisition condition, an extraction method is here presented for the lip shape from region around the lip due to fuzzy reasoning. We studied on set up of the membership function of condition part. The proposed method uses a* color histogram and habcolor histogram of the region around the lip when sets up of membership function of condition part. This paper clarified that the lip was able to be extracted without the no special conditions such as the lipstick or lighting. The experimental result indicates the effectiveness of the propose method; about 98.7 percent of facial images data was extracted its shape.

  19. From remote sensing data about information extraction for 3D geovisualization - Development of a workflow

    International Nuclear Information System (INIS)

    With an increased availability of high (spatial) resolution remote sensing imagery since the late nineties, the need to develop operative workflows for the automated extraction, provision and communication of information from such data has grown. Monitoring requirements, aimed at the implementation of environmental or conservation targets, management of (environmental-) resources, and regional planning as well as international initiatives, especially the joint initiative of the European Commission and ESA (European Space Agency) for Global Monitoring for Environment and Security (GMES) play also a major part. This thesis addresses the development of an integrated workflow for the automated provision of information derived from remote sensing data. Considering applied data and fields of application, this work aims to design the workflow as generic as possible. Following research questions are discussed: What are the requirements of a workflow architecture that seamlessly links the individual workflow elements in a timely manner and secures accuracy of the extracted information effectively? How can the workflow retain its efficiency if mounds of data are processed? How can the workflow be improved with regards to automated object-based image analysis (OBIA)? Which recent developments could be of use? What are the limitations or which workarounds could be applied in order to generate relevant results? How can relevant information be prepared target-oriented and communicated effectively? How can the more recently developed freely available virtual globes be used for the delivery of conditioned information under consideration of the third dimension as an additional, explicit carrier of information? Based on case studies comprising different data sets and fields of application it is demonstrated how methods to extract and process information as well as to effectively communicate results can be improved and successfully combined within one workflow. It is shown that (1

  20. Digital surface modelling and 3D information extraction from spaceborne very high resolution stereo pairs

    OpenAIRE

    POLI DANIELA; Caravaggi I.

    2012-01-01

    This report discusses the potentials of VHR stereo imagery for automatic digital surface modelling (DSM) and 3D information extraction on large metropolitan cities. Stereo images acquired by GeoEye-1 on Dakar and Guatemala City and by WorldView-2 on Panama City, Constitucion (Chile), Kabul, Teheran, Kathmandu and San Salvador were processed following a rigorous photogrammetric approach. The work focusing on evaluating the quality of the DSMs in relation to the image and terrain characteristic...

  1. Monadic Datalog and the Expressive Power of Languages for Web Information Extraction

    OpenAIRE

    Gottlob, Georg; Koch, Christoph

    2002-01-01

    Research on information extraction from Web pages (wrapping) has seen much activity recently (particularly systems implementations), but little work has been done on formally studying the expressiveness of the formalisms proposed or on the theoretical foundations of wrapping. In this paper, we first study monadic datalog over trees as a wrapping language. We show that this simple language is equivalent to monadic second order logic (MSO) in its ability to specify wrappers. We believe that MSO...

  2. The feasibility of using natural language processing to extract clinical information from breast pathology reports

    OpenAIRE

    Buckley, Julliette M.; Coopey, Suzanne B.; John Sharko; Fernanda Polubriaginof; Brian Drohan; Belli, Ahmet K.; Kim, Elizabeth M. H.; Garber, Judy E.; Smith, Barbara L; Gadd, Michele A.; Specht, Michelle C.; Roche, Constance A.; Gudewicz, Thomas M.; Hughes, Kevin S.

    2012-01-01

    Objective: The opportunity to integrate clinical decision support systems into clinical practice is limited due to the lack of structured, machine readable data in the current format of the electronic health record. Natural language processing has been designed to convert free text into machine readable data. The aim of the current study was to ascertain the feasibility of using natural language processing to extract clinical information from >76,000 breast pathology reports. Approach and Pro...

  3. Term identification in the biomedical literature.

    Science.gov (United States)

    Krauthammer, Michael; Nenadic, Goran

    2004-12-01

    Sophisticated information technologies are needed for effective data acquisition and integration from a growing body of the biomedical literature. Successful term identification is key to getting access to the stored literature information, as it is the terms (and their relationships) that convey knowledge across scientific articles. Due to the complexities of a dynamically changing biomedical terminology, term identification has been recognized as the current bottleneck in text mining, and--as a consequence--has become an important research topic both in natural language processing and biomedical communities. This article overviews state-of-the-art approaches in term identification. The process of identifying terms is analysed through three steps: term recognition, term classification, and term mapping. For each step, main approaches and general trends, along with the major problems, are discussed. By assessing previous work in context of the overall term identification process, the review also tries to delineate needs for future work in the field. PMID:15542023

  4. An Approach to Extract Informative Rules for Web Page Recommendation by Genetic Programming

    Science.gov (United States)

    Kim, Jaekwang; Yoon, Kwangho; Lee, Jee-Hyong

    Clickstreams in users' navigation logs have various data which are related to users' web surfing. Those are visit counts, stay times, product types, etc. When we observe these data, we can divide clickstreams into sub-clickstreams so that the pages in a sub-clickstream share more contexts with each other than with the pages in other sub-clickstreams. In this paper, we propose a method which extracts more informative rules from clickstreams for web page recommendation based on genetic programming and association rules. First, we split clickstreams into sub-clickstreams by contexts for generating more informative rules. In order to split clickstreams in consideration of context, we extract six features from users' navigation logs. A set of split rules is generated by combining those features through genetic programming, and then informative rules for recommendation are extracted with the association rule mining algorithm. Through experiments, we verify that the proposed method is more effective than the other methods in various conditions.

  5. Semi-Automatic Mapping Generation for the DBpedia Information Extraction Framework

    Directory of Open Access Journals (Sweden)

    Arup Sarkar, Ujjal Marjit, Utpal Biswas

    2013-03-01

    Full Text Available DBpedia is one of the very well known live projectsfrom the Semantic Web. It is likeamirror version ofthe Wikipedia site in Semantic Web. Initially itpublishes the information collected from theWikipedia, but only that part which is relevant tothe Semantic Web.Collecting information forSemantic Web from the Wikipedia is demonstratedas the extraction of structured data. DBpedianormally do this by using a specially designedframework called DBpedia Information ExtractionFramework. This extraction framework do itsworks thorough the evaluation of the similarproperties from the DBpedia Ontology and theWikipedia template. This step is known as DBpediamapping.At present mostof the mapping jobs aredone complete manually.In this paper a newframework is introduced considering the issuesrelated to the template to ontology mapping. A semi-automatic mapping tool for the DBpedia projectisproposedwith the capability of automaticsuggestion generation for the end usersso thatusers can identify the similar Ontology and templateproperties.Proposed framework is useful since afterselection of similar properties, the necessary code tomaintain the mapping between Ontology andtemplate is generated automatically.

  6. TagLine: Information Extraction for Semi-Structured Text in Medical Progress Notes.

    Science.gov (United States)

    Finch, Dezon K; McCart, James A; Luther, Stephen L

    2014-01-01

    Statistical text mining and natural language processing have been shown to be effective for extracting useful information from medical documents. However, neither technique is effective at extracting the information stored in semi-structure text elements. A prototype system (TagLine) was developed to extract information from the semi-structured text using machine learning and a rule based annotator. Features for the learning machine were suggested by prior work, and by examining text, and selecting attributes that help distinguish classes of text lines. Classes were derived empirically from text and guided by an ontology developed by the VHA's Consortium for Health Informatics Research (CHIR). Decision trees were evaluated for class predictions on 15,103 lines of text achieved an overall accuracy of 98.5 percent. The class labels applied to the lines were then used for annotating semi-structured text elements. TagLine achieved F-measure over 0.9 for each of the structures, which included tables, slots and fillers. PMID:25954358

  7. Road Extraction from High-resolution Remote Sensing Images Based on Multiple Information Fusion

    Directory of Open Access Journals (Sweden)

    LI Xiao-feng

    2016-02-01

    Full Text Available Road extraction from high-resolution remote sensing images has been considered to be a significant but very difficult task.Especially the spectrum of some buildings is similar with that of roads,which makes the surfaces being connect with each other after classification and difficult to be distinguished.Based on the cooperation between road surfaces and edges,this paper presents an approach to purify roads from high-resolution remote sensing images.Firstly,we try to improve the extraction accuracy of road surfaces and edges respectively.The logic cooperation between these two binary images is used to separate road and non-road objects.Then the road objects are confirmed by the cooperation between surfaces and edges.And the effective shape indices(e.g.polar moment of inertia and narrow extent index are applied to eliminate non-road objects.So the road information is refined.The experiments indicate that the proposed approach is efficient for eliminating non-road information and extracting road information from high-resolution remote sensing image.

  8. TagLine: Information Extraction for Semi-Structured Text in Medical Progress Notes

    Science.gov (United States)

    Finch, Dezon K.; McCart, James A.; Luther, Stephen L.

    2014-01-01

    Statistical text mining and natural language processing have been shown to be effective for extracting useful information from medical documents. However, neither technique is effective at extracting the information stored in semi-structure text elements. A prototype system (TagLine) was developed to extract information from the semi-structured text using machine learning and a rule based annotator. Features for the learning machine were suggested by prior work, and by examining text, and selecting attributes that help distinguish classes of text lines. Classes were derived empirically from text and guided by an ontology developed by the VHA’s Consortium for Health Informatics Research (CHIR). Decision trees were evaluated for class predictions on 15,103 lines of text achieved an overall accuracy of 98.5 percent. The class labels applied to the lines were then used for annotating semi-structured text elements. TagLine achieved F-measure over 0.9 for each of the structures, which included tables, slots and fillers. PMID:25954358

  9. MEDSYNDIKATE--a natural language system for the extraction of medical information from findings reports.

    Science.gov (United States)

    Hahn, Udo; Romacker, Martin; Schulz, Stefan

    2002-12-01

    MEDSYNDIKATE is a natural language processor, which automatically acquires medical information from findings reports. In the course of text analysis their contents is transferred to conceptual representation structures, which constitute a corresponding text knowledge base. MEDSYNDIKATE is particularly adapted to deal properly with text structures, such as various forms of anaphoric reference relations spanning several sentences. The strong demands MEDSYNDIKATE poses on the availability of expressive knowledge sources are accounted for by two alternative approaches to acquire medical domain knowledge (semi)automatically. We also present data for the information extraction performance of MEDSYNDIKATE in terms of the semantic interpretation of three major syntactic patterns in medical documents. PMID:12460632

  10. Multiple Features Based Approach to Extract Bio-molecular Event Triggers Using Conditional Random Field

    Directory of Open Access Journals (Sweden)

    Amit Majumder

    2012-11-01

    Full Text Available The purpose of Biomedical Natural Language Processing (BioNLP is to capture biomedical phenomena from textual data by extracting relevant entities, information and relations between biomedical entities (i.e. proteins and genes. In general, in most of the published papers, only binary relations were extracted. In a recent past, the focus is shifted towards extracting more complex relations in the form of bio-molecular events that may include several entities or other relations. In this paper we propose an approach that enables event trigger extraction of relatively complex bio-molecular events. We approach this problem as a detection of bio-molecular event trigger using the well-known algorithm, namely Conditional Random Field (CRF. We apply our experiments on development set. It shows the overall average recall, precision and F-measure values of 64.27504%, 69.97559% and 67.00429%, respectively for the event detection.

  11. Effective use of Latent Semantic Indexing and Computational Linguistics in Biological and Biomedical Applications

    Directory of Open Access Journals (Sweden)

    Hongyu eChen

    2013-01-01

    Full Text Available Text mining is rapidly becoming an essential technique for the annotation and analysis of large biological data sets. Biomedical literature currently increases at a rate of several thousand papers per week, making automated information retrieval methods the only feasible method of managing this expanding corpus. With the increasing prevalence of open-access journals and constant growth of publicly-available repositories of biomedical literature, literature mining has become much more effective with respect to the extraction of biomedically-relevant data. In recent years, text mining of popular databases such as MEDLINE has evolved from basic term-searches to more sophisticated natural language processing techniques, indexing and retrieval methods, structural analysis and integration of literature with associated metadata. In this review, we will focus on Latent Semantic Indexing (LSI, a computational linguistics technique increasingly used for a variety of biological purposes. It is noted for its ability to consistently outperform benchmark Boolean text searches and co-occurrence models at information retrieval and its power to extract indirect relationships within a data set. LSI has been used successfully to formulate new hypotheses, generate novel connections from existing data, and validate empirical data.

  12. Automated Building Extraction from High-Resolution Satellite Imagery in Urban Areas Using Structural, Contextual, and Spectral Information

    Directory of Open Access Journals (Sweden)

    Jin Xiaoying

    2005-01-01

    Full Text Available High-resolution satellite imagery provides an important new data source for building extraction. We demonstrate an integrated strategy for identifying buildings in 1-meter resolution satellite imagery of urban areas. Buildings are extracted using structural, contextual, and spectral information. First, a series of geodesic opening and closing operations are used to build a differential morphological profile (DMP that provides image structural information. Building hypotheses are generated and verified through shape analysis applied to the DMP. Second, shadows are extracted using the DMP to provide reliable contextual information to hypothesize position and size of adjacent buildings. Seed building rectangles are verified and grown on a finely segmented image. Next, bright buildings are extracted using spectral information. The extraction results from the different information sources are combined after independent extraction. Performance evaluation of the building extraction on an urban test site using IKONOS satellite imagery of the City of Columbia, Missouri, is reported. With the combination of structural, contextual, and spectral information, of the building areas are extracted with a quality percentage .

  13. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1976-01-01

    Advances in Biomedical Engineering, Volume 5, is a collection of papers that deals with application of the principles and practices of engineering to basic and applied biomedical research, development, and the delivery of health care. The papers also describe breakthroughs in health improvements, as well as basic research that have been accomplished through clinical applications. One paper examines engineering principles and practices that can be applied in developing therapeutic systems by a controlled delivery system in drug dosage. Another paper examines the physiological and materials vari

  14. Biomedical enhancements as justice.

    Science.gov (United States)

    Nam, Jeesoo

    2015-02-01

    Biomedical enhancements, the applications of medical technology to make better those who are neither ill nor deficient, have made great strides in the past few decades. Using Amartya Sen's capability approach as my framework, I argue in this article that far from being simply permissible, we have a prima facie moral obligation to use these new developments for the end goal of promoting social justice. In terms of both range and magnitude, the use of biomedical enhancements will mark a radical advance in how we compensate the most disadvantaged members of society. PMID:24117708

  15. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1976-01-01

    Advances in Biomedical Engineering, Volume 6, is a collection of papers that discusses the role of integrated electronics in medical systems and the usage of biological mathematical models in biological systems. Other papers deal with the health care systems, the problems and methods of approach toward rehabilitation, as well as the future of biomedical engineering. One paper discusses the use of system identification as it applies to biological systems to estimate the values of a number of parameters (for example, resistance, diffusion coefficients) by indirect means. More particularly, the i

  16. Biomedical engineering entrepreneurship

    CERN Document Server

    Lee, Jen-Shih

    2014-01-01

    This book is written for undergraduate and graduate students in biomedical engineering wanting to learn how to pursue a career in building up their entrepreneur ventures. Practicing engineers wanting to apply their innovations for healthcare will also find this book useful. The 21st century is the Biotech Century where many nations are investing heavily in biotechnology. As a result, tremendous business opportunities exist for biomedical engineering graduates who are interested in becoming successful entrepreneurs. However, many challenges await these entrepreneurs intending to invent safe and

  17. Automated concept-level information extraction to reduce the need for custom software and rules development

    Science.gov (United States)

    Nguyen, Thien M; Goryachev, Sergey; Fiore, Louis D

    2011-01-01

    Objective Despite at least 40 years of promising empirical performance, very few clinical natural language processing (NLP) or information extraction systems currently contribute to medical science or care. The authors address this gap by reducing the need for custom software and rules development with a graphical user interface-driven, highly generalizable approach to concept-level retrieval. Materials and methods A ‘learn by example’ approach combines features derived from open-source NLP pipelines with open-source machine learning classifiers to automatically and iteratively evaluate top-performing configurations. The Fourth i2b2/VA Shared Task Challenge's concept extraction task provided the data sets and metrics used to evaluate performance. Results Top F-measure scores for each of the tasks were medical problems (0.83), treatments (0.82), and tests (0.83). Recall lagged precision in all experiments. Precision was near or above 0.90 in all tasks. Discussion With no customization for the tasks and less than 5 min of end-user time to configure and launch each experiment, the average F-measure was 0.83, one point behind the mean F-measure of the 22 entrants in the competition. Strong precision scores indicate the potential of applying the approach for more specific clinical information extraction tasks. There was not one best configuration, supporting an iterative approach to model creation. Conclusion Acceptable levels of performance can be achieved using fully automated and generalizable approaches to concept-level information extraction. The described implementation and related documentation is available for download. PMID:21697292

  18. Robust relationship extraction in the biomedical domain

    OpenAIRE

    Thomas, Philippe

    2015-01-01

    Seit Jahrhunderten wird menschliches Wissen in Form von natürlicher Sprache ausgetauscht und in Dokumenten schriftlich aufgezeichnet. In den letzten Jahren konnte man auf dem Gebiet der Lebenswissenschaften eine exponentielle Zunahme wissenschaftlicher Publikationen beobachten. Diese Dissertation untersucht die automatische Extraktion von Beziehungen zwischen Eigennamen. Innerhalb dieses Gebietes beschäftigt sich die Arbeit mit der Steigerung der Robustheit für die Relationsextraktion. Zunäc...

  19. Neural Networks and Information Extraction: New developments in astronomical information retrieval for electronic publications

    Science.gov (United States)

    Lesteven, S.; Murtagh, F.; Poincot, P.; Creze, M.; Egret, D.; Murtagh, F.

    1996-12-01

    The inlet of electronic publication in astronomy offers a wealth of new possibilities for retrieving and accessing astronomical information. We describe results obtained in prototyping a Kohonen selforganising feature (a neural network approach) as an interface to a large document collection. This tool permits to display density maps and clustering tendencies of the document collection using, in a first step, the keywords of the articles. The resulting clickable map provides direct access to the abstract services. In a second part, we discuss new possibilities for increasing links between electronic texts and astronomical services. The first application is an automatic tagging of object names in an electronic text, in order to link that object name with the SIMBAD data available for the object.

  20. A Feature Extraction Method Based on Information Theory for Fault Diagnosis of Reciprocating Machinery

    Directory of Open Access Journals (Sweden)

    Huaqing Wang

    2009-04-01

    Full Text Available This paper proposes a feature extraction method based on information theory for fault diagnosis of reciprocating machinery. A method to obtain symptom parameter waves is defined in the time domain using the vibration signals, and an information wave is presented based on information theory, using the symptom parameter waves. A new way to determine the difference spectrum of envelope information waves is also derived, by which the feature spectrum can be extracted clearly and machine faults can be effectively differentiated. This paper also compares the proposed method with the conventional Hilbert-transform-based envelope detection and with a wavelet analysis technique. Practical examples of diagnosis for a rolling element bearing used in a diesel engine are provided to verify the effectiveness of the proposed method. The verification results show that the bearing faults that typically occur in rolling element bearings, such as outer-race, inner-race, and roller defects, can be effectively identified by the proposed method, while these bearing faults are difficult to detect using either of the other techniques it was compared to.

  1. Electrode Selection for Noninvasive Fetal Electrocardiogram Extraction using Mutual Information Criteria

    Science.gov (United States)

    Sameni, R.; Vrins, F.; Parmentier, F.; Hérail, C.; Vigneron, V.; Verleysen, M.; Jutten, C.; Shamsollahi, M. B.

    2006-11-01

    Blind source separation (BSS) techniques have revealed to be promising approaches for the noninvasive extraction of fetal cardiac signals from maternal abdominal recordings. From previous studies, it is now believed that a carefully selected array of electrodes well-placed over the abdomen of a pregnant woman contains the required `information' for BSS, to extract the complete fetal components. Based on this idea, previous works have involved array recording systems and sensor selection strategies based on the Mutual Information (MI) criterion. In this paper the previous works have been extended, by considering the 3-dimensional aspects of the cardiac electrical activity. The proposed method has been tested on simulated and real maternal abdominal recordings. The results show that the new sensor selection strategy together with the MI criterion, can be effectively used to select the channels containing the most `information' concerning the fetal ECG components from an array of 72 recordings. The method is hence believed to be useful for the selection of the most informative channels in online applications, considering the different fetal positions and movements.

  2. MedIEQ-Quality labelling of medical web content using multilingual information extraction.

    Science.gov (United States)

    Mayer, Miquel Angel; Karkaletsis, Vangelis; Stamatakis, Kostas; Leis, Angela; Villarroel, Dagmar; Thomeczek, Christian; Labský, Martin; López-Ostenero, Fernando; Honkela, Timo

    2006-01-01

    Quality of Internet health information is essential because it has the potential to benefit or harm a large number of people and it is therefore essential to provide consumers with some tools to aid them in assessing the nature of the information they are accessing and how they should use it without jeopardizing their relationship with their doctor. Organizations around the world are working on establishing standards of quality in the accreditation of health-related web content. For the full success of these initiatives, they must be equipped with technologies that enable the automation of the rating process and allow the continuous monitoring of labelled web sites alerting the labelling agency. In this paper we describe the European project MedIEQ (Quality Labelling of Medical Web Content Using Multilingual Information Extraction) that integrates the efforts of relevant organizations on medical quality labelling, multilingual information retrieval and extraction and semantic resources, from six different European countries (Spain, Germany, Greece, Finland, Czech Republic and Switzerland). The main objectives of MedIEQ are: first, to develop a scheme for the quality labelling of medical web content and provide the tools supporting the creation, maintenance and access of labelling data according to this scheme and second, to specify a methodology for the content analysis of medical web sites according to the MedIEQ scheme and develop the tools that will implement it. PMID:17095816

  3. The Feature Extraction Based on Texture Image Information for Emotion Sensing in Speech

    Directory of Open Access Journals (Sweden)

    Kun-Ching Wang

    2014-09-01

    Full Text Available In this paper, we present a novel texture image feature for Emotion Sensing in Speech (ESS. This idea is based on the fact that the texture images carry emotion-related information. The feature extraction is derived from time-frequency representation of spectrogram images. First, we transform the spectrogram as a recognizable image. Next, we use a cubic curve to enhance the image contrast. Then, the texture image information (TII derived from the spectrogram image can be extracted by using Laws’ masks to characterize emotional state. In order to evaluate the effectiveness of the proposed emotion recognition in different languages, we use two open emotional databases including the Berlin Emotional Speech Database (EMO-DB and eNTERFACE corpus and one self-recorded database (KHUSC-EmoDB, to evaluate the performance cross-corpora. The results of the proposed ESS system are presented using support vector machine (SVM as a classifier. Experimental results show that the proposed TII-based feature extraction inspired by visual perception can provide significant classification for ESS systems. The two-dimensional (2-D TII feature can provide the discrimination between different emotions in visual expressions except for the conveyance pitch and formant tracks. In addition, the de-noising in 2-D images can be more easily completed than de-noising in 1-D speech.

  4. Extracting lithologic information from ASTER multispectral thermal infrared data in the eastern Kunlun

    Science.gov (United States)

    Xu, Kai; Kong, Chunfang; Shuai, Yanmin; Cao, Chunxiang; Yan, Shouxun

    2007-11-01

    In this paper, mechanisms of mineral radiation transfer, atmospheric correction and surface temperature retrieve, method of minerals identification based on emissivity spectral features are studied. Mineral radiation transfer can model the mechanisms of spectral formation and variation, and is one of study methods of spectral mechanism. Along with the variation of mineral granularity, the shape and absorption depth of mineral emissivity spectral will all variate. However, the law of emissivity variation with emission angle of different minerals is identical. Along with the increasement of emission angle, emissivity decrease. The more emissivity is small, the more variation range and speed are large. The reflectance mixture of mineral is non-linear, and can be lineated using mineral radiative transfer model. After the mixture spectral is lineated, the precision of linear unmixing of spectral and mineral content extraction will be improved greatly. The atmospheric correction and surface temperature retrieve of thermal remote sensing data will affect extraction lithologic information greatly. In this paper, using the MODTRAN model to atmospheric correction, and using split-window algorithm for retrieving surface temperature from ASTER thermal infrared data. With the minerals emissivity spectral features and the index (QI, CI and SI), retrieving Si02 content of rock quantitatively using ASTER thermal infrared data. The method can be used to extract lithologic information.

  5. Implantable CMOS Biomedical Devices

    Directory of Open Access Journals (Sweden)

    Toshihiko Noda

    2009-11-01

    Full Text Available The results of recent research on our implantable CMOS biomedical devices are reviewed. Topics include retinal prosthesis devices and deep-brain implantation devices for small animals. Fundamental device structures and characteristics as well as in vivo experiments are presented.

  6. Biomedical applications in EELA.

    Science.gov (United States)

    Cardenas, Miguel; Hernández, Vicente; Mayo, Rafael; Blanquer, Ignacio; Perez-Griffo, Javier; Isea, Raul; Nuñez, Luis; Mora, Henry Ricardo; Fernández, Manuel

    2006-01-01

    The current demand for Grid Infrastructures to bring collabarating groups between Latina America and Europe has created the EELA proyect. This e-infrastructure is used by Biomedical groups in Latina America and Europe for the studies of ocnological analisis, neglected diseases, sequence alignments and computation plygonetics. PMID:16823158

  7. Bevalac biomedical facility

    International Nuclear Information System (INIS)

    This paper describes the physical layout of the Bevalac Facility and the research programs carried out at the facility. Beam time on the Bevalac is divided between two disciplines: one-third for biomedical research and two-thirds for nuclear science studies. The remainder of the paper discusses the beam delivery system including dosimetry, beam sharing and beam scanning

  8. Biomedical applications of photochemistry

    OpenAIRE

    Chan, BP

    2010-01-01

    Photochemistry is the study of photochemical reactions between light and molecules. Recently, there have been increasing interests in using photochemical reactions in the fields of biomaterials and tissue engineering. This work revisits the components and mechanisms of photochemistry and reviews biomedical applications of photochemistry in various disciplines, including oncology, molecular biology, and biosurgery, with particular emphasis on tissue engineering. Finally, potential toxicities a...

  9. NASA Biomedical Informatics Capabilities and Needs

    Science.gov (United States)

    Johnson-Throop, Kathy A.

    2009-01-01

    To improve on-orbit clinical capabilities by developing and providing operational support for intelligent, robust, reliable, and secure, enterprise-wide and comprehensive health care and biomedical informatics systems with increasing levels of autonomy, for use on Earth, low Earth orbit & exploration class missions. Biomedical Informatics is an emerging discipline that has been defined as the study, invention, and implementation of structures and algorithms to improve communication, understanding and management of medical information. The end objective of biomedical informatics is the coalescing of data, knowledge, and the tools necessary to apply that data and knowledge in the decision-making process, at the time and place that a decision needs to be made.

  10. Automated DICOM metadata and volumetric anatomical information extraction for radiation dosimetry

    Science.gov (United States)

    Papamichail, D.; Ploussi, A.; Kordolaimi, S.; Karavasilis, E.; Papadimitroulas, P.; Syrgiamiotis, V.; Efstathopoulos, E.

    2015-09-01

    Patient-specific dosimetry calculations based on simulation techniques have as a prerequisite the modeling of the modality system and the creation of voxelized phantoms. This procedure requires the knowledge of scanning parameters and patients’ information included in a DICOM file as well as image segmentation. However, the extraction of this information is complicated and time-consuming. The objective of this study was to develop a simple graphical user interface (GUI) to (i) automatically extract metadata from every slice image of a DICOM file in a single query and (ii) interactively specify the regions of interest (ROI) without explicit access to the radiology information system. The user-friendly application developed in Matlab environment. The user can select a series of DICOM files and manage their text and graphical data. The metadata are automatically formatted and presented to the user as a Microsoft Excel file. The volumetric maps are formed by interactively specifying the ROIs and by assigning a specific value in every ROI. The result is stored in DICOM format, for data and trend analysis. The developed GUI is easy, fast and and constitutes a very useful tool for individualized dosimetry. One of the future goals is to incorporate a remote access to a PACS server functionality.

  11. Evaluation of information retrieval and text mining tools on automatic named entity extraction. Intelligence and security informatics. Proceedings

    OpenAIRE

    Kumar, Nishant; De Beer, Jan; Vanthienen, Jan; Moens, Marie-Francine

    2006-01-01

    We will report evaluation of Automatic Named Entity Extraction feature of IR tools on Dutch, French, and English text. The aim is to analyze the competency of off-the-shelf information extraction tools in recognizing entity types including person, organization, location, vehicle, time, & currency from unstructured text. Within such an evaluation one can compare the effectiveness of different approaches for identifying named entities.

  12. Red Tide Information Extraction Based on Multi-source Remote Sensing Data in Haizhou Bay

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    [Objective] The aim was to extract red tide information in Haizhou Bay on the basis of multi-source remote sensing data.[Method] Red tide in Haizhou Bay was studied based on multi-source remote sensing data,such as IRS-P6 data on October 8,2005,Landsat 5-TM data on May 20,2006,MODIS 1B data on October 6,2006 and HY-1B second-grade data on April 22,2009,which were firstly preprocessed through geometric correction,atmospheric correction,image resizing and so on.At the same time,the synchronous environment mon...

  13. Extracting information from two-dimensional electrophoresis gels by partial least squares regression

    DEFF Research Database (Denmark)

    Jessen, Flemming; Lametsch, R.; Bendixen, E.;

    2002-01-01

    disappear depending on the experimental conditions. Such biomarkers are found by comparing the relative volumes of individual spots in the individual gels. Multivariate statistical analysis and modelling of 2-DE data for comparison and classification is an alternative approach utilising the combination of...... all proteins/spots in the gels. In the present study it is demonstrated how information can be extracted by multivariate data analysis. The strategy is based on partial least squares regression followed by variable selection to find proteins that individually or in combination with other proteins vary...

  14. A Methodology to Extract Information from the Brain Waves in a Multi-Core Environment

    OpenAIRE

    Krishnakumar Venkatasubramanian; M. Rajasekhara Babu

    2013-01-01

    Brain Computer Interface (BCI) is one of the most dynamic fields in the world of Artificial Intelligence. It involves a direct neural interface between the subject and the machine, and the information is extracted from the brain in the form of waves. This raw brain-wave needs to be classified, de-noised, translated and suitably stored. These steps involve the use of a number of techniques like, thede-noising involves the use of Discrete Wavelet Transform (DWT) [1] or Recurrent Quantum Neural ...

  15. Multi-Paradigm and Multi-Lingual Information Extraction as Support for Medical Web Labelling Authorities

    Directory of Open Access Journals (Sweden)

    Martin Labsky

    2010-10-01

    Full Text Available Until recently, quality labelling of medical web content has been a pre-dominantly manual activity. However, the advances in automated text processing opened the way to computerised support of this activity. The core enabling technology is information extraction (IE. However, the heterogeneity of websites offering medical content imposes particular requirements on the IE techniques to be applied. In the paper we discuss these requirements and describe a multi-paradigm approach to IE addressing them. Experiments on multi-lingual data are reported. The research has been carried out within the EU MedIEQ project.

  16. Analysis on health information extracted from an urban professional population in Beijing

    Institute of Scientific and Technical Information of China (English)

    ZHANG Tie-mei; ZHANG Yan; LIU Bin; JIA Hong-bo; LIU Yun-jie; ZHU Ling; LUO Sen-lin; HAN Yi-wen; ZHANG Yan; YANG Shu-wen; LIU An-nan; MA Lan-jun; ZHAO Yan-yan

    2011-01-01

    Background The assembled data from a population could provide information on health trends within the population.The aim of this research was to extract and know basic health information from an urban professional population in Beijing.Methods Data analysis was carried out in a population who underwent a routine medical check-up and aged >20 years,including 30 058 individuals.General information,data from physical examinations and blood samples were collected in the same method.The health status was separated into three groups by the criteria generated in this study,i.e.,people with common chronic diseases,people in a sub-clinic situation,and healthy people.The proportion of both common diseases suffered and health risk distribution of different age groups were also analyzed.Results The proportion of people with common chronic diseases,in the sub-clinic group and in the healthy group was 28.6%,67.8% and 3.6% respectively.There were significant differences in the health situation in different age groups.Hypertension was on the top of list of self-reported diseases.The proportion of chronic diseases increased significantly in people after 35 years of age.Meanwhile,the proportion of sub-clinic conditions was decreasing at the same rate.The complex risk factors to health in this population were metabolic disturbances (61.3%),risk for tumor (2.7%),abnormal results of morphological examination (8.2%) and abnormal results of lab tests of serum (27.8%).Conclusions Health information could be extracted from a complex data set from the heath check-ups of the general population.The information should be applied to support prevention and control chronic diseases as well as for directing intervention for patients with risk factors for disease.

  17. Biomedical signals, imaging, and informatics

    CERN Document Server

    Bronzino, Joseph D

    2014-01-01

    Known as the bible of biomedical engineering, The Biomedical Engineering Handbook, Fourth Edition, sets the standard against which all other references of this nature are measured. As such, it has served as a major resource for both skilled professionals and novices to biomedical engineering.Biomedical Signals, Imaging, and Informatics, the third volume of the handbook, presents material from respected scientists with diverse backgrounds in biosignal processing, medical imaging, infrared imaging, and medical informatics.More than three dozen specific topics are examined, including biomedical s

  18. Inexperienced clinicians can extract pathoanatomic information from MRI narrative reports with high reproducability for use in research/quality assurance

    DEFF Research Database (Denmark)

    Kent, Peter; Briggs, Andrew M; Albert, Hanne Birgit;

    2011-01-01

    Background Although reproducibility in reading MRI images amongst radiologists and clinicians has been studied previously, no studies have examined the reproducibility of inexperienced clinicians in extracting pathoanatomic information from magnetic resonance imaging (MRI) narrative reports and...... pathoanatomic information from radiologist-generated MRI narrative reports. Methods Twenty MRI narrative reports were randomly extracted from an institutional database. A group of three physiotherapy students independently reviewed the reports and coded the presence of 14 common pathoanatomic findings using a...

  19. Developing an Approach to Prioritize River Restoration using Data Extracted from Flood Risk Information System Databases.

    Science.gov (United States)

    Vimal, S.; Tarboton, D. G.; Band, L. E.; Duncan, J. M.; Lovette, J. P.; Corzo, G.; Miles, B.

    2015-12-01

    Prioritizing river restoration requires information on river geometry. In many states in the US detailed river geometry has been collected for floodplain mapping and is available in Flood Risk Information Systems (FRIS). In particular, North Carolina has, for its 100 Counties, developed a database of numerous HEC-RAS models which are available through its Flood Risk Information System (FRIS). These models that include over 260 variables were developed and updated by numerous contractors. They contain detailed surveyed or LiDAR derived cross-sections and modeled flood extents for different extreme event return periods. In this work, over 4700 HEC-RAS models' data was integrated and upscaled to utilize detailed cross-section information and 100-year modelled flood extent information to enable river restoration prioritization for the entire state of North Carolina. We developed procedures to extract geomorphic properties such as entrenchment ratio, incision ratio, etc. from these models. Entrenchment ratio quantifies the vertical containment of rivers and thereby their vulnerability to flooding and incision ratio quantifies the depth per unit width. A map of entrenchment ratio for the whole state was derived by linking these model results to a geodatabase. A ranking of highly entrenched counties enabling prioritization for flood allowance and mitigation was obtained. The results were shared through HydroShare and web maps developed for their visualization using Google Maps Engine API.

  20. Feature extraction and learning using context cue and Rényi entropy based mutual information

    DEFF Research Database (Denmark)

    Pan, Hong; Olsen, Søren Ingvor; Zhu, Yaping

    2015-01-01

    Feature extraction and learning play a critical role for visual perception tasks. We focus on improving the robustness of the kernel descriptors (KDES) by embedding context cues and further learning a compact and discriminative feature codebook for feature reduction using Rényi entropy based mutual...... improving the robustness of CKD. For feature learning and reduction, we propose a novel codebook learning method, based on a Rényi quadratic entropy based mutual information measure called Cauchy-Schwarz Quadratic Mutual Information (CSQMI), to learn a compact and discriminative CKD codebook. Projecting the...... original full-dimensional CKD onto the codebook, we reduce the dimensionality of CKD while preserving its discriminability. Moreover, the latent connection between Rényi quadratic entropy and the mapping data in kernel feature space further facilitates us to capture the geometric structure as well as the...

  1. Audio-Visual Speech Recognition Using Lip Information Extracted from Side-Face Images

    Directory of Open Access Journals (Sweden)

    Koji Iwano

    2007-03-01

    Full Text Available This paper proposes an audio-visual speech recognition method using lip information extracted from side-face images as an attempt to increase noise robustness in mobile environments. Our proposed method assumes that lip images can be captured using a small camera installed in a handset. Two different kinds of lip features, lip-contour geometric features and lip-motion velocity features, are used individually or jointly, in combination with audio features. Phoneme HMMs modeling the audio and visual features are built based on the multistream HMM technique. Experiments conducted using Japanese connected digit speech contaminated with white noise in various SNR conditions show effectiveness of the proposed method. Recognition accuracy is improved by using the visual information in all SNR conditions. These visual features were confirmed to be effective even when the audio HMM was adapted to noise by the MLLR method.

  2. Solution of Multiple——Point Statistics to Extracting Information from Remotely Sensed Imagery

    Institute of Scientific and Technical Information of China (English)

    Ge Yong; Bai Hexiang; Cheng Qiuming

    2008-01-01

    Two phenomena of similar objects with different spectra and different objects with similar spectrum often result in the difficulty of separation and identification of all types of geographical objects only using spectral information.Therefore,there is a need to incorporate spatial structural and spatial association properties of the surfaces of objects into image processing to improve the accuracy of classification of remotely sensed imagery.In the current article,a new method is proposed on the basis of the principle of multiple-point statistics for combining spectral information and spatial information for image classification.The method was validated by applying to a case study on road extraction based on Landsat TM taken over the Chinese YeHow River delta on August 8,1999. The classification results have shown that this new method provides overall better results than the traditional methods such as maximum likelihood classifier (MLC)

  3. DEVELOPMENT OF AUTOMATIC EXTRACTION METHOD FOR ROAD UPDATE INFORMATION BASED ON PUBLIC WORK ORDER OUTLOOK

    Science.gov (United States)

    Sekimoto, Yoshihide; Nakajo, Satoru; Minami, Yoshitaka; Yamaguchi, Syohei; Yamada, Harutoshi; Fuse, Takashi

    Recently, disclosure of statistic data, representing financial effects or burden for public work, through each web site of national or local government, enables us to discuss macroscopic financial trends. However, it is still difficult to grasp a basic property nationwide how each spot was changed by public work. In this research, our research purpose is to collect road update information reasonably which various road managers provide, in order to realize efficient updating of various maps such as car navigation maps. In particular, we develop the system extracting public work concerned and registering summary including position information to database automatically from public work order outlook, released by each local government, combinating some web mining technologies. Finally, we collect and register several tens of thousands from web site all over Japan, and confirm the feasibility of our method.

  4. Foreground and Background Lexicons and Word Sense Disambiguation for Information Extraction

    CERN Document Server

    Kilgarriff, A

    1999-01-01

    Lexicon acquisition from machine-readable dictionaries and corpora is currently a dynamic field of research, yet it is often not clear how lexical information so acquired can be used, or how it relates to structured meaning representations. In this paper I look at this issue in relation to Information Extraction (hereafter IE), and one subtask for which both lexical and general knowledge are required, Word Sense Disambiguation (WSD). The analysis is based on the widely-used, but little-discussed distinction between an IE system's foreground lexicon, containing the domain's key terms which map onto the database fields of the output formalism, and the background lexicon, containing the remainder of the vocabulary. For the foreground lexicon, human lexicography is required. For the background lexicon, automatic acquisition is appropriate. For the foreground lexicon, WSD will occur as a by-product of finding a coherent semantic interpretation of the input. WSD techniques as discussed in recent literature are suit...

  5. Optical Polarizationin Biomedical Applications

    CERN Document Server

    Tuchin, Valery V; Zimnyakov, Dmitry A

    2006-01-01

    Optical Polarization in Biomedical Applications introduces key developments in optical polarization methods for quantitative studies of tissues, while presenting the theory of polarization transfer in a random medium as a basis for the quantitative description of polarized light interaction with tissues. This theory uses the modified transfer equation for Stokes parameters and predicts the polarization structure of multiple scattered optical fields. The backscattering polarization matrices (Jones matrix and Mueller matrix) important for noninvasive medical diagnostic are introduced. The text also describes a number of diagnostic techniques such as CW polarization imaging and spectroscopy, polarization microscopy and cytometry. As a new tool for medical diagnosis, optical coherent polarization tomography is analyzed. The monograph also covers a range of biomedical applications, among them cataract and glaucoma diagnostics, glucose sensing, and the detection of bacteria.

  6. Toxicology of Biomedical Polymers

    Directory of Open Access Journals (Sweden)

    P. V. Vedanarayanan

    1987-04-01

    Full Text Available This paper deals with the various types of polymers, used in the fabrication of medical devices, their diversity of applications and toxic hazards which may arise out of their application. The potential toxicity of monomers and the various additives used in the manufacture of biomedical polymers have been discussed along with hazards which may arise out of processing of devices such as sterilization. The importance of quality control and stringent toxicity evaluation methods have been emphasised since in our country, at present, there are no regulations covering the manufacturing and marketing of medical devices. Finally the question of the general and subtle long term systemic toxicity of biomedical polymers have been brought to attention with the suggestion that this question needs to be resolved permanently by appropriate studies.

  7. Biomimicry in biomedical research

    OpenAIRE

    Zhang, Ge

    2012-01-01

    Biomimicry (literally defined as the imitation of life or nature) has sparked a variety of human innovations and inspired countless cutting-edge designs. From spider silk-made artificial skin to lotus leaf-inspired self-cleaning materials, biomimicry endeavors to solve human problems. Biomimetic approaches have contributed significantly to advances biomedical research during recent years. Using polyacrylamide gels to mimic the elastic modulus of different biological tissues, Disher’s lab has ...

  8. Toxicology of Biomedical Polymers

    OpenAIRE

    P. V. Vedanarayanan; A. C. Fernandez

    1987-01-01

    This paper deals with the various types of polymers, used in the fabrication of medical devices, their diversity of applications and toxic hazards which may arise out of their application. The potential toxicity of monomers and the various additives used in the manufacture of biomedical polymers have been discussed along with hazards which may arise out of processing of devices such as sterilization. The importance of quality control and stringent toxicity evaluation methods have been emphasi...

  9. Extracting Urban Ground Object Information from Images and LiDAR Data

    Science.gov (United States)

    Yi, Lina; Zhao, Xuesheng; Li, Luan; Zhang, Guifeng

    2016-06-01

    To deal with the problem of urban ground object information extraction, the paper proposes an object-oriented classification method using aerial image and LiDAR data. Firstly, we select the optimal segmentation scales of different ground objects and synthesize them to get accurate object boundaries. Then, this paper uses ReliefF algorithm to select the optimal feature combination and eliminate the Hughes phenomenon. Eventually, the multiple classifier combination method is applied to get the outcome of the classification. In order to validate the feasible of this method, this paper selects two experimental regions in Stuttgart and Germany (Region A and B, covers 0.21 km2 and 1.1 km2 respectively). The aim of the first experiment on the Region A is to get the optimal segmentation scales and classification features. The overall accuracy of the classification reaches to 93.3 %. The purpose of the experiment on region B is to validate the application-ability of this method for a large area, which is turned out to be reaches 88.4 % overall accuracy. In the end of this paper, the conclusion shows that the proposed method can be performed accurately and efficiently in terms of urban ground information extraction and be of high application value.

  10. Urban impervious surface information extracting and its eco-environment effect analysis

    Science.gov (United States)

    Gao, Zhihong; Wu, Naiming

    2015-12-01

    Urban impervious surface is not only a major indicator of urbanization but also a key factor for environmental quality evaluation. NDISI is applied for enhancing and extracting impervious surface information in this study. NDVI derived from measurements of the optical imagery reflectance of sunlight in the red and near-infrared wavelengths, can reveal the vegetation cover condition. LST plays an important role in energy exchange between the land surface and the atmosphere. The objective of this paper is to extract the urban impervious surface information and its eco-envionment effect. Experiment results indicate that NDISI is effective and easy-to-use. And the correlation coefficient among NDISI, NDVI and LST are -0.82, 0.95 and -0.7. Combined with the field survey meteorological site data, this study reveals that the urban impervious surface area has a strong positive exponential relationship with the LST. This suggests that the areas with high NDISI value will accelerate the increase in LST much more than the areas with low NDISI value. And urban impervious surface area is the most important factor contributing to the development of the UHI while vegetation cover (high NDVI area) can significantly reduce the LST.

  11. Extraction and Analysis of Information Related to Research & Development Declared Under an Additional Protocol

    International Nuclear Information System (INIS)

    The additional protocol (AP) provides important tools to strengthen and improve the effectiveness and efficiency of the safeguards system. Safeguards are designed to verify that States comply with their international commitments not to use nuclear material or to engage in nuclear-related activities for the purpose of developing nuclear weapons or other nuclear explosive devices. Under an AP based on INFCIRC/540, a State must provide to the IAEA additional information about, and inspector access to, all parts of its nuclear fuel cycle. In addition, the State has to supply information about its nuclear fuel cycle-related research and development (R&D) activities. The majority of States declare their R&D activities under the AP Articles 2.a.(i), 2.a.(x), and 2.b.(i) as part of initial declarations and their annual updates under the AP. In order to verify consistency and completeness of information provided under the AP by States, the Agency has started to analyze declared R&D information by identifying interrelationships between States in different R&D areas relevant to safeguards. The paper outlines the quality of R&D information provided by States to the Agency, describes how the extraction and analysis of relevant declarations are currently carried out at the Agency and specifies what kinds of difficulties arise during evaluation in respect to cross-linking international projects and finding gaps in reporting. In addition, the paper tries to elaborate how the reporting quality of AP information with reference to R&D activities and the assessment process of R&D information could be improved. (author)

  12. Overview of image processing tools to extract physical information from JET videos

    Science.gov (United States)

    Craciunescu, T.; Murari, A.; Gelfusa, M.; Tiseanu, I.; Zoita, V.; EFDA Contributors, JET

    2014-11-01

    In magnetic confinement nuclear fusion devices such as JET, the last few years have witnessed a significant increase in the use of digital imagery, not only for the surveying and control of experiments, but also for the physical interpretation of results. More than 25 cameras are routinely used for imaging on JET in the infrared (IR) and visible spectral regions. These cameras can produce up to tens of Gbytes per shot and their information content can be very different, depending on the experimental conditions. However, the relevant information about the underlying physical processes is generally of much reduced dimensionality compared to the recorded data. The extraction of this information, which allows full exploitation of these diagnostics, is a challenging task. The image analysis consists, in most cases, of inverse problems which are typically ill-posed mathematically. The typology of objects to be analysed is very wide, and usually the images are affected by noise, low levels of contrast, low grey-level in-depth resolution, reshaping of moving objects, etc. Moreover, the plasma events have time constants of ms or tens of ms, which imposes tough conditions for real-time applications. On JET, in the last few years new tools and methods have been developed for physical information retrieval. The methodology of optical flow has allowed, under certain assumptions, the derivation of information about the dynamics of video objects associated with different physical phenomena, such as instabilities, pellets and filaments. The approach has been extended in order to approximate the optical flow within the MPEG compressed domain, allowing the manipulation of the large JET video databases and, in specific cases, even real-time data processing. The fast visible camera may provide new information that is potentially useful for disruption prediction. A set of methods, based on the extraction of structural information from the visual scene, have been developed for the

  13. Overview of image processing tools to extract physical information from JET videos

    International Nuclear Information System (INIS)

    In magnetic confinement nuclear fusion devices such as JET, the last few years have witnessed a significant increase in the use of digital imagery, not only for the surveying and control of experiments, but also for the physical interpretation of results. More than 25 cameras are routinely used for imaging on JET in the infrared (IR) and visible spectral regions. These cameras can produce up to tens of Gbytes per shot and their information content can be very different, depending on the experimental conditions. However, the relevant information about the underlying physical processes is generally of much reduced dimensionality compared to the recorded data. The extraction of this information, which allows full exploitation of these diagnostics, is a challenging task. The image analysis consists, in most cases, of inverse problems which are typically ill-posed mathematically. The typology of objects to be analysed is very wide, and usually the images are affected by noise, low levels of contrast, low grey-level in-depth resolution, reshaping of moving objects, etc. Moreover, the plasma events have time constants of ms or tens of ms, which imposes tough conditions for real-time applications. On JET, in the last few years new tools and methods have been developed for physical information retrieval. The methodology of optical flow has allowed, under certain assumptions, the derivation of information about the dynamics of video objects associated with different physical phenomena, such as instabilities, pellets and filaments. The approach has been extended in order to approximate the optical flow within the MPEG compressed domain, allowing the manipulation of the large JET video databases and, in specific cases, even real-time data processing. The fast visible camera may provide new information that is potentially useful for disruption prediction. A set of methods, based on the extraction of structural information from the visual scene, have been developed for the

  14. Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery.

    Science.gov (United States)

    Gonzalez, Graciela H; Tahsin, Tasnia; Goodale, Britton C; Greene, Anna C; Greene, Casey S

    2016-01-01

    Precision medicine will revolutionize the way we treat and prevent disease. A major barrier to the implementation of precision medicine that clinicians and translational scientists face is understanding the underlying mechanisms of disease. We are starting to address this challenge through automatic approaches for information extraction, representation and analysis. Recent advances in text and data mining have been applied to a broad spectrum of key biomedical questions in genomics, pharmacogenomics and other fields. We present an overview of the fundamental methods for text and data mining, as well as recent advances and emerging applications toward precision medicine. PMID:26420781

  15. THE STUDY ON HEIGHT INFORMATION EXTRACTION OF CULTURAL FEATURES IN REMOTE SENSING IMAGES BASED ON SHADOW AREAS

    Directory of Open Access Journals (Sweden)

    Z. Bao-Ming

    2012-09-01

    Full Text Available Cultural feature is important element in geospatial information library and the height information is important information of cultural features. The existences of the height information and its precision have direct influence over topographic map, especially the quality of large-scale and medium-scale topographic map, and the level of surveying and mapping support. There are a lot of methods about height information extraction, in which the main methods are ground survey (field direct measurement spatial sensor and photogrammetric ways. However, automatic extraction is very tough. This paper has had an emphasis on segmentation algorithm on shadow areas under multiple constraints and realized automatic extraction of height information by using shadow. Binarization image can be obtained using gray threshold estimated under the multiple constraints. On the interesting area, spot elimination and region splitting are made. After region labeling and non-shadowed regions elimination, shadow area of cultural features can be found. Then height of the cultural features can be calculated using shadow length, sun altitude angle, azimuth angle, and sensor altitude angle, azimuth angle. A great many of experiments have shown that mean square error of the height information of cultural features extraction is close to 2 meter and automatic extraction rate is close to 70%.

  16. Extracting duration information in a picture category decoding task using hidden Markov Models

    Science.gov (United States)

    Pfeiffer, Tim; Heinze, Nicolai; Frysch, Robert; Deouell, Leon Y.; Schoenfeld, Mircea A.; Knight, Robert T.; Rose, Georg

    2016-04-01

    Objective. Adapting classifiers for the purpose of brain signal decoding is a major challenge in brain-computer-interface (BCI) research. In a previous study we showed in principle that hidden Markov models (HMM) are a suitable alternative to the well-studied static classifiers. However, since we investigated a rather straightforward task, advantages from modeling of the signal could not be assessed. Approach. Here, we investigate a more complex data set in order to find out to what extent HMMs, as a dynamic classifier, can provide useful additional information. We show for a visual decoding problem that besides category information, HMMs can simultaneously decode picture duration without an additional training required. This decoding is based on a strong correlation that we found between picture duration and the behavior of the Viterbi paths. Main results. Decoding accuracies of up to 80% could be obtained for category and duration decoding with a single classifier trained on category information only. Significance. The extraction of multiple types of information using a single classifier enables the processing of more complex problems, while preserving good training results even on small databases. Therefore, it provides a convenient framework for online real-life BCI utilizations.

  17. A study of land use/land cover information extraction classification technology based on DTC

    Science.gov (United States)

    Wang, Ping; Zheng, Yong-guo; Yang, Feng-jie; Jia, Wei-jie; Xiong, Chang-zhen

    2008-10-01

    Decision Tree Classification (DTC) is one organizational form of the multi-level recognition system, which changes the complicated classification into simple categories, and then gradually resolves it. The paper does LULC Decision Tree Classification research on some areas of Gansu Province in the west of China. With the mid-resolution remote sensing data as the main data resource, the authors adopt decision-making classification technology method, taking advantage of its character that it imitates the processing pattern of human judgment and thinking and its fault-tolerant character, and also build the decision tree LULC classical pattern. The research shows that the methods and techniques can increase the level of automation and accuracy of LULC information extraction, and better carry out LULC information extraction on the research areas. The main aspects of the research are as follows: 1. We collected training samples firstly, established a comprehensive database which is supported by remote sensing and ground data; 2. By utilizing CART system, and based on multiply sources and time phases remote sensing data and other assistance data, the DTC's technology effectively combined the unsupervised classification results with the experts' knowledge together. The method and procedure for distilling the decision tree information were specifically developed. 3. In designing the decision tree, based on the various object of types classification rules, we established and pruned DTC'S model for the purpose of achieving effective treatment of subdivision classification, and completed the land use and land cover classification of the research areas. The accuracy of evaluation showed that the classification accuracy reached upwards 80%.

  18. Face Contour Extraction of Information%人脸轮廓信息的提取

    Institute of Scientific and Technical Information of China (English)

    原瑾

    2011-01-01

    边缘提取在模式识别、机器视觉、图像分析及图像编码等领域都有着重要的研究价值。人脸检测技术是一种人脸识别技术的前提。文章针对人脸检测中人脸定位提出了人脸轮廓信息提取技术,确定人脸检测的主要区域。首先介绍了几种边缘检测算子,然后提出了动态阈值方法来改进图像阈值,提高了边缘检测精度。%Edge extraction has important research value in the fields of pattern recognition, machine vision, image analysis and image coding. Face detection technology is prerequisite of face recognition technology. In view of person face localization in person face detection, the dissertation proposes an extraction technology of face outline information to identify the main regional of face. This article first introduced several edge detection operators, and then proposed the method of dynamic threshold value to improves the image threshold value, which increased the edge detection accuracy.

  19. Developing a Process Model for the Forensic Extraction of Information from Desktop Search Applications

    Directory of Open Access Journals (Sweden)

    Timothy Pavlic

    2008-03-01

    Full Text Available Desktop search applications can contain cached copies of files that were deleted from the file system. Forensic investigators see this as a potential source of evidence, as documents deleted by suspects may still exist in the cache. Whilst there have been attempts at recovering data collected by desktop search applications, there is no methodology governing the process, nor discussion on the most appropriate means to do so. This article seeks to address this issue by developing a process model that can be applied when developing an information extraction application for desktop search applications, discussing preferred methods and the limitations of each. This work represents a more structured approach than other forms of current research.

  20. Information Extraction for System-Software Safety Analysis: Calendar Year 2007 Year-End Report

    Science.gov (United States)

    Malin, Jane T.

    2008-01-01

    This annual report describes work to integrate a set of tools to support early model-based analysis of failures and hazards due to system-software interactions. The tools perform and assist analysts in the following tasks: 1) extract model parts from text for architecture and safety/hazard models; 2) combine the parts with library information to develop the models for visualization and analysis; 3) perform graph analysis on the models to identify possible paths from hazard sources to vulnerable entities and functions, in nominal and anomalous system-software configurations; 4) perform discrete-time-based simulation on the models to investigate scenarios where these paths may play a role in failures and mishaps; and 5) identify resulting candidate scenarios for software integration testing. This paper describes new challenges in a NASA abort system case, and enhancements made to develop the integrated tool set.

  1. Extracting spatial information from noise measurements of multi-spatial-mode quantum states

    Science.gov (United States)

    Marino, A. M.; Clark, J. B.; Glorieux, Q.; Lett, P. D.

    2012-11-01

    We show that it is possible to use the spatial quantum correlations present in twin beams to extract information about the shape of a binary amplitude mask in the path of one of the beams. The scheme, based on noise measurements through homodyne detection, is useful in the regime where the number of photons is low enough that direct detection with a photodiode is difficult but high enough that photon counting is not an option. We find that under some conditions the use of quantum states of light leads to an enhancement of the sensitivity in the estimation of the shape of the mask over what can be achieved with a classical state with equivalent properties (mean photon flux and noise properties). In addition, we show that the level of enhancement that is obtained is a result of the quantum correlations and cannot be explained with only classical correlations.

  2. The Ontology for Biomedical Investigations

    OpenAIRE

    Anita Bandrowski; Ryan Brinkman; Mathias Brochhausen; Brush, Matthew H.; Bill Bug; Chibucos, Marcus C.; Kevin Clancy; Mélanie Courtot; Dirk Derom; Michel Dumontier; Liju Fan; Jennifer Fostel; Gilberto Fragoso; Frank Gibson; Alejandra Gonzalez-Beltran

    2016-01-01

    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using i...

  3. Generating Explanations for Biomedical Queries

    OpenAIRE

    Erdem, Esra; Oztok, Umut

    2013-01-01

    We introduce novel mathematical models and algorithms to generate (shortest or k different) explanations for biomedical queries, using answer set programming. We implement these algorithms and integrate them in BIOQUERY-ASP. We illustrate the usefulness of these methods with some complex biomedical queries related to drug discovery, over the biomedical knowledge resources PHARMGKB, DRUGBANK, BIOGRID, CTD, SIDER, DISEASE ONTOLOGY and ORPHADATA. To appear in Theory and Practice of Logic Program...

  4. Statistics in biomedical research

    Directory of Open Access Journals (Sweden)

    González-Manteiga, Wenceslao

    2007-06-01

    Full Text Available The discipline of biostatistics is nowadays a fundamental scientific component of biomedical, public health and health services research. Traditional and emerging areas of application include clinical trials research, observational studies, physiology, imaging, and genomics. The present article reviews the current situation of biostatistics, considering the statistical methods traditionally used in biomedical research, as well as the ongoing development of new methods in response to the new problems arising in medicine. Clearly, the successful application of statistics in biomedical research requires appropriate training of biostatisticians. This training should aim to give due consideration to emerging new areas of statistics, while at the same time retaining full coverage of the fundamentals of statistical theory and methodology. In addition, it is important that students of biostatistics receive formal training in relevant biomedical disciplines, such as epidemiology, clinical trials, molecular biology, genetics, and neuroscience.La Bioestadística es hoy en día una componente científica fundamental de la investigación en Biomedicina, salud pública y servicios de salud. Las áreas tradicionales y emergentes de aplicación incluyen ensayos clínicos, estudios observacionales, fisología, imágenes, y genómica. Este artículo repasa la situación actual de la Bioestadística, considerando los métodos estadísticos usados tradicionalmente en investigación biomédica, así como los recientes desarrollos de nuevos métodos, para dar respuesta a los nuevos problemas que surgen en Medicina. Obviamente, la aplicación fructífera de la estadística en investigación biomédica exige una formación adecuada de los bioestadísticos, formación que debería tener en cuenta las áreas emergentes en estadística, cubriendo al mismo tiempo los fundamentos de la teoría estadística y su metodología. Es importante, además, que los estudiantes de

  5. Biomedical Sensors and Instruments

    CERN Document Server

    Tagawa, Tatsuo

    2011-01-01

    The living body is a difficult object to measure: accurate measurements of physiological signals require sensors and instruments capable of high specificity and selectivity that do not interfere with the systems under study. As a result, detailed knowledge of sensor and instrument properties is required to be able to select the "best" sensor from one of the many designed to meet these challenges. From the underlying principles to practical applications, this updated edition of Biomedical Sensors and Instruments provides an easy-to-understand introduction to the various kinds of biome

  6. Principles of Biomedical Engineering

    CERN Document Server

    Madihally, Sundararajan V

    2010-01-01

    Describing the role of engineering in medicine today, this comprehensive volume covers a wide range of the most important topics in this burgeoning field. Supported with over 145 illustrations, the book discusses bioelectrical systems, mechanical analysis of biological tissues and organs, biomaterial selection, compartmental modeling, and biomedical instrumentation. Moreover, you find a thorough treatment of the concept of using living cells in various therapeutics and diagnostics.Structured as a complete text for students with some engineering background, the book also makes a valuable refere

  7. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1973-01-01

    Advances in Biomedical Engineering, Volume 3, is a collection of papers that discusses circulatory system models, linguistics in computer usage, and clinical applications on patient monitoring. One paper describes the use of comparative models of overall circulatory mechanics that include models of the cardiac pump, of the vascular systems, and of the overall systems behavior. Another paper describes a model in processing medical language data that employs an explicit semantic structure, becoming the basis for the computer-based, artificial intelligence of the system. One paper cites studies b

  8. Biomedical photonics handbook

    CERN Document Server

    Vo-Dinh, Tuan

    2003-01-01

    1.Biomedical Photonics: A Revolution at the Interface of Science and Technology, T. Vo-DinhPHOTONICS AND TISSUE OPTICS2.Optical Properties of Tissues, J. Mobley and T. Vo-Dinh3.Light-Tissue Interactions, V.V. Tuchin 4.Theoretical Models and Algorithms in Optical Diffusion Tomography, S.J. Norton and T. Vo-DinhPHOTONIC DEVICES5.Laser Light in Biomedicine and the Life Sciences: From the Present to the Future, V.S. Letokhov6.Basic Instrumentation in Photonics, T. Vo-Dinh7.Optical Fibers and Waveguides for Medical Applications, I. Gannot and

  9. Biomedical signals and systems

    CERN Document Server

    Tranquillo, Joseph V

    2013-01-01

    Biomedical Signals and Systems is meant to accompany a one-semester undergraduate signals and systems course. It may also serve as a quick-start for graduate students or faculty interested in how signals and systems techniques can be applied to living systems. The biological nature of the examples allows for systems thinking to be applied to electrical, mechanical, fluid, chemical, thermal and even optical systems. Each chapter focuses on a topic from classic signals and systems theory: System block diagrams, mathematical models, transforms, stability, feedback, system response, control, time

  10. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1973-01-01

    Advances in Biomedical Engineering, Volume 2, is a collection of papers that discusses the basic sciences, the applied sciences of engineering, the medical sciences, and the delivery of health services. One paper discusses the models of adrenal cortical control, including the secretion and metabolism of cortisol (the controlled process), as well as the initiation and modulation of secretion of ACTH (the controller). Another paper discusses hospital computer systems-application problems, objective evaluation of technology, and multiple pathways for future hospital computer applications. The pos

  11. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1974-01-01

    Advances in Biomedical Engineering, Volume 4, is a collection of papers that deals with gas chromatography, mass spectroscopy and the analysis of minute samples, as well as the role of the government in regulating the production, usage, safety, and efficacy of medical devices. One paper reviews the use of mass spectrometry and computer technology in relation to gas-phase analytical methods based on gas chromatograph-mass spectrometer instruments and gas chromatograph-mass spectrometer-computer analytical systems. Many health practitioners, government and private health agencies, the legal prof

  12. EnvMine: A text-mining system for the automatic extraction of contextual information

    Directory of Open Access Journals (Sweden)

    de Lorenzo Victor

    2010-06-01

    Full Text Available Abstract Background For ecological studies, it is crucial to count on adequate descriptions of the environments and samples being studied. Such a description must be done in terms of their physicochemical characteristics, allowing a direct comparison between different environments that would be difficult to do otherwise. Also the characterization must include the precise geographical location, to make possible the study of geographical distributions and biogeographical patterns. Currently, there is no schema for annotating these environmental features, and these data have to be extracted from textual sources (published articles. So far, this had to be performed by manual inspection of the corresponding documents. To facilitate this task, we have developed EnvMine, a set of text-mining tools devoted to retrieve contextual information (physicochemical variables and geographical locations from textual sources of any kind. Results EnvMine is capable of retrieving the physicochemical variables cited in the text, by means of the accurate identification of their associated units of measurement. In this task, the system achieves a recall (percentage of items retrieved of 92% with less than 1% error. Also a Bayesian classifier was tested for distinguishing parts of the text describing environmental characteristics from others dealing with, for instance, experimental settings. Regarding the identification of geographical locations, the system takes advantage of existing databases such as GeoNames to achieve 86% recall with 92% precision. The identification of a location includes also the determination of its exact coordinates (latitude and longitude, thus allowing the calculation of distance between the individual locations. Conclusion EnvMine is a very efficient method for extracting contextual information from different text sources, like published articles or web pages. This tool can help in determining the precise location and physicochemical

  13. Intelligent information extraction to aid science decision making in autonomous space exploration

    Science.gov (United States)

    Merényi, Erzsébet; Tasdemir, Kadim; Farrand, William H.

    2008-04-01

    Effective scientific exploration of remote targets such as solar system objects increasingly calls for autonomous data analysis and decision making on-board. Today, robots in space missions are programmed to traverse from one location to another without regard to what they might be passing by. By not processing data as they travel, they can miss important discoveries, or will need to travel back if scientists on Earth find the data warrant backtracking. This is a suboptimal use of resources even on relatively close targets such as the Moon or Mars. The farther mankind ventures into space, the longer the delay in communication, due to which interesting findings from data sent back to Earth are made too late to command a (roving, floating, or orbiting) robot to further examine a given location. However, autonomous commanding of robots in scientific exploration can only be as reliable as the scientific information extracted from the data that is collected and provided for decision making. In this paper, we focus on the discovery scenario, where information extraction is accomplished with unsupervised clustering. For high-dimensional data with complicated structure, detailed segmentation that identifies all significant groups and discovers the small, surprising anomalies in the data, is a challenging task at which conventional algorithms often fail. We approach the problem with precision manifold learning using self-organizing neural maps with non-standard features developed in the course of our research. We demonstrate the effectiveness and robustness of this approach on multi-spectral imagery from the Mars Exploration Rovers Pancam, and on synthetic hyperspectral imagery.

  14. Facilitating biomedical researchers' interrogation of electronic health record data: Ideas from outside of biomedical informatics.

    Science.gov (United States)

    Hruby, Gregory W; Matsoukas, Konstantina; Cimino, James J; Weng, Chunhua

    2016-04-01

    Electronic health records (EHR) are a vital data resource for research uses, including cohort identification, phenotyping, pharmacovigilance, and public health surveillance. To realize the promise of EHR data for accelerating clinical research, it is imperative to enable efficient and autonomous EHR data interrogation by end users such as biomedical researchers. This paper surveys state-of-art approaches and key methodological considerations to this purpose. We adapted a previously published conceptual framework for interactive information retrieval, which defines three entities: user, channel, and source, by elaborating on channels for query formulation in the context of facilitating end users to interrogate EHR data. We show the current progress in biomedical informatics mainly lies in support for query execution and information modeling, primarily due to emphases on infrastructure development for data integration and data access via self-service query tools, but has neglected user support needed during iteratively query formulation processes, which can be costly and error-prone. In contrast, the information science literature has offered elaborate theories and methods for user modeling and query formulation support. The two bodies of literature are complementary, implying opportunities for cross-disciplinary idea exchange. On this basis, we outline the directions for future informatics research to improve our understanding of user needs and requirements for facilitating autonomous interrogation of EHR data by biomedical researchers. We suggest that cross-disciplinary translational research between biomedical informatics and information science can benefit our research in facilitating efficient data access in life sciences. PMID:26972838

  15. Enriching a biomedical event corpus with meta-knowledge annotation

    Directory of Open Access Journals (Sweden)

    Thompson Paul

    2011-10-01

    Full Text Available Abstract Background Biomedical papers contain rich information about entities, facts and events of biological relevance. To discover these automatically, we use text mining techniques, which rely on annotated corpora for training. In order to extract protein-protein interactions, genotype-phenotype/gene-disease associations, etc., we rely on event corpora that are annotated with classified, structured representations of important facts and findings contained within text. These provide an important resource for the training of domain-specific information extraction (IE systems, to facilitate semantic-based searching of documents. Correct interpretation of these events is not possible without additional information, e.g., does an event describe a fact, a hypothesis, an experimental result or an analysis of results? How confident is the author about the validity of her analyses? These and other types of information, which we collectively term meta-knowledge, can be derived from the context of the event. Results We have designed an annotation scheme for meta-knowledge enrichment of biomedical event corpora. The scheme is multi-dimensional, in that each event is annotated for 5 different aspects of meta-knowledge that can be derived from the textual context of the event. Textual clues used to determine the values are also annotated. The scheme is intended to be general enough to allow integration with different types of bio-event annotation, whilst being detailed enough to capture important subtleties in the nature of the meta-knowledge expressed in the text. We report here on both the main features of the annotation scheme, as well as its application to the GENIA event corpus (1000 abstracts with 36,858 events. High levels of inter-annotator agreement have been achieved, falling in the range of 0.84-0.93 Kappa. Conclusion By augmenting event annotations with meta-knowledge, more sophisticated IE systems can be trained, which allow interpretative

  16. Understanding Metabolomics in Biomedical Research.

    Science.gov (United States)

    Kim, Su Jung; Kim, Su Hee; Kim, Ji Hyun; Hwang, Shin; Yoo, Hyun Ju

    2016-03-01

    The term "omics" refers to any type of specific study that provides collective information on a biological system. Representative omics includes genomics, proteomics, and metabolomics, and new omics is constantly being added, such as lipidomics or glycomics. Each omics technique is crucial to the understanding of various biological systems and complements the information provided by the other approaches. The main strengths of metabolomics are that metabolites are closely related to the phenotypes of living organisms and provide information on biochemical activities by reflecting the substrates and products of cellular metabolism. The transcriptome does not always correlate with the proteome, and the translated proteome might not be functionally active. Therefore, their changes do not always result in phenotypic alterations. Unlike the genome or proteome, the metabolome is often called the molecular phenotype of living organisms and is easily translated into biological conditions and disease states. Here, we review the general strategies of mass spectrometry-based metabolomics. Targeted metabolome or lipidome analysis is discussed, as well as nontargeted approaches, with a brief explanation of the advantages and disadvantages of each platform. Biomedical applications that use mass spectrometry-based metabolomics are briefly introduced. PMID:26676338

  17. Sentence Simplification Aids Protein-Protein Interaction Extraction

    OpenAIRE

    Jonnalagadda, Siddhartha; Gonzalez, Graciela

    2010-01-01

    Accurate systems for extracting Protein-Protein Interactions (PPIs) automatically from biomedical articles can help accelerate biomedical research. Biomedical Informatics researchers are collaborating to provide metaservices and advance the state-of-art in PPI extraction. One problem often neglected by current Natural Language Processing systems is the characteristic complexity of the sentences in biomedical literature. In this paper, we report on the impact that automatic simplification of s...

  18. Biomedical Device Technology Principles and Design

    CERN Document Server

    Chan, Anthony Y K

    2008-01-01

    For many years, the tools available to physicians were limited to a few simple handpieces such as stethoscopes, thermometers and syringes; medical professionals primarily relied on their senses and skills to perform diagnosis and disease mitigation. Today, diagnosis of medical problems is heavily dependent on the analysis of information made available by sophisticated medical machineries such as electrocardiographs, ultrasound scanners and laboratory analyzers. Patient treatments often involve specialized equipment such as cardiac pacemakers and electrosurgical units. Such biomedical instrumen

  19. Biomedical Informatics Doctoral Programme and Lifelong Education

    Czech Academy of Sciences Publication Activity Database

    Zvárová, Jana; Dostálová, T.; Zvára Jr., Karel; Heroutová, Helena

    Amsterdam: IOS Press, 2010 - (Safran, C.; Reti, S.; Marin, S.). s. 1426-1426 ISBN 978-1-60750-587-7. [MEDINFO 2010. World Congress on Medical and Health Informatics /13./. 13.09.2010-16.09.2010, Cape Town] R&D Projects: GA MŠk(CZ) 1M06014 Institutional research plan: CEZ:AV0Z10300504 Keywords : biomedical informatics * education * e-learning * communication * information technologies Subject RIV: IN - Informatics, Computer Science

  20. Trends in modeling Biomedical Complex Systems

    OpenAIRE

    Remondini Daniel; Castellani Gastone; Romano Paolo; Milanesi Luciano; Liò Petro

    2009-01-01

    Abstract In this paper we provide an introduction to the techniques for multi-scale complex biological systems, from the single bio-molecule to the cell, combining theoretical modeling, experiments, informatics tools and technologies suitable for biological and biomedical research, which are becoming increasingly multidisciplinary, multidimensional and information-driven. The most important concepts on mathematical modeling methodologies and statistical inference, bioinformatics and standards...

  1. Biomedical research in a Digital Health Framework

    OpenAIRE

    Cano, Isaac; Lluch-Ariet, Magí; Gomez-Cabrero, David; Maier, Dieter; Kalko, Susana; Cascante, Marta; Tegnér, Jesper; Miralles, Felip; Herrera, Diego; Roca, Josep; ,

    2014-01-01

    This article describes a Digital Health Framework (DHF), benefitting from the lessons learnt during the three-year life span of the FP7 Synergy-COPD project. The DHF aims to embrace the emerging requirements - data and tools - of applying systems medicine into healthcare with a three-tier strategy articulating formal healthcare, informal care and biomedical research. Accordingly, it has been constructed based on three key building blocks, namely, novel integrated care services with the suppor...

  2. How to Mine Information from Each Instance to Extract an Abbreviated and Credible Logical Rule

    Directory of Open Access Journals (Sweden)

    Limin Wang

    2014-10-01

    Full Text Available Decision trees are particularly promising in symbolic representation and reasoning due to their comprehensible nature, which resembles the hierarchical process of human decision making. However, their drawbacks, caused by the single-tree structure,cannot be ignored. A rigid decision path may cause the majority class to overwhelm otherclass when dealing with imbalanced data sets, and pruning removes not only superfluousnodes, but also subtrees. The proposed learning algorithm, flexible hybrid decision forest(FHDF, mines information implicated in each instance to form logical rules on the basis of a chain rule of local mutual information, then forms different decision tree structures and decision forests later. The most credible decision path from the decision forest can be selected to make a prediction. Furthermore, functional dependencies (FDs, which are extracted from the whole data set based on association rule analysis, perform embedded attribute selection to remove nodes rather than subtrees, thus helping to achieve different levels of knowledge representation and improve model comprehension in the framework of semi-supervised learning. Naive Bayes replaces the leaf nodes at the bottom of the tree hierarchy, where the conditional independence assumption may hold. This technique reduces the potential for overfitting and overtraining and improves the prediction quality and generalization. Experimental results on UCI data sets demonstrate the efficacy of the proposed approach.

  3. A methodology for the extraction of quantitative information from electron microscopy images at the atomic level

    Science.gov (United States)

    Galindo, P. L.; Pizarro, J.; Guerrero, E.; Guerrero-Lebrero, M. P.; Scavello, G.; Yáñez, A.; Núñez-Moraleda, B. M.; Maestre, J. M.; Sales, D. L.; Herrera, M.; Molina, S. I.

    2014-06-01

    In this paper we describe a methodology developed at the University of Cadiz (Spain) in the past few years for the extraction of quantitative information from electron microscopy images at the atomic level. This work is based on a coordinated and synergic activity of several research groups that have been working together over the last decade in two different and complementary fields: Materials Science and Computer Science. The aim of our joint research has been to develop innovative high-performance computing techniques and simulation methods in order to address computationally challenging problems in the analysis, modelling and simulation of materials at the atomic scale, providing significant advances with respect to existing techniques. The methodology involves several fundamental areas of research including the analysis of high resolution electron microscopy images, materials modelling, image simulation and 3D reconstruction using quantitative information from experimental images. These techniques for the analysis, modelling and simulation allow optimizing the control and functionality of devices developed using materials under study, and have been tested using data obtained from experimental samples.

  4. A Knowledge-Driven Approach to Extract Disease-Related Biomarkers from the Literature

    OpenAIRE

    À. Bravo; Cases, M.; Queralt-Rosinach, N.; Sanz, F.; Furlong, L. I.

    2014-01-01

    The biomedical literature represents a rich source of biomarker information. However, both the size of literature databases and their lack of standardization hamper the automatic exploitation of the information contained in these resources. Text mining approaches have proven to be useful for the exploitation of information contained in the scientific publications. Here, we show that a knowledge-driven text mining approach can exploit a large literature database to extract a dataset of biomark...

  5. Biomedical digital assistant for ubiquitous healthcare.

    Science.gov (United States)

    Lee, Tae-Soo; Hong, Joo-Hyun; Cho, Myeong-Chan

    2007-01-01

    The concept of ubiquitous healthcare service, which emerged as one of measures to solve healthcare problems in aged society, means that patients can receive services such as prevention, diagnosis, therapy and prognosis management at any time and in any place with the help of advanced information and communication technology. This service requires not only biomedical digital assistant that can monitor continuously the patients' health condition regardless of time and place, but also wired and wireless communication devices and telemedicine servers that provide doctors with data on patients' present health condition. In order to implement a biomedical digital assistant that is portable and wearable to patients, the present study developed a device that minimizes size, weight and power consumption, measures ECG and PPG signals, and even monitors moving patients' state. The biomedical sensor with the function of wireless communication was designed to be highly portable and wearable, to be operable 24 hours with small-size batteries, and to monitor the subject's heart rate, step count and respiratory rate in his daily life. The biomedical signal receiving device was implemented in two forms, PDA and cellular phone. The movement monitoring device embedded in the battery pack of a cellular phone does not have any problem in operating 24 hours, but the real-time biomedical signal receiving device implemented with PDA operated up to 6 hours due to the limited battery capacity of PDA. This problem is expected to be solved by reducing wireless communication load through improving the processing and storage functions of the sensor. The developed device can transmit a message on the patient's emergency to the remote server through the cellular phone network, and is expected to play crucial roles in the health management of chronic-aged patients in their daily life. PMID:18002325

  6. Multiscale computer modeling in biomechanics and biomedical engineering

    CERN Document Server

    2013-01-01

    This book reviews the state-of-the-art in multiscale computer modeling, in terms of both accomplishments and challenges. The information in the book is particularly useful for biomedical engineers, medical physicists and researchers in systems biology, mathematical biology, micro-biomechanics and biomaterials who are interested in how to bridge between traditional biomedical engineering work at the organ and tissue scales, and the newer arenas of cellular and molecular bioengineering.

  7. Information Extraction and Dependency on Open Government Data (ogd) for Environmental Monitoring

    Science.gov (United States)

    Abdulmuttalib, Hussein

    2016-06-01

    Environmental monitoring practices support decision makers of different government / private institutions, besides environmentalists and planners among others. This support helps them act towards the sustainability of our environment, and also take efficient measures for protecting human beings in general, but it is difficult to explore useful information from 'OGD' and assure its quality for the purpose. On the other hand, Monitoring itself comprises detecting changes as happens, or within the mitigation period range, which means that any source of data, that is to be used for monitoring, should replicate the information related to the period of environmental monitoring, or otherwise it's considered almost useless or history. In this paper the assessment of information extraction and structuring from Open Government Data 'OGD', that can be useful to environmental monitoring is performed, looking into availability, usefulness to environmental monitoring of a certain type, checking its repetition period and dependences. The particular assessment is being performed on a small sample selected from OGD, bearing in mind the type of the environmental change monitored, such as the increase and concentrations of built up areas, and reduction of green areas, or monitoring the change of temperature in a specific area. The World Bank mentioned in its blog that Data is open if it satisfies both conditions of, being technically open, and legally open. The use of Open Data thus, is regulated by published terms of use, or an agreement which implies some conditions without violating the above mentioned two conditions. Within the scope of the paper I wish to share the experience of using some OGD for supporting an environmental monitoring work, that is performed to mitigate the production of carbon dioxide, by regulating energy consumption, and by properly designing the test area's landscapes, thus using Geodesign tactics, meanwhile wish to add to the results achieved by many

  8. Overview of BioCreAtIvE: critical assessment of information extraction for biology

    Directory of Open Access Journals (Sweden)

    Hirschman Lynette

    2005-05-01

    Full Text Available Abstract Background The goal of the first BioCreAtIvE challenge (Critical Assessment of Information Extraction in Biology was to provide a set of common evaluation tasks to assess the state of the art for text mining applied to biological problems. The results were presented in a workshop held in Granada, Spain March 28–31, 2004. The articles collected in this BMC Bioinformatics supplement entitled "A critical assessment of text mining methods in molecular biology" describe the BioCreAtIvE tasks, systems, results and their independent evaluation. Results BioCreAtIvE focused on two tasks. The first dealt with extraction of gene or protein names from text, and their mapping into standardized gene identifiers for three model organism databases (fly, mouse, yeast. The second task addressed issues of functional annotation, requiring systems to identify specific text passages that supported Gene Ontology annotations for specific proteins, given full text articles. Conclusion The first BioCreAtIvE assessment achieved a high level of international participation (27 groups from 10 countries. The assessment provided state-of-the-art performance results for a basic task (gene name finding and normalization, where the best systems achieved a balanced 80% precision / recall or better, which potentially makes them suitable for real applications in biology. The results for the advanced task (functional annotation from free text were significantly lower, demonstrating the current limitations of text-mining approaches where knowledge extrapolation and interpretation are required. In addition, an important contribution of BioCreAtIvE has been the creation and release of training and test data sets for both tasks. There are 22 articles in this special issue, including six that provide analyses of results or data quality for the data sets, including a novel inter-annotator consistency assessment for the test set used in task 2.

  9. Commercialising biomedical technology.

    Science.gov (United States)

    Craig, D L

    1989-06-01

    Engineers and scientists working with biomedical technology are a highly inventive lot. However, it is disappointing to see how few of the products of that inventiveness ever see the light of day outside the hospitals or institutions in which they are developed. This is usually because the developers do not know how to go about commercialising their products. The two basic options in commercialising a new product are to license the product to an existing company, or to establish a new company to manufacture and market it. Whichever approach is taken, a "Business Plan" is an essential requirement. This is a selling document which is needed either to convince an existing company that it would be profitable for it to license the product, or to convince an investor/financier to fund the establishment of a new company to commercialise it. PMID:2764795

  10. MEMS biomedical implants

    Institute of Scientific and Technical Information of China (English)

    Tai Yuchong

    2012-01-01

    The field of micro-electro-mechanical systems (MEMS) has advanced tremendously for the last 20 years. Most commercially noticeably, the field has successfully advanced from pressure sensors to micro physical sensors, such as accelerometers and gyros, for handheld electronics application. In parallel, MEMS has also advanced into micro total analysis system(TAS) and/or lab-on-a-chip applications. This article would discuss a relatively new but promising future direction towards MEMS biomedical implants. Specifically, Parylene C has been explored to be used as a good MEMS implant material and will be discussed in detail. Demonstrated implant devices, such as retinal and spinal cord implants, are presented in this article.

  11. A Semantics and Data-Driven Biomedical Multimedia Software System

    Directory of Open Access Journals (Sweden)

    Shih-Hsi Liu

    2010-08-01

    Full Text Available Developing a large-scale biomedical multimedia software system is always a challenging task: Satisfaction of sundry and stringent biomedical multimedia related requirements and standards; Heterogeneous software deployment and communication environments; and tangling correlation between data/contents and software functionalities, among others. This paper introduces a novel biomedical multimedia software system developed under Service-Oriented Architecture (SOA. Such a system takes the advantage of interoperability of SOA to solve the heterogeneity and correlation problems. The paper also classifies the system into services, annotation, ontologies, semantics matching, and QoS optimization aspects which may potentially solve the requirements problem: By establishing data ontology with respect to data properties, contents, QoS, and biomedical regulations and expanding service ontology to describe more functional and QoS specifications supported by services, appropriate services for processing biomedical multimedia data may be discovered, performed, tuned up or replaced as needed. Lastly, a biomedical education project that improves the performance of feature extraction and classification processed afterwards is introduced to illustrate the advantages of our software system developed under SOA.

  12. Biomedical applications of nisin.

    Science.gov (United States)

    Shin, J M; Gwak, J W; Kamarajan, P; Fenno, J C; Rickard, A H; Kapila, Y L

    2016-06-01

    Nisin is a bacteriocin produced by a group of Gram-positive bacteria that belongs to Lactococcus and Streptococcus species. Nisin is classified as a Type A (I) lantibiotic that is synthesized from mRNA and the translated peptide contains several unusual amino acids due to post-translational modifications. Over the past few decades, nisin has been used widely as a food biopreservative. Since then, many natural and genetically modified variants of nisin have been identified and studied for their unique antimicrobial properties. Nisin is FDA approved and generally regarded as a safe peptide with recognized potential for clinical use. Over the past two decades the application of nisin has been extended to biomedical fields. Studies have reported that nisin can prevent the growth of drug-resistant bacterial strains, such as methicillin-resistant Staphylococcus aureus, Streptococcus pneumoniae, Enterococci and Clostridium difficile. Nisin has now been shown to have antimicrobial activity against both Gram-positive and Gram-negative disease-associated pathogens. Nisin has been reported to have anti-biofilm properties and can work synergistically in combination with conventional therapeutic drugs. In addition, like host-defence peptides, nisin may activate the adaptive immune response and have an immunomodulatory role. Increasing evidence indicates that nisin can influence the growth of tumours and exhibit selective cytotoxicity towards cancer cells. Collectively, the application of nisin has advanced beyond its role as a food biopreservative. Thus, this review will describe and compare studies on nisin and provide insight into its future biomedical applications. PMID:26678028

  13. GDRMS: a system for automatic extraction of the disease-centre relation

    Science.gov (United States)

    Yang, Ronggen; Zhang, Yue; Gong, Lejun

    2012-01-01

    With the rapidly increasing of biomedical literature, the deluge of new articles is leading to information overload. Extracting the available knowledge from the huge amount of biomedical literature has become a major challenge. GDRMS is developed as a tool that extracts the relationship between disease and gene, gene and gene from biomedical literatures using text mining technology. It is a ruled-based system which also provides disease-centre network visualization, constructs the disease-gene database, and represents a gene engine for understanding the function of the gene. The main focus of GDRMS is to provide a valuable opportunity to explore the relationship between disease and gene for the research community about etiology of disease.

  14. Analysis Methods for Extracting Knowledge from Large-Scale WiFi Monitoring to Inform Building Facility Planning

    DEFF Research Database (Denmark)

    Ruiz-Ruiz, Antonio; Blunck, Henrik; Prentow, Thor Siiger;

    2014-01-01

    realistic data to inform facility planning. In this paper, we propose analysis methods to extract knowledge from large sets of network collected WiFi traces to better inform facility management and planning in large building complexes. The analysis methods, which build on a rich set of temporal and spatial....... Spatio-temporal visualization tools built on top of these methods enable planners to inspect and explore extracted information to inform facility-planning activities. To evaluate the methods, we present results for a large hospital complex covering more than 10 hectares. The evaluation is based on WiFi...... traces collected in the hospital’s WiFi infrastructure over two weeks observing around 18000 different devices recording more than a billion individual WiFi measurements. For the presented analysis methods we present quantitative performance results, e.g., demonstrating over 95% accuracy for correct...

  15. Biomedical semantics in the Semantic Web.

    Science.gov (United States)

    Splendiani, Andrea; Burger, Albert; Paschke, Adrian; Romano, Paolo; Marshall, M Scott

    2011-01-01

    The Semantic Web offers an ideal platform for representing and linking biomedical information, which is a prerequisite for the development and application of analytical tools to address problems in data-intensive areas such as systems biology and translational medicine. As for any new paradigm, the adoption of the Semantic Web offers opportunities and poses questions and challenges to the life sciences scientific community: which technologies in the Semantic Web stack will be more beneficial for the life sciences? Is biomedical information too complex to benefit from simple interlinked representations? What are the implications of adopting a new paradigm for knowledge representation? What are the incentives for the adoption of the Semantic Web, and who are the facilitators? Is there going to be a Semantic Web revolution in the life sciences?We report here a few reflections on these questions, following discussions at the SWAT4LS (Semantic Web Applications and Tools for Life Sciences) workshop series, of which this Journal of Biomedical Semantics special issue presents selected papers from the 2009 edition, held in Amsterdam on November 20th. PMID:21388570

  16. Biomedical research in a Digital Health Framework.

    Science.gov (United States)

    Cano, Isaac; Lluch-Ariet, Magí; Gomez-Cabrero, David; Maier, Dieter; Kalko, Susana; Cascante, Marta; Tegnér, Jesper; Miralles, Felip; Herrera, Diego; Roca, Josep

    2014-11-28

    This article describes a Digital Health Framework (DHF), benefitting from the lessons learnt during the three-year life span of the FP7 Synergy-COPD project. The DHF aims to embrace the emerging requirements--data and tools--of applying systems medicine into healthcare with a three-tier strategy articulating formal healthcare, informal care and biomedical research. Accordingly, it has been constructed based on three key building blocks, namely, novel integrated care services with the support of information and communication technologies, a personal health folder (PHF) and a biomedical research environment (DHF-research). Details on the functional requirements and necessary components of the DHF-research are extensively presented. Finally, the specifics of the building blocks strategy for deployment of the DHF, as well as the steps toward adoption are analyzed. The proposed architectural solutions and implementation steps constitute a pivotal strategy to foster and enable 4P medicine (Predictive, Preventive, Personalized and Participatory) in practice and should provide a head start to any community and institution currently considering to implement a biomedical research platform. PMID:25472554

  17. Biomedical engineering frontier research and converging technologies

    CERN Document Server

    Jun, Ho-Wook; Shin, Jennifer; Lee, SangHoon

    2016-01-01

    This book provides readers with an integrative overview of the latest research and developments in the broad field of biomedical engineering. Each of the chapters offers a timely review written by leading biomedical engineers and aims at showing how the convergence of scientific and engineering fields with medicine has created a new basis for practically solving problems concerning human health, wellbeing and disease. While some of the latest frontiers of biomedicine, such as neuroscience and regenerative medicine, are becoming increasingly dependent on new ideas and tools from other disciplines, the paradigm shift caused by technological innovations in the fields of information science, nanotechnology, and robotics is opening new opportunities in healthcare, besides dramatically changing the ways we actually practice science. At the same time, a new generation of engineers, fluent in many different scientific “languages,” is creating entirely new fields of research that approach the “old” questions f...

  18. In-shore ship extraction from HR optical remote sensing image via salience structure and GIS information

    Science.gov (United States)

    Ren, Xiaoyuan; Jiang, Libing; Tang, Xiao-an

    2015-12-01

    In order to solve the problem of in-shore ship extraction from remote sensing image, a novel method for in-shore ship extraction from high resolution (HR) optical remote sensing image is proposed via salience structure feature and GIS information. Firstly, the berth ROI is located in the image with the aid of the prior GIS auxiliary information. Secondly, the salient corner features at ship bow are extracted from the berth ROI precisely. Finally, a recursive algorithm concerning the symmetric geometry of the ship target is conducted to discriminate the multi docked in-shore targets into mono in-shore ships. The results of the experiments show that the method proposed in this paper can detect the majority of large and medium scale in-shore ships from the optical remote sensing image, including both the mono and the multi adjacent docked in-shore ship cases.

  19. Extracting conformational structure information of benzene molecules via laser-induced electron diffraction

    Directory of Open Access Journals (Sweden)

    Yuta Ito

    2016-05-01

    Full Text Available We have measured the angular distributions of high energy photoelectrons of benzene molecules generated by intense infrared femtosecond laser pulses. These electrons arise from the elastic collisions between the benzene ions with the previously tunnel-ionized electrons that have been driven back by the laser field. Theory shows that laser-free elastic differential cross sections (DCSs can be extracted from these photoelectrons, and the DCS can be used to retrieve the bond lengths of gas-phase molecules similar to the conventional electron diffraction method. From our experimental results, we have obtained the C-C and C-H bond lengths of benzene with a spatial resolution of about 10 pm. Our results demonstrate that laser induced electron diffraction (LIED experiments can be carried out with the present-day ultrafast intense lasers already. Looking ahead, with aligned or oriented molecules, more complete spatial information of the molecule can be obtained from LIED, and applying LIED to probe photo-excited molecules, a “molecular movie” of the dynamic system may be created with sub-Ångström spatial and few-ten femtosecond temporal resolutions.

  20. Quantum measurement information as a key to energy extraction from local vacuums

    International Nuclear Information System (INIS)

    In this paper, a protocol is proposed in which energy extraction from local vacuum states is possible by using quantum measurement information for the vacuum state of quantum fields. In the protocol, Alice, who stays at a spatial point, excites the ground state of the fields by a local measurement. Consequently, wave packets generated by Alice's measurement propagate the vacuum to spatial infinity. Let us assume that Bob stays away from Alice and fails to catch the excitation energy when the wave packets pass in front of him. Next Alice announces her local measurement result to Bob by classical communication. Bob performs a local unitary operation depending on the measurement result. In this process, positive energy is released from the fields to Bob's apparatus of the unitary operation. In the field systems, wave packets are generated with negative energy around Bob's location. Soon afterwards, the negative-energy wave packets begin to chase after the positive-energy wave packets generated by Alice and form loosely bound states.

  1. The Effect of Giving Moringa Leaves Extract to Pregnant Women Working in Informal Sector on DNA Damage

    OpenAIRE

    Muis, Masyita; Hadju, Veni; S. Russeng, Syamsiar; Burhanuddin, Laode

    2015-01-01

    Moringa leaves are the leaves of the Moringa tree containing various macro and micro nutrients and active ingredients that act as antioxidants. We assess the effect of leaf extracts of Moringa in pregnant women informal workers to DNA damage This study design was randomized, double-blind, controlled trials. Pregnant women working in informal sector (generally the laborers and sellers). Statistical analysis using paired and independent t-tests. Characteristics of the subjects before t...

  2. Sequential Data Mining for Information Extraction from Texts Fouille de données séquentielles pour l’extraction d’information dans les textes

    Directory of Open Access Journals (Sweden)

    Thierry Charnois

    2010-09-01

    Full Text Available This paper shows the benefit of using data mining methods for Biological Natural Language Processing. A method for discovering linguistic patterns based on a recursive sequential pattern mining is proposed. It does not require a sentence parsing nor other resource except a training data set. It produces understandable results and we show its interest in the extraction of relations between named entities. For the named entities recognition problem, we propose a method based on a new kind of patterns taking account the sequence and its context.

  3. Handbook on advanced design and manufacturing technologies for biomedical devices

    CERN Document Server

    2013-01-01

    The last decades have seen remarkable advances in computer-aided design, engineering and manufacturing technologies, multi-variable simulation tools, medical imaging, biomimetic design, rapid prototyping, micro and nanomanufacturing methods and information management resources, all of which provide new horizons for the Biomedical Engineering fields and the Medical Device Industry. Handbook on Advanced Design and Manufacturing Technologies for Biomedical Devices covers such topics in depth, with an applied perspective and providing several case studies that help to analyze and understand the key factors of the different stages linked to the development of a novel biomedical device, from the conceptual and design steps, to the prototyping and industrialization phases. Main research challenges and future potentials are also discussed, taking into account relevant social demands and a growing market already exceeding billions of dollars. In time, advanced biomedical devices will decisively change methods and resu...

  4. Terahertz Imaging for Biomedical Applications Pattern Recognition and Tomographic Reconstruction

    CERN Document Server

    Yin, Xiaoxia; Abbott, Derek

    2012-01-01

    Terahertz Imaging for Biomedical Applications: Pattern Recognition and Tomographic Reconstruction presents the necessary algorithms needed to assist screening, diagnosis, and treatment, and these algorithms will play a critical role in the accurate detection of abnormalities present in biomedical imaging. Terahertz biomedical imaging has become an area of interest due to its ability to simultaneously acquire both image and spectral information. Terahertz imaging systems are being commercialized with an increasing number of trials performed in a biomedical setting. Terahertz tomographic imaging and detection technology contributes to the ability to identify opaque objects with clear boundaries,and would be useful to both in vivo and ex vivo environments. This book also: Introduces terahertz radiation techniques and provides a number of topical examples of signal and image processing, as well as machine learning Presents the most recent developments in an emerging field, terahertz radiation Utilizes new methods...

  5. Publication speed and advanced online publication: Are biomedical Indian journals slow?

    Directory of Open Access Journals (Sweden)

    Akash Shah

    2016-01-01

    Full Text Available Objective: The aim of this study was to identify the publication speed (peer review time and publication time of biomedical Indian journals and identify the journals having the facility of advance online publication (AOP. Materials and Methods: Biomedical Indian journals were identified from the Journal Citation Report of 2013. Thirty original articles published between January 2012 and June 2014 were systematically selected from each journal. Information about the date of submission, revision, and acceptance were extracted from the full text of the articles. Median peer review time (submission to acceptance and publication time (acceptance to AOP/electronic publication were calculated for each journal. Results: Of the 19 journals studied, 5 (26.3%, 15 (78.9%, and 6 (31.6% journals did not mention details about date of submission, date of revision, and date of acceptance, respectively. The individual median peer review time of the journals ranged from 87 to 377.5 days and the combined median peer review time (interquartile range was 143.5 days (105.5, 238. The individual median publication time ranged from 14 to 349 days. The publication time for journals with AOP was significantly lesser (29.5 [19.6, 50.6] vs. 146.5 [126.5, 202.5]; P = 0.02 compared to journals without AOP. Impact factor of the journal did not correlate with the publication speed. The facility of AOP was provided by 6 (31.6% journals. Conclusions: Overall, the peer review time and publication time of biomedical Indian journals included in our study seems to be fairly long. Less than one-third of biomedical Indian journals provide the facility of AOP.

  6. Cluster-Based Query Expansion Using Language Modeling for Biomedical Literature Retrieval

    Science.gov (United States)

    Xu, Xuheng

    2011-01-01

    The tremendously huge volume of biomedical literature, scientists' specific information needs, long terms of multiples words, and fundamental problems of synonym and polysemy have been challenging issues facing the biomedical information retrieval community researchers. Search engines have significantly improved the efficiency and effectiveness of…

  7. For 481 biomedical open access journals, articles are not searchable in the Directory of Open Access Journals nor in conventional biomedical databases

    DEFF Research Database (Denmark)

    Liljekvist, Mads Svane; Andresen, Kristoffer; Pommergaard, Hans-Christian;

    2015-01-01

    Background. Open access (OA) journals allows access to research papers free of charge to the reader. Traditionally, biomedical researchers use databases like MEDLINE and EMBASE to discover new advances. However, biomedical OA journals might not fulfill such databases' criteria, hindering...... dissemination. The Directory of Open Access Journals (DOAJ) is a database exclusively listing OA journals. The aim of this study was to investigate DOAJ's coverage of biomedical OA journals compared with the conventional biomedical databases. Methods. Information on all journals listed in four conventional...... biomedical databases (MEDLINE, PubMed Central, EMBASE and SCOPUS) and DOAJ were gathered. Journals were included if they were (1) actively publishing, (2) full OA, (3) prospectively indexed in one or more database, and (4) of biomedical subject. Impact factor and journal language were also collected. DOAJ...

  8. Extraction as a source of additional information when concentrations in multicomponent systems are simultaneously determined

    International Nuclear Information System (INIS)

    Using as an example photometric determination of Nd and Sm in their joint presence, the possibility to use the influence of extraction on analytic signal increase is considered. It is shown that interligand exchange in extracts in combination with simultaneous determination of concentrations can be used as a simple means increasing the accuracy of determination. 5 refs.; 2 figs.; 3 tabs

  9. Molecular Biomedical Imaging Laboratory (MBIL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Molecular Biomedical Imaging Laboratory (MBIL) is adjacent-a nd has access-to the Department of Radiology and Imaging Sciences clinical imaging facilities. MBIL...

  10. Extracting key information from historical data to quantify the transmission dynamics of smallpox

    Directory of Open Access Journals (Sweden)

    Brockmann Stefan O

    2008-08-01

    Full Text Available Abstract Background Quantification of the transmission dynamics of smallpox is crucial for optimizing intervention strategies in the event of a bioterrorist attack. This article reviews basic methods and findings in mathematical and statistical studies of smallpox which estimate key transmission parameters from historical data. Main findings First, critically important aspects in extracting key information from historical data are briefly summarized. We mention different sources of heterogeneity and potential pitfalls in utilizing historical records. Second, we discuss how smallpox spreads in the absence of interventions and how the optimal timing of quarantine and isolation measures can be determined. Case studies demonstrate the following. (1 The upper confidence limit of the 99th percentile of the incubation period is 22.2 days, suggesting that quarantine should last 23 days. (2 The highest frequency (61.8% of secondary transmissions occurs 3–5 days after onset of fever so that infected individuals should be isolated before the appearance of rash. (3 The U-shaped age-specific case fatality implies a vulnerability of infants and elderly among non-immune individuals. Estimates of the transmission potential are subsequently reviewed, followed by an assessment of vaccination effects and of the expected effectiveness of interventions. Conclusion Current debates on bio-terrorism preparedness indicate that public health decision making must account for the complex interplay and balance between vaccination strategies and other public health measures (e.g. case isolation and contact tracing taking into account the frequency of adverse events to vaccination. In this review, we summarize what has already been clarified and point out needs to analyze previous smallpox outbreaks systematically.

  11. Extracting respiratory information from seismocardiogram signals acquired on the chest using a miniature accelerometer

    International Nuclear Information System (INIS)

    Seismocardiography (SCG) is a non-invasive measurement of the vibrations of the chest caused by the heartbeat. SCG signals can be measured using a miniature accelerometer attached to the chest, and are thus well-suited for unobtrusive and long-term patient monitoring. Additionally, SCG contains information relating to both cardiovascular and respiratory systems. In this work, algorithms were developed for extracting three respiration-dependent features of the SCG signal: intensity modulation, timing interval changes within each heartbeat, and timing interval changes between successive heartbeats. Simultaneously with a reference respiration belt, SCG signals were measured from 20 healthy subjects and a respiration rate was estimated using each of the three SCG features and the reference signal. The agreement between each of the three accelerometer-derived respiration rate measurements was computed with respect to the respiration rate derived from the reference respiration belt. The respiration rate obtained from the intensity modulation in the SCG signal was found to be in closest agreement with the respiration rate obtained from the reference respiration belt: the bias was found to be 0.06 breaths per minute with a 95% confidence interval of −0.99 to 1.11 breaths per minute. The limits of agreement between the respiration rates estimated using SCG (intensity modulation) and the reference were within the clinically relevant ranges given in existing literature, demonstrating that SCG could be used for both cardiovascular and respiratory monitoring. Furthermore, phases of each of the three SCG parameters were investigated at four instances of a respiration cycle—start inspiration, peak inspiration, start expiration, and peak expiration—and during breath hold (apnea). The phases of the three SCG parameters observed during the respiration cycle were congruent with existing literature and physiologically expected trends. (paper)

  12. Extraction, interpretation and validation of information for comparing samples in metabolic LC/MS data sets.

    Science.gov (United States)

    Jonsson, Par; Bruce, Stephen J; Moritz, Thomas; Trygg, Johan; Sjöström, Michael; Plumb, Robert; Granger, Jennifer; Maibaum, Elaine; Nicholson, Jeremy K; Holmes, Elaine; Antti, Henrik

    2005-05-01

    LC/MS is an analytical technique that, due to its high sensitivity, has become increasingly popular for the generation of metabolic signatures in biological samples and for the building of metabolic data bases. However, to be able to create robust and interpretable (transparent) multivariate models for the comparison of many samples, the data must fulfil certain specific criteria: (i) that each sample is characterized by the same number of variables, (ii) that each of these variables is represented across all observations, and (iii) that a variable in one sample has the same biological meaning or represents the same metabolite in all other samples. In addition, the obtained models must have the ability to make predictions of, e.g. related and independent samples characterized accordingly to the model samples. This method involves the construction of a representative data set, including automatic peak detection, alignment, setting of retention time windows, summing in the chromatographic dimension and data compression by means of alternating regression, where the relevant metabolic variation is retained for further modelling using multivariate analysis. This approach has the advantage of allowing the comparison of large numbers of samples based on their LC/MS metabolic profiles, but also of creating a means for the interpretation of the investigated biological system. This includes finding relevant systematic patterns among samples, identifying influential variables, verifying the findings in the raw data, and finally using the models for predictions. The presented strategy was here applied to a population study using urine samples from two cohorts, Shanxi (People's Republic of China) and Honolulu (USA). The results showed that the evaluation of the extracted information data using partial least square discriminant analysis (PLS-DA) provided a robust, predictive and transparent model for the metabolic differences between the two populations. The presented findings

  13. Hydroxyapatite coatings for biomedical applications

    CERN Document Server

    Zhang, Sam

    2013-01-01

    Hydroxyapatite coatings are of great importance in the biological and biomedical coatings fields, especially in the current era of nanotechnology and bioapplications. With a bonelike structure that promotes osseointegration, hydroxyapatite coating can be applied to otherwise bioinactive implants to make their surface bioactive, thus achieving faster healing and recovery. In addition to applications in orthopedic and dental implants, this coating can also be used in drug delivery. Hydroxyapatite Coatings for Biomedical Applications explores developments in the processing and property characteri

  14. Modified chitosans for biomedical applications

    OpenAIRE

    Yalınca, Zülal

    2013-01-01

    ABSTRACT: The subject of this thesis is the exploration of the suitability of chitosan and some of its derivatives for some chosen biomedical applications. Chitosan-graft-poly (N-vinyl imidazole), Chitosan-tripolyphosphate and ascorbyl chitosan were synthesized and characterized for specific biomedical applications in line with their chemical functionalities. Chitosan-graft-poly (N-vinyl imidazole), Chi-graft-PNVI, was synthesized by two methods; via an N-protection route and without N-pr...

  15. A COMPARATIVE ANALYSIS OF WEB INFORMATION EXTRACTION TECHNIQUES DEEP LEARNING vs. NAÏVE BAYES vs. BACK PROPAGATION NEURAL NETWORKS IN WEB DOCUMENT EXTRACTION

    Directory of Open Access Journals (Sweden)

    J. Sharmila

    2016-01-01

    Full Text Available Web mining related exploration is getting the chance to be more essential these days in view of the reason that a lot of information is overseen through the web. Web utilization is expanding in an uncontrolled way. A particular framework is required for controlling such extensive measure of information in the web space. Web mining is ordered into three noteworthy divisions: Web content mining, web usage mining and web structure mining. Tak-Lam Wong has proposed a web content mining methodology in the exploration with the aid of Bayesian Networks (BN. In their methodology, they were learning on separating the web data and characteristic revelation in view of the Bayesian approach. Roused from their investigation, we mean to propose a web content mining methodology, in view of a Deep Learning Algorithm. The Deep Learning Algorithm gives the interest over BN on the basis that BN is not considered in any learning architecture planning like to propose system. The main objective of this investigation is web document extraction utilizing different grouping algorithm and investigation. This work extricates the data from the web URL. This work shows three classification algorithms, Deep Learning Algorithm, Bayesian Algorithm and BPNN Algorithm. Deep Learning is a capable arrangement of strategies for learning in neural system which is connected like computer vision, speech recognition, and natural language processing and biometrics framework. Deep Learning is one of the simple classification technique and which is utilized for subset of extensive field furthermore Deep Learning has less time for classification. Naive Bayes classifiers are a group of basic probabilistic classifiers in view of applying Bayes hypothesis with concrete independence assumptions between the features. At that point the BPNN algorithm is utilized for classification. Initially training and testing dataset contains more URL. We extract the content presently from the dataset. The

  16. Automatic Extraction of Femur Contours from Calibrated X-Ray Images using Statistical Information

    Directory of Open Access Journals (Sweden)

    Xiao Dong

    2007-09-01

    Full Text Available Automatic identification and extraction of bone contours from x-ray images is an essential first step task for further medical image analysis. In this paper we propose a 3D statistical model based framework for the proximal femur contour extraction from calibrated x-ray images. The automatic initialization to align the 3D model with the x-ray images is solved by an Estimation of Bayesian Network Algorithm to fit a simplified multiple component geometrical model of the proximal femur to the x-ray data. Landmarks can be extracted from the geometrical model for the initialization of the 3D statistical model. The contour extraction is then accomplished by a joint registration and segmentation procedure. We iteratively updates the extracted bone contours and an instanced 3D model to fit the x-ray images. Taking the projected silhouettes of the instanced 3D model on the registered x-ray images as templates, bone contours can be extracted by a graphical model based Bayesian inference. The 3D model can then be updated by a non-rigid 2D/3D registration between the 3D statistical model and the extracted bone contours. Preliminary experiments on clinical data sets verified its validity.

  17. Post-processing of Deep Web Information Extraction Based on Domain Ontology

    OpenAIRE

    Peng, T.; L. Liu

    2013-01-01

    Many methods are utilized to extract and process query results in deep Web, which rely on the different structures of Web pages and various designing modes of databases. However, some semantic meanings and relations are ignored. So, in this paper, we present an approach for post-processing deep Web query results based on domain ontology which can utilize the semantic meanings and relations. A block identification model (BIM) based on node similarity is defined to extract data blocks that ...

  18. Bio-SCoRes: A Smorgasbord Architecture for Coreference Resolution in Biomedical Text.

    Science.gov (United States)

    Kilicoglu, Halil; Demner-Fushman, Dina

    2016-01-01

    Coreference resolution is one of the fundamental and challenging tasks in natural language processing. Resolving coreference successfully can have a significant positive effect on downstream natural language processing tasks, such as information extraction and question answering. The importance of coreference resolution for biomedical text analysis applications has increasingly been acknowledged. One of the difficulties in coreference resolution stems from the fact that distinct types of coreference (e.g., anaphora, appositive) are expressed with a variety of lexical and syntactic means (e.g., personal pronouns, definite noun phrases), and that resolution of each combination often requires a different approach. In the biomedical domain, it is common for coreference annotation and resolution efforts to focus on specific subcategories of coreference deemed important for the downstream task. In the current work, we aim to address some of these concerns regarding coreference resolution in biomedical text. We propose a general, modular framework underpinned by a smorgasbord architecture (Bio-SCoRes), which incorporates a variety of coreference types, their mentions and allows fine-grained specification of resolution strategies to resolve coreference of distinct coreference type-mention pairs. For development and evaluation, we used a corpus of structured drug labels annotated with fine-grained coreference information. In addition, we evaluated our approach on two other corpora (i2b2/VA discharge summaries and protein coreference dataset) to investigate its generality and ease of adaptation to other biomedical text types. Our results demonstrate the usefulness of our novel smorgasbord architecture. The specific pipelines based on the architecture perform successfully in linking coreferential mention pairs, while we find that recognition of full mention clusters is more challenging. The corpus of structured drug labels (SPL) as well as the components of Bio-SCoRes and

  19. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

    Science.gov (United States)

    Taylor, Chris F; Field, Dawn; Sansone, Susanna-Assunta; Aerts, Jan; Apweiler, Rolf; Ashburner, Michael; Ball, Catherine A; Binz, Pierre-Alain; Bogue, Molly; Booth, Tim; Brazma, Alvis; Brinkman, Ryan R; Clark, Adam Michael; Deutsch, Eric W; Fiehn, Oliver; Fostel, Jennifer; Ghazal, Peter; Gibson, Frank; Gray, Tanya; Grimes, Graeme; Hancock, John M; Hardy, Nigel W; Hermjakob, Henning; Julian, Randall K; Kane, Matthew; Kettner, Carsten; Kinsinger, Christopher; Kolker, Eugene; Kuiper, Martin; Le Novère, Nicolas; Leebens-Mack, Jim; Lewis, Suzanna E; Lord, Phillip; Mallon, Ann-Marie; Marthandan, Nishanth; Masuya, Hiroshi; McNally, Ruth; Mehrle, Alexander; Morrison, Norman; Orchard, Sandra; Quackenbush, John; Reecy, James M; Robertson, Donald G; Rocca-Serra, Philippe; Rodriguez, Henry; Rosenfelder, Heiko; Santoyo-Lopez, Javier; Scheuermann, Richard H; Schober, Daniel; Smith, Barry; Snape, Jason; Stoeckert, Christian J; Tipton, Keith; Sterk, Peter; Untergasser, Andreas; Vandesompele, Jo; Wiemann, Stefan

    2009-01-01

    The Minimum Information for Biological and Biomedical Investigations (MIBBI) project provides a resource for those exploring the range of extant minimum information checklists and fosters coordinated development of such checklists. PMID:18688244

  20. Network and Ensemble Enabled Entity Extraction in Informal Text (NEEEEIT) final report.

    Energy Technology Data Exchange (ETDEWEB)

    Kegelmeyer, W. Philip,; Shead, Timothy M. [Sandia National Laboratories, Albuquerque, NM; Dunlavy, Daniel M. [Sandia National Laboratories, Albuquerque, NM

    2013-09-01

    This SAND report summarizes the activities and outcomes of the Network and Ensemble Enabled Entity Extraction in Informal Text (NEEEEIT) LDRD project, which addressed improving the accuracy of conditional random fields for named entity recognition through the use of ensemble methods. Conditional random fields (CRFs) are powerful, flexible probabilistic graphical models often used in supervised machine learning prediction tasks associated with sequence data. Specifically, they are currently the best known option for named entity recognition (NER) in text. NER is the process of labeling words in sentences with semantic identifiers such as %E2%80%9Cperson%E2%80%9D, %E2%80%9Cdate%E2%80%9D, or %E2%80%9Corganization%E2%80%9D. Ensembles are a powerful statistical inference meta-method that can make most supervised machine learning methods more accurate, faster, or both. Ensemble methods are normally best suited to %E2%80%9Cunstable%E2%80%9D classification methods with high variance error. CRFs applied to NER are very stable classifiers, and as such, would initially seem to be resistant to the benefits of ensembles. The NEEEEIT project nonetheless worked out how to generalize ensemble methods to CRFs, demonstrated that accuracy can indeed be improved by proper use of ensemble techniques, and generated a new CRF code, %E2%80%9CpyCrust%E2%80%9D and a surrounding application environment, %E2%80%9CNEEEEIT%E2%80%9D, which implement those improvements. The summary practical advice that results from this work, then, is: When making use of CRFs for label prediction tasks in machine learning, use the pyCrust CRF base classifier with NEEEEIT's bagging ensemble implementation. (If those codes are not available, then de-stablize your CRF code via every means available, and generate the bagged training sets by hand.) If you have ample pre-processing computational time, do %E2%80%9Cforward feature selection%E2%80%9D to find and remove counter-productive feature classes. Conversely

  1. Information Extraction of Web Document Based on Htmlparser%基于HTMLParser的Web文献信息提取

    Institute of Scientific and Technical Information of China (English)

    龚真平

    2011-01-01

    Web anlalyzing based on HTMLParser could extract the information of Link,image,meta and title of the links.Using HTMLParser extracts the information of title,key words,abstract,author,sources,ect.in Web document,when store in MySql database after cleaning%基于HTMLParser对网页进行解析,可抽取标签间的Link、image、meta和title等信息。使用HTMLParser来提取Web文献中的题名、关键字、摘要、作者、来源等信息,清洗后存入MySql数据库当中,以备后续数据挖掘使用。对此进行了论述。

  2. All India Seminar on Biomedical Engineering 2012

    CERN Document Server

    Bhatele, Mukta

    2013-01-01

    This book is a collection of articles presented by researchers and practitioners, including engineers, biologists, health professionals and informatics/computer scientists, interested in both theoretical advances and applications of information systems, artificial intelligence, signal processing, electronics and other engineering tools in areas related to biology and medicine in the All India Seminar on Biomedical Engineering 2012 (AISOBE 2012), organized by The Institution of Engineers (India), Jabalpur Local Centre, Jabalpur, India during November 3-4, 2012. The content of the book is useful to doctors, engineers, researchers and academicians as well as industry professionals.

  3. Author Keywords in Biomedical Journal Articles

    OpenAIRE

    Névéol, Aurélie; Doğan, Rezarta Islamaj; Lu, Zhiyong

    2010-01-01

    As an information retrieval system, PubMed® aims at providing efficient access to documents cited in MEDLINE®. For this purpose, it relies on matching representations of documents, as provided by authors and indexers to user queries. In this paper, we describe the growth of author keywords in biomedical journal articles and present a comparative study of author keywords and MeSH® indexing terms assigned by MEDLINE indexers to PubMed Central Open Access articles. A similarity metric is used to...

  4. The biomedical discourse relation bank

    Directory of Open Access Journals (Sweden)

    Joshi Aravind

    2011-05-01

    Full Text Available Abstract Background Identification of discourse relations, such as causal and contrastive relations, between situations mentioned in text is an important task for biomedical text-mining. A biomedical text corpus annotated with discourse relations would be very useful for developing and evaluating methods for biomedical discourse processing. However, little effort has been made to develop such an annotated resource. Results We have developed the Biomedical Discourse Relation Bank (BioDRB, in which we have annotated explicit and implicit discourse relations in 24 open-access full-text biomedical articles from the GENIA corpus. Guidelines for the annotation were adapted from the Penn Discourse TreeBank (PDTB, which has discourse relations annotated over open-domain news articles. We introduced new conventions and modifications to the sense classification. We report reliable inter-annotator agreement of over 80% for all sub-tasks. Experiments for identifying the sense of explicit discourse connectives show the connective itself as a highly reliable indicator for coarse sense classification (accuracy 90.9% and F1 score 0.89. These results are comparable to results obtained with the same classifier on the PDTB data. With more refined sense classification, there is degradation in performance (accuracy 69.2% and F1 score 0.28, mainly due to sparsity in the data. The size of the corpus was found to be sufficient for identifying the sense of explicit connectives, with classifier performance stabilizing at about 1900 training instances. Finally, the classifier performs poorly when trained on PDTB and tested on BioDRB (accuracy 54.5% and F1 score 0.57. Conclusion Our work shows that discourse relations can be reliably annotated in biomedical text. Coarse sense disambiguation of explicit connectives can be done with high reliability by using just the connective as a feature, but more refined sense classification requires either richer features or more

  5. Biomedical journals: keeping up and reading critically.

    Science.gov (United States)

    Chase, Karen L; DiGiacomo, Ronald F; Van Hoosier, Gerald L

    2006-09-01

    By extrapolation from studies of physicians, knowledge and practice of laboratory animal medicine and science are expected to become progressively more outdated the longer practitioners are out of school. Keeping up with current literature and practice is a challenge that necessitates the use of many different sources of continuing education. Both veterinarians and physicians consistently list journals as the most beneficial source of new information. Accordingly, they must select from the veterinary and biomedical literature articles that report original studies and systematic reviews and recognize and respond to valid new knowledge to improve diagnostic and therapeutic approaches and maintain consistent clinical skills. Other objectives include selecting journals for general information and for information relevant or specific to one's field of research. Lastly, candidates for board certification need to read articles from journals that potentially provide the basis for questions on the examination. 'High-impact' journals should be identified, and articles should be reviewed critically. In a survey of recent candidates for laboratory animal medicine board examination, these journals included Contemporary Topics (now JAALAS), Comparative Medicine, ILAR Journal, and Laboratory Animals. Strategies for coping with the challenge of staying current with the literature include wise use of technology, journal clubs, and consultation with colleagues. A laboratory animal practitioner can become a better scientist and clinician by evaluating the research performed by others. Thorough, critical review of biomedical literature is paramount to these goals. PMID:16995641

  6. How to Select a Journal to Submit and Publish Your Biomedical Paper?

    Directory of Open Access Journals (Sweden)

    Farhad Shokraneh

    2012-03-01

    Full Text Available Introduction: selection of journal for publication purpose is one of concerns of biomedical researchers. They apply various criteria to choose appropriate journal. Here, we have tried to collect main criteria biomedical researchers use to select a journal to submit their work. Methods: we collected these criteria through focus group conversations with researchers during our careers, feedbacks from participants of our scientific writing workshops and non-systematic reviewing of some related literature. Results: we have presented a summative and informative guidance in selection of biomedical journals for biomedical paper submission and publication. Conclusion: Categorized criteria as a mnemonic tool for authors may help the authors in journal selection process.

  7. Advances in biomedical dosimetry

    International Nuclear Information System (INIS)

    Full text: Radiation dosimetry, the accurate determination of the absorbed dose within an irradiated body or a piece of material, is a prerequisite for all applications of ionizing radiation. This has been known since the very first radiation applications in medicine and biology, and increasing efforts are being made by radiation researchers to develop more reliable, effective and safe instruments, and to further improve dosimetric accuracy for all types of radiation used. Development of new techniques and instrumentation was particularly fast in the field of both medical diagnostic and therapeutic radiology. Thus, in Paris in October the IAEA held the latest symposium in its continuing series on dosimetry in medicine and biology. The last one was held in Vienna in 1975. High-quality dosimetry is obviously of great importance for human health, whether the objectives lie in the prevention and control of risks associated with the nuclear industry, in medical uses of radioactive substances or X-ray beams for diagnostic purposes, or in the application of photon, electron or neutron beams in radiotherapy. The symposium dealt with the following subjects: General aspects of dosimetry; Special physical and biomedical aspects; Determination of absorbed dose; Standardization and calibration of dosimetric systems; and Development of dosimetric systems. The forty or so papers presented and the discussions that followed them brought out a certain number of dominant themes, among which three deserve particular mention. - The recent generalization of the International System of Units having prompted a fundamental reassessment of the dosimetric quantities to be considered in calibrating measuring instruments, various proposals were advanced by the representatives of national metrology laboratories to replace the quantity 'exposure' (SI unit = coulomb/kg) by 'Kerma' or 'absorbed dose' (unit joule/kg, the special name of which is 'gray'), this latter being closer to the practical

  8. Implantable biomedical devices on bioresorbable substrates

    Science.gov (United States)

    Rogers, John A; Kim, Dae-Hyeong; Omenetto, Fiorenzo; Kaplan, David L; Litt, Brian; Viventi, Jonathan; Huang, Yonggang; Amsden, Jason

    2014-03-04

    Provided herein are implantable biomedical devices, methods of administering implantable biomedical devices, methods of making implantable biomedical devices, and methods of using implantable biomedical devices to actuate a target tissue or sense a parameter associated with the target tissue in a biological environment. Each implantable biomedical device comprises a bioresorbable substrate, an electronic device having a plurality of inorganic semiconductor components supported by the bioresorbable substrate, and a barrier layer encapsulating at least a portion of the inorganic semiconductor components. Upon contact with a biological environment the bioresorbable substrate is at least partially resorbed, thereby establishing conformal contact between the implantable biomedical device and the target tissue in the biological environment.

  9. Introductory Course in Biomedical Ethics in the Obstetrics-Gynecology Residency.

    Science.gov (United States)

    Elkins, Thomas E.

    1988-01-01

    Information used in a brief lecture that introduces a biomedical ethics curriculum in an obstetrics and gynecology residency is described. Major components include theories of philosophic ethics (formalist and consequentialist) and principles of biomedical ethics (honesty, contract-keeping, nonmaleficence, justice, autonomy, beneficence,…

  10. Unstable markup: A template-based information extraction from web sites with unstable markup

    OpenAIRE

    Kolchin, Maxim; Kozlov, Fedor

    2014-01-01

    This paper presents results of a work on crawling CEUR Workshop proceedings web site to a Linked Open Data (LOD) dataset in the framework of ESWC 2014 Semantic Publishing Challenge 2014. Our approach is based on using an extensible template-dependent crawler and DBpedia for linking extracted entities, such as the names of universities and countries.

  11. Comparison of Qinzhou bay wetland landscape information extraction by three methods

    Directory of Open Access Journals (Sweden)

    X. Chang

    2014-04-01

    and OO is 219 km2, 193.70 km2, 217.40 km2 respectively. The result indicates that SC is in the f irst place, followed by OO approach, and the third DT method when used to extract Qingzhou Bay coastal wetland.

  12. Flexible sensors for biomedical technology.

    Science.gov (United States)

    Vilela, Diana; Romeo, Agostino; Sánchez, Samuel

    2016-02-01

    Flexible sensing devices have gained a great deal of attention among the scientific community in recent years. The application of flexible sensors spans over several fields, including medicine, industrial automation, robotics, security, and human-machine interfacing. In particular, non-invasive health-monitoring devices are expected to play a key role in the improvement of patient life and in reducing costs associated with clinical and biomedical diagnostic procedures. Here, we focus on recent advances achieved in flexible devices applied on the human skin for biomedical and healthcare purposes. PMID:26675174

  13. Study on extraction of crop information using time-series MODIS data in the Chao Phraya Basin of Thailand

    Science.gov (United States)

    Tingting, Lv; Chuang, Liu

    2010-03-01

    In order to acquire the crop-related information in Chao Phraya Basin, time-series MODIS data were used in this paper. Although the spatial resolution of MODIS data is not very high, it is still useful for detecting very large-scale phenomenon, such as changes in seasonal vegetation patterns. After the data processing a general crop-related LULC (land use and land cover) map, cropping intensity map and cropping patterns map were produced. Analysis of these maps showed that the main land use type in the study area was farmland, most of which was dominated by rice. Rice fields mostly concentrated in the flood plains and double or triple rice-cropping system was commonly employed in this area. Maize, cassava, sugarcane and other upland crops were mainly distributed in the high alluvial terraces. Because these area often have water shortage problem particularly in the dry season which can support only one crop in a year, the cropping intensity was very low. However, some upland areas can be cultivated twice a year with crops which have short growing seasons. The crop information extracted from MODIS data sets were assessed by CBERS data, statistic data and so on. It was shown that MODIS derived crop information coincided well with the statistic data at the provincial level. At the same time, crop information extracted by MODIS data sets and CBERS were compared with each other which also showed similar spatial patterns.

  14. Biomedical Application of Laser

    Institute of Scientific and Technical Information of China (English)

    K. X. He; Alan Chow; Jiada Mo; Wang Zhuo

    2004-01-01

    @@ INTRODUCTION Lasers have revolutionized research and development in medicine and dentistry. They have led to development and production of many new products. Laser applications in diagnosis, treatment and surgery are enormous and have led to speedy and more efficient results, as well as better and quicker healing Processes. The applications could be classified in terms of areas of uses or in terms of instruments/products.In this paper, discussions will not be grouped in a particular fashion, but will be on specific applications. A lot of information on these applications can be found in the Internet. Such information will be mentioned in related discussions and will be given in the appendix.

  15. Parsing Citations in Biomedical Articles Using Conditional Random Fields

    OpenAIRE

    Zhang, Qing; Cao, Yong-Gang; Yu, Hong

    2011-01-01

    Citations are used ubiquitously in biomedical full-text articles and play an important role for representing both the rhetorical structure and the semantic content of the articles. As a result, text mining systems will significantly benefit from a tool that automatically extracts the content of a citation. In this study, we applied the supervised machine-learning algorithms Conditional Random Fields (CRFs) to automatically parse a citation into its fields (e.g., Author, Title, Journal, and Ye...

  16. Keyword Extraction from a Document using Word Co-occurrence Statistical Information

    Science.gov (United States)

    Matsuo, Yutaka; Ishizuka, Mitsuru

    We present a new keyword extraction algorithm that applies to a single document without using a large corpus. Frequent terms are extracted first, then a set of co-occurrence between each term and the frequent terms, i.e., occurrences in the same sentences, is generated. The distribution of co-occurrence shows the importance of a term in the document as follows. If the probability distribution of co-occurrence between term a and the frequent terms is biased to a particular subset of the frequent terms, then term a is likely to be a keyword. The degree of the biases of the distribution is measured by χ²-measure. We show our algorithm performs well for indexing technical papers.

  17. Extracting Information about the Initial State from the Black Hole Radiation

    Science.gov (United States)

    Lochan, Kinjalk; Padmanabhan, T.

    2016-02-01

    The crux of the black hole information paradox is related to the fact that the complete information about the initial state of a quantum field in a collapsing spacetime is not available to future asymptotic observers, belying the expectations from a unitary quantum theory. We study the imprints of the initial quantum state contained in a specific class of distortions of the black hole radiation and identify the classes of in states that can be partially or fully reconstructed from the information contained within. Even for the general in state, we can uncover some specific information. These results suggest that a classical collapse scenario ignores this richness of information in the resulting spectrum and a consistent quantum treatment of the entire collapse process might allow us to retrieve much more information from the spectrum of the final radiation.

  18. Extracting Information about the Initial State from the Black Hole Radiation.

    Science.gov (United States)

    Lochan, Kinjalk; Padmanabhan, T

    2016-02-01

    The crux of the black hole information paradox is related to the fact that the complete information about the initial state of a quantum field in a collapsing spacetime is not available to future asymptotic observers, belying the expectations from a unitary quantum theory. We study the imprints of the initial quantum state contained in a specific class of distortions of the black hole radiation and identify the classes of in states that can be partially or fully reconstructed from the information contained within. Even for the general in state, we can uncover some specific information. These results suggest that a classical collapse scenario ignores this richness of information in the resulting spectrum and a consistent quantum treatment of the entire collapse process might allow us to retrieve much more information from the spectrum of the final radiation. PMID:26894699

  19. Sentence Simplification Aids Protein-Protein Interaction Extraction

    CERN Document Server

    Jonnalagadda, Siddhartha

    2010-01-01

    Accurate systems for extracting Protein-Protein Interactions (PPIs) automatically from biomedical articles can help accelerate biomedical research. Biomedical Informatics researchers are collaborating to provide metaservices and advance the state-of-art in PPI extraction. One problem often neglected by current Natural Language Processing systems is the characteristic complexity of the sentences in biomedical literature. In this paper, we report on the impact that automatic simplification of sentences has on the performance of a state-of-art PPI extraction system, showing a substantial improvement in recall (8%) when the sentence simplification method is applied, without significant impact to precision.

  20. Ontology-based information extraction from the configuration command line of network routers

    OpenAIRE

    Martínez Manzanilla, Anny Gabriela; Yannuzzi, Marcelo; Serral Gracià, René; Ramirez Almonte, Wilson

    2014-01-01

    Knowledge extraction is increasingly attracting the attention of researchers from different disciplines, as a means to automate complex tasks that rely on bulk textual resources. However, the configuration of many devices in the networking field continues to be a labor intensive task, based on the human interpretation and manual entry of commands through a text-based user interface. Typically, these Command-Line Interfaces (CLIs) are both device and vendor-specific, and thus, commands differ ...

  1. Amplitude extraction in pseudoscalar-meson photoproduction: towards a situation of complete information

    OpenAIRE

    Nys, Jannes; Vrancx, Tom; Ryckebusch, Jan

    2015-01-01

    A complete set for pseudoscalar-meson photoproduction is a minimum set of observables from which one can determine the underlying reaction amplitudes unambiguously. The complete sets considered in this work involve single- and double-polarization observables. It is argued that for extracting amplitudes from data, the transversity representation of the reaction amplitudes offers advantages over alternate representations. It is shown that with the available single-polarization data for the p({\\...

  2. TennisSense: a platform for extracting semantic information from multi-camera tennis data

    OpenAIRE

    Ó Conaire, Ciarán; Kelly, Philip; Connaghan, Damien; O''Connor, Noel E.

    2009-01-01

    In this paper, we introduce TennisSense, a technology platform for the digital capture, analysis and retrieval of tennis training and matches. Our algorithms for extracting useful metadata from the overhead court camera are described and evaluated. We track the tennis ball using motion images for ball candidate detection and then link ball candidates into locally linear tracks. From these tracks we can infer when serves and rallies take place. Using background subtraction and hysteresis-type ...

  3. Extracting information from non adiabatic dynamics: excited symmetric states of the Bose-Hubbard model

    OpenAIRE

    Lacki, M.; Delande, D; Zakrzewski, J.

    2011-01-01

    Using Fourier transform on a time series generated by unitary evolution, we extract many-body eigenstates of the Bose-Hubbard model corresponding to low energy excitations, which are generated when the insulator-superfluid phase transition is realized in a typical experiment. The analysis is conducted in a symmetric external potential both without and with and disorder. A simple classification of excitations in the absence disorder is provided. The evolution is performed assuming the presence...

  4. Comparison of methods of extracting information for meta-analysis of observational studies in nutritional epidemiology

    OpenAIRE

    Bae, Jong-Myon

    2016-01-01

    OBJECTIVES: A common method for conducting a quantitative systematic review (QSR) for observational studies related to nutritional epidemiology is the “highest versus lowest intake” method (HLM), in which only the information concerning the effect size (ES) of the highest category of a food item is collected on the basis of its lowest category. However, in the interval collapsing method (ICM), a method suggested to enable a maximum utilization of all available information, the ES information ...

  5. Use of dual isotope tracers in biomedical research

    NARCIS (Netherlands)

    Stellaard, F

    2005-01-01

    Biomedical stable isotope studies involve administration of tracer and measurement of isotope enrichment in blood, urine, feces or breath. The aim of the studies is to gather quantitative information about a specific metabolic function. However, the measured isotope enrichment may be affected by oth

  6. Schroedinger Eigenmaps for the Analysis of Bio-Medical Data

    CERN Document Server

    Czaja, Wojciech

    2011-01-01

    We introduce Schroedinger Eigenmaps, a new semi-supervised manifold learning and recovery technique. This method is based on an implementation of graph Schroedinger operators with appropriately constructed barrier potentials as carriers of labeled information. We apply it to analyze two complex bio-medical datasets: multispectral retinal images and microarray gene expressions.

  7. A New Paradigm for the Extraction of Information:Application to Enhancement of Visual Information in a Medical Application

    Institute of Scientific and Technical Information of China (English)

    V. Courboulay; A. Histace; M. Ménard; C.Cavaro-Menard

    2004-01-01

    The noninvasive evaluation of the cardiac function presents a great interest for the diagnosis of cardiovascular diseases. Tagged cardiac MRI allows the measurement of anatomical and functional myocardial parameters. This protocol generates a dark grid which is deformed with the myocardium displacement on both Short-Axis (SA) and Long-Axis (LA) frames in a time sequence. Visual evaluation of the grid deformation allows the estimation of the displacement inside the myocardium. The work described in this paper aims to make robust and reliable the visual enhancement of the grid tags on cardiac MRI sequences, thanks to an informational formalism based on Extreme Physical Informational (EPI). This approach leads to the development of an original diffusion pre-processing allowing us to make better the robustness of the visual detection and the following of the grid of tags.

  8. Science gateways for biomedical big data analysis

    NARCIS (Netherlands)

    S. Shahand

    2015-01-01

    Biomedical researchers are facing data deluge challenges such as dealing with large volume of complex heterogeneous data and complex and computationally demanding data processing methods. Such scale and complexity of biomedical research requires multi-disciplinary collaboration between scientists fr

  9. Biomedical applications of supermagnetic nanoparticles

    Czech Academy of Sciences Publication Activity Database

    Horák, Daniel; Babič, Michal; Kubinová, Šárka; Schmiedtová, M.; Poledne, R.; Herynek, V.; Sundstrom, T.; Altanerova, V.; Borisova, T.

    Prague : Institute of Macromolecular Chemistry AS CR, 2015. s. 18. [Research Postdoctoral Colloquium. 14.05.2015, Prague] R&D Projects: GA MŠk(CZ) EE2.3.30.0029; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61389013 ; RVO:68378041 Keywords : biomedical applications * supermagnetic nanoparticles Subject RIV: CE - Biochemistry

  10. National Space Biomedical Research Institute

    Science.gov (United States)

    2004-01-01

    This report outlines the National Space Biomedical Research Institute's (NSBRI) activities during FY 2004, the Institute's seventh year. It is prepared in accordance with Cooperative Agreement NCC 9-58 between NASA's Lyndon B. Johnson Space Center (JSC) and the Institute's lead institution, Baylor College of Medicine.

  11. Integrated Biomaterials for Biomedical Technology

    CERN Document Server

    Ramalingam, Murugan; Ramakrishna, Seeram; Kobayashi, Hisatoshi

    2012-01-01

    This cutting edge book provides all the important aspects dealing with the basic science involved in materials in biomedical technology, especially structure and properties, techniques and technological innovations in material processing and characterizations, as well as the applications. The volume consists of 12 chapters written by acknowledged experts of the biomaterials field and covers a wide range of topics and applications.

  12. Mathematical modeling in biomedical imaging

    CERN Document Server

    2009-01-01

    This volume gives an introduction to a fascinating research area to applied mathematicians. It is devoted to providing the exposition of promising analytical and numerical techniques for solving challenging biomedical imaging problems, which trigger the investigation of interesting issues in various branches of mathematics.

  13. UMLS Content Views Appropriate for NLP Processing of the Biomedical Literature vs. Clinical Text

    OpenAIRE

    Demner-Fushman, Dina; Mork, James G; Shooshan, Sonya E.; Aronson, Alan R.

    2010-01-01

    Identification of medical terms in free text is a first step in such Natural Language Processing (NLP) tasks as automatic indexing of biomedical literature and extraction of patients’ problem lists from the text of clinical notes. Many tools developed to perform these tasks use biomedical knowledge encoded in the Unified Medical Language System (UMLS) Metathesaurus. We continue our exploration of automatic approaches to creation of subsets (UMLS content views) which can support NLP processing...

  14. The New Biomedical Technology

    OpenAIRE

    Scoggin, Charles H.

    1985-01-01

    New methods for studying the genetic information of humans in health and disease are emerging from basic science laboratories. Because these approaches are yielding fundamental insights for diagnosing and treating disease, it is important that practitioners begin to understand these methods and how they are used. Methods for genetic analysis using recombinant DNA techniques consist of isolation, separation, propagation in microorganisms and molecular hybridization of DNA. The study of RNA all...

  15. Entropy-Based Algorithms in the Analysis of Biomedical Signals

    Directory of Open Access Journals (Sweden)

    Borowska Marta

    2015-12-01

    Full Text Available Biomedical signals are frequently noisy and incomplete. They produce complex and high-dimensional data sets. In these mentioned cases, the results of traditional methods of signal processing can be skewed by noise or interference present in the signal. Information entropy, as a measure of disorder or uncertainty in the data, was introduced by Shannon. To date, many different types of entropy methods have appeared with many different application areas. The purpose of this paper is to present a short overview of some methods of entropy analysis and to discuss their suitability for use in the analysis of biomedical signals.

  16. New roles & responsibilities of hospital biomedical engineering.

    Science.gov (United States)

    Frisch, P H; Stone, B; Booth, P; Lui, W

    2014-01-01

    Over the last decade the changing healthcare environment has required hospitals and specifically Biomedical Engineering to critically evaluate, optimize and adapt their operations. The focus is now on new technologies, changes to the environment of care, support requirements and financial constraints. Memorial Sloan Kettering Cancer Center (MSKCC), an NIH-designated comprehensive cancer center, has been transitioning to an increasing outpatient care environment. This transition is driving an increase in-patient acuity coupled with the need for added urgency of support and response time. New technologies, regulatory requirements and financial constraints have impacted operating budgets and in some cases, resulted in a reduction in staffing. Specific initiatives, such as the Joint Commission's National Patient Safety Goals, requirements for an electronic medical record, meaningful use and ICD10 have caused institutions to reevaluate their operations and processes including requiring Biomedical Engineering to manage new technologies, integrations and changes in the electromagnetic environment, while optimizing operational workflow and resource utilization. This paper addresses the new and expanding responsibilities and approach of Biomedical Engineering organizations, specifically at MSKCC. It is suggested that our experience may be a template for other organizations facing similar problems. Increasing support is necessary for Medical Software - Medical Device Data Systems in the evolving wireless environment, including RTLS and RFID. It will be necessary to evaluate the potential impact on the growing electromagnetic environment, on connectivity resulting in the need for dynamic and interactive testing and the growing demand to establish new and needed operational synergies with Information Technology operations and other operational groups within the institution, such as nursing, facilities management, central supply, and the user departments. PMID:25570742

  17. Automated Methods to Extract Patient New Information from Clinical Notes in Electronic Health Record Systems

    Science.gov (United States)

    Zhang, Rui

    2013-01-01

    The widespread adoption of Electronic Health Record (EHR) has resulted in rapid text proliferation within clinical care. Clinicians' use of copying and pasting functions in EHR systems further compounds this by creating a large amount of redundant clinical information in clinical documents. A mixture of redundant information (especially outdated…

  18. A new fast method for earthquake-triggered secondary geological hazard information extraction from high-resolution remote sensing imagery

    International Nuclear Information System (INIS)

    Earthquake-triggered secondary geological hazards usually significantly augment the destruction caused by an earthquake due to their rapid impact, long duration and high repeatability. Seismic disaster losses are often exacerbated and can cause substantial difficulties for rescue, relief and post-disaster reconstruction. The quick acquisition of disaster information is important to aid relief efforts in the 72 critical hours after an earthquake occurs. Currently, computer-aided interpretation of remotely sensed imagery of a single time phase plays a central role in information extraction for geological hazards, whereas automated interpretation is relatively limited. Because high-resolution remotely sensed imagery is rich in textures and spatial details of the imaged objects, such as their size, shape and neighborhood relationship, geologic hazard investigations employing such imagery can offer more accurate results. In this paper, a rapid method for earthquake-triggered secondary geological hazard information extraction from high-resolution remotely sensed imagery is proposed and is demonstrated to be a fast and automatic method that uses multiple image features of a hazard

  19. BIOMEDICAL WASTE MANAGEMENT AND THEIR POSSIBLE HEALTH RISKS WITH CONTROLLING MEASURES IN BAREILLY CITY, UP, INDIA

    Directory of Open Access Journals (Sweden)

    Amrita Singh

    2014-12-01

    Full Text Available Biomedical waste has become a serious health hazard in many countries including India. The purpose of the study is to get background information about the disposal of hospital wastes and their health risks on our society. The MoEF notified Bio-medical waste and handling rules 1998 in July 1998. According to it every hospital generating Bio-medical waste needs to set a proper treatment facility nearby to ensure degradation of Bio-medical waste as the untreated Bio-medical waste should not be kept beyond 48 hours. In this research we try to elaborate the effects of Bio-medical waste and will also discuss its treatment techniques in Bareilly city. The studies were carried out for a three month i.e. from January 2012 to March 2012. The objective of this study was to critically evaluate the existing management practices of biomedical waste and its possible health risks on our environment. A detailed study of major hospitals (Government and Private of Bareilly city was carried out to assess the current situation of Bio-medical waste generation and management. The results of the study demonstrate that there is a need of strict enforcement of legal provisions and a better environmental management system for the disposal of biomedical waste.

  20. Algal lectins as promising biomolecules for biomedical research.

    Science.gov (United States)

    Singh, Ram Sarup; Thakur, Shivani Rani; Bansal, Parveen

    2015-02-01

    Lectins are natural bioactive ubiquitous proteins or glycoproteins of non-immune response that bind reversibly to glycans of glycoproteins, glycolipids and polysaccharides possessing at least one non-catalytic domain causing agglutination. Some of them consist of several carbohydrate-binding domains which endow them with the properties of cell agglutination or precipitation of glycoconjugates. Lectins are rampant in nature from plants, animals and microorganisms. Among microorganisms, algae are the potent source of lectins with unique properties specifically from red algae. The demand of peculiar and neoteric biologically active substances has intensified the developments on isolation and biomedical applications of new algal lectins. Comprehensively, algal lectins are used in biomedical research for antiviral, antinociceptive, anti-inflammatory, anti-tumor activities, etc. and in pharmaceutics for the fabrication of cost-effective protein expression systems and nutraceutics. In this review, an attempt has been made to collate the information on various biomedical applications of algal lectins. PMID:23855360

  1. Advanced Biomedical Computing Center (ABCC) | DSITP

    Science.gov (United States)

    The Advanced Biomedical Computing Center (ABCC), located in Frederick Maryland (MD), provides HPC resources for both NIH/NCI intramural scientists and the extramural biomedical research community. Its mission is to provide HPC support, to provide collaborative research, and to conduct in-house research in various areas of computational biology and biomedical research.

  2. Biomedical informatics discovering knowledge in big data

    CERN Document Server

    Holzinger, Andreas

    2014-01-01

    This book provides a broad overview of the topic Bioinformatics (medical informatics + biological information) with a focus on data, information and knowledge. From data acquisition and storage to visualization, privacy, regulatory, and other practical and theoretical topics, the author touches on several fundamental aspects of the innovative interface between the medical and computational domains that form biomedical informatics. Each chapter starts by providing a useful inventory of definitions and commonly used acronyms for each topic, and throughout the text, the reader finds several real-world examples, methodologies, and ideas that complement the technical and theoretical background. Also at the beginning of each chapter a new section called "key problems", has been added, where the author discusses possible traps and unsolvable or major problems. This new edition includes new sections at the end of each chapter, called "future outlook and research avenues," providing pointers to future challenges.

  3. Direct measurement of single soft lipid nano-tubes: nano-scale information extracted in non-invasive manner

    OpenAIRE

    Yamamoto, Akihisa; Ichikawa, Masatoshi

    2012-01-01

    We investigated the dynamics of single soft nano-tubes of phospholipids to extract nano-scale information such as size of tube, which are several tens to hundreds of nano-meters thick. The scaling law of the nano-tube dynamics in quasi-2-dimensional space was revealed to be constituent with that of a polymer. The dynamic properties of the tubes obtained from direct observation by fluorescent microscopy, such as their persistence length, enable us to access the nano-scale characteristics throu...

  4. Factors affecting the extraction of absorbed dose information in 3d polymer gel dosimeters by X-ray computed tomography

    International Nuclear Information System (INIS)

    It has been shown that a post irradiation change in the linear attenuation coefficient, μ of a polymer gel dosimeter can be measured by use of X-ray computerised tomography (CT). It is postulated that the change in μ may be primarily due to a change in physical density, ρ of the polymer gel dosimeter. In this work we examine the relationship between μ and ρ in a polymer gel dosimeter and consider the implications of a density change in relation to spatial resolution of the dosimeter. Other factors affecting the extraction of accurate dose information from polymer gel dosimeters are considered, such as imaging protocols and phantom design

  5. Exploiting the performance of dictionary-based bio-entity name recognition in biomedical literature.

    Science.gov (United States)

    Yang, Zhihao; Lin, Hongfei; Li, Yanpeng

    2008-08-01

    Bio-entity name recognition is the key step for information extraction from biomedical literature. This paper presents a dictionary-based bio-entity name recognition approach. The approach expands the bio-entity name dictionary via the Abbreviation Definitions identifying algorithm, improves the recall rate through the improved edit distance algorithm and adopts some post-processing methods including Pre-keyword and Post-keyword expansion, Part of Speech expansion, merge of adjacent bio-entity names and the exploitation of the contextual cues to further improve the performance. Experiment results show that with this approach even an internal dictionary-based system could achieve a fairly good performance. PMID:18467180

  6. Functional network and its application to extract information from chaotic communication

    Institute of Scientific and Technical Information of China (English)

    李卫斌; 焦李成

    2004-01-01

    In chaotic communication system, the useful signal is hidden in chaotic signal, so the general method does not work well. Due to the random feature of chaotic signal, a functional network-based method is presented. In this method,the neural functions are selected from some complete function set for the functional network to reconstruct the chaotic signal, so the useful signal hidden in chaotic background is extracted. In addition, its learning algorithm is presented here and the example proves its good preformance.

  7. SEMANTIC INFORMATION EXTRACTION FROM MULTISPECTRAL GEOSPATIAL IMAGERY VIA A FLEXIBLE FRAMEWORK

    Energy Technology Data Exchange (ETDEWEB)

    Gleason, Shaun Scott [ORNL; Ferrell, Regina Kay [ORNL; Cheriyadat, Anil M [ORNL; Vatsavai, Raju [ORNL; De, Soumya [Missouri University of Science and Technology

    2010-01-01

    Identification and automatic labeling of facilities in high-resolution satellite images is a challenging task as the current thematic classification schemes and the low-level image features are not good enough to capture complex objects and their spatial relationships. In this paper we present a novel algorithm framework for automated semantic labeling of large image collections. The framework consists of various segmentation, feature extraction, vector quantization, and Latent Dirichlet Allocation modules. Initial experimental results show promise as well as the challenges in semantic classification technology development for nuclear proliferation monitoring.

  8. Hydrography, Spring locations in Arizona incorporating information extracted from both the USGS Geonames database and from USGS Digital Line Graphs (DLG's)., Published in 1993, Arizona State Land Department.

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — This Hydrography dataset as of 1993. It is described as 'Spring locations in Arizona incorporating information extracted from both the USGS Geonames database and...

  9. Wavelet analysis of molecular dynamics: Efficient extraction of time-frequency information in ultrafast optical processes

    Energy Technology Data Exchange (ETDEWEB)

    Prior, Javier; Castro, Enrique [Departamento de Física Aplicada, Universidad Politécnica de Cartagena, Cartagena 30202 (Spain); Chin, Alex W. [Theory of Condensed Matter Group, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Almeida, Javier; Huelga, Susana F.; Plenio, Martin B. [Institut für Theoretische Physik, Albert-Einstein-Allee 11, Universität Ulm, D-89069 Ulm (Germany)

    2013-12-14

    New experimental techniques based on nonlinear ultrafast spectroscopies have been developed over the last few years, and have been demonstrated to provide powerful probes of quantum dynamics in different types of molecular aggregates, including both natural and artificial light harvesting complexes. Fourier transform-based spectroscopies have been particularly successful, yet “complete” spectral information normally necessitates the loss of all information on the temporal sequence of events in a signal. This information though is particularly important in transient or multi-stage processes, in which the spectral decomposition of the data evolves in time. By going through several examples of ultrafast quantum dynamics, we demonstrate that the use of wavelets provide an efficient and accurate way to simultaneously acquire both temporal and frequency information about a signal, and argue that this greatly aids the elucidation and interpretation of physical process responsible for non-stationary spectroscopic features, such as those encountered in coherent excitonic energy transport.

  10. [Big data, medical language and biomedical terminology systems].

    Science.gov (United States)

    Schulz, Stefan; López-García, Pablo

    2015-08-01

    A variety of rich terminology systems, such as thesauri, classifications, nomenclatures and ontologies support information and knowledge processing in health care and biomedical research. Nevertheless, human language, manifested as individually written texts, persists as the primary carrier of information, in the description of disease courses or treatment episodes in electronic medical records, and in the description of biomedical research in scientific publications. In the context of the discussion about big data in biomedicine, we hypothesize that the abstraction of the individuality of natural language utterances into structured and semantically normalized information facilitates the use of statistical data analytics to distil new knowledge out of textual data from biomedical research and clinical routine. Computerized human language technologies are constantly evolving and are increasingly ready to annotate narratives with codes from biomedical terminology. However, this depends heavily on linguistic and terminological resources. The creation and maintenance of such resources is labor-intensive. Nevertheless, it is sensible to assume that big data methods can be used to support this process. Examples include the learning of hierarchical relationships, the grouping of synonymous terms into concepts and the disambiguation of homonyms. Although clear evidence is still lacking, the combination of natural language technologies, semantic resources, and big data analytics is promising. PMID:26077872

  11. Toward a Structured Information Retrieval System on the Web: Automatic Structure Extraction of Web Pages

    OpenAIRE

    Géry, Mathias; Chevallet, Jean-Pierre

    2001-01-01

    The World Wide Web is a distributed, heterogeneous and semi-structured information space. With the growth of available data, retrieving interesting information is becoming quite difficult and classical search engines give often very poor results. The Web is changing very quickly, and search engines mainly use old and well-known IR techniques. One of the main problems is the lack of explicit HTML page structure, and more generally the lack of explicit Web sites structure. We show in this paper...

  12. Time-resolved photoemission by attosecond streaking: extraction of time information

    OpenAIRE

    Nagele, S; Pazourek, R; Feist, J.; Doblhoff-Dier, K; Lemell, C.; Tőkési, K; Burgdörfer, J.

    2011-01-01

    Attosecond streaking of atomic photoemission holds the promise to provide unprecedented information on the release time of the photoelectron. We show that attosecond streaking phase shifts indeed contain timing (or spectral phase) information associated with the Eisenbud-Wigner-Smith time delay matrix of quantum scattering. However, this is only accessible if the influence of the streaking infrared (IR) field on the emission process is properly accounted for. The IR probe field can strongly m...

  13. Investigation of the Impact of Extracting and Exchanging Health Information by Using Internet and Social Networks

    Science.gov (United States)

    Pistolis, John; Zimeras, Stelios; Chardalias, Kostas; Roupa, Zoe; Fildisis, George; Diomidous, Marianna

    2016-01-01

    Introduction: Social networks (1) have been embedded in our daily life for a long time. They constitute a powerful tool used nowadays for both searching and exchanging information on different issues by using Internet searching engines (Google, Bing, etc.) and Social Networks (Facebook, Twitter etc.). In this paper, are presented the results of a research based on the frequency and the type of the usage of the Internet and the Social Networks by the general public and the health professionals. Objectives: The objectives of the research were focused on the investigation of the frequency of seeking and meticulously searching for health information in the social media by both individuals and health practitioners. The exchanging of information is a procedure that involves the issues of reliability and quality of information. Methods: In this research, by using advanced statistical techniques an effort is made to investigate the participant’s profile in using social networks for searching and exchanging information on health issues. Results: Based on the answers 93 % of the people, use the Internet to find information on health-subjects. Considering principal component analysis, the most important health subjects were nutrition (0.719 %), respiratory issues (0.79 %), cardiological issues (0.777%), psychological issues (0.667%) and total (73.8%). Conclusions: The research results, based on different statistical techniques revealed that the 61.2% of the males and 56.4% of the females intended to use the social networks for searching medical information. Based on the principal components analysis, the most important sources that the participants mentioned, were the use of the Internet and social networks for exchanging information on health issues. These sources proved to be of paramount importance to the participants of the study. The same holds for nursing, medical and administrative staff in hospitals. PMID:27482135

  14. Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy

    International Nuclear Information System (INIS)

    Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis

  15. Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Konuma, Tsuyoshi [Icahn School of Medicine at Mount Sinai, Department of Structural and Chemical Biology (United States); Harada, Erisa [Suntory Foundation for Life Sciences, Bioorganic Research Institute (Japan); Sugase, Kenji, E-mail: sugase@sunbor.or.jp, E-mail: sugase@moleng.kyoto-u.ac.jp [Kyoto University, Department of Molecular Engineering, Graduate School of Engineering (Japan)

    2015-12-15

    Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.

  16. Multilingual information identification and extraction from imaged documents using optical correlator

    Science.gov (United States)

    Stalcup, Bruce W.; Brower, James; Vaughn, Lou; Vertuno, Mike

    2002-11-01

    Most organizations usually have large archives of paper documents that they maintain. These archives typically contain valuable information and data, which are imaged to provide electronic access. However, once a document is either printed or imaged, these organizations had no efficient method of retrieving information from these documents. The only methods available to retrieve information from them were to either manually read them or to convert them to ASCII text using optical character recognition (OCR). For most of the archives with large numbers of documents, these methods are problematic. Manual searches are not feasible. OCR, on the other hand, can be CPU intensive and prone to error. In addition, for many foreign languages, OCR engines do not exist. By contrast, our system provides an innovative approach to the problem of retrieving information from imaged document archives utilizing a client/server architecture. Since its beginning in 1999, we have made significant advances in the development of a system that employs optical correlation (OC) technology (either software or hardware) to access directly the textual and graphic information contained in imaged paper documents therefore eliminating the OCR process. It provides a fast, accurate means of accessing this information directly from multilingual documents. In addition, our system can also rapidly and accurately detect the presence of duplicate documents within an archive using optical correlation techniques. In this paper, we describe the present system and selected examples of its capabilities. We also present some performance results (accuracy, speed, etc.) against test document sets.

  17. Current practice of public involvement activities in biomedical research and innovation: a systematic qualitative review.

    Directory of Open Access Journals (Sweden)

    Jonas Lander

    Full Text Available BACKGROUND: A recent report from the British Nuffield Council on Bioethics associated 'emerging biotechnologies' with a threefold challenge: 1 uncertainty about outcomes, 2 diverse public views on the values and implications attached to biotechnologies and 3 the possibility of creating radical changes regarding societal relations and practices. To address these challenges, leading international institutions stress the need for public involvement activities (PIAs. The objective of this study was to assess the state of PIA reports in the field of biomedical research. METHODS: PIA reports were identified via a systematic literature search. Thematic text analysis was employed for data extraction. RESULTS: After filtering, 35 public consultation and 11 public participation studies were included in this review. Analysis and synthesis of all 46 PIA studies resulted in 6 distinguishable PIA objectives and 37 corresponding PIA methods. Reports of outcome translation and PIA evaluation were found in 9 and 10 studies respectively (20% and 22%. The paper presents qualitative details. DISCUSSION: The state of PIAs on biomedical research and innovation is characterized by a broad range of methods and awkward variation in the wording of objectives. Better comparability of PIAs might improve the translation of PIA findings into further policy development. PIA-specific reporting guidelines would help in this regard. The modest level of translation efforts is another pointer to the "deliberation to policy gap". The results of this review could inform the design of new PIAs and future efforts to improve PIA comparability and outcome translation.

  18. Architecture and data processing alternatives for the TSE computer. Volume 2: Extraction of topological information from an image by the Tse computer

    Science.gov (United States)

    Jones, J. R.; Bodenheimer, R. E.

    1976-01-01

    A simple programmable Tse processor organization and arithmetic operations necessary for extraction of the desired topological information are described. Hardware additions to this organization are discussed along with trade-offs peculiar to the tse computing concept. An improved organization is presented along with the complementary software for the various arithmetic operations. The performance of the two organizations is compared in terms of speed, power, and cost. Software routines developed to extract the desired information from an image are included.

  19. Resolving anaphoras for the extraction of drug-drug interactions in pharmacological documents

    OpenAIRE

    Segura-Bedmar, Isabel; Crespo, Mario; de Pablo-Sánchez, César; Martínez, Paloma

    2010-01-01

    Background Drug-drug interactions are frequently reported in the increasing amount of biomedical literature. Information Extraction (IE) techniques have been devised as a useful instrument to manage this knowledge. Nevertheless, IE at the sentence level has a limited effect because of the frequent references to previous entities in the discourse, a phenomenon known as 'anaphora'. DrugNerAR, a drug anaphora resolution system is presented to address the problem of co-referring expressions in ph...

  20. Mathematics and physics of emerging biomedical imaging

    International Nuclear Information System (INIS)

    Although the mathematical sciences were used in a general way for image processing, they were of little importance in biomedical work until the development in the 1970s of computed tomography (CT) for the imaging of x-rays and isotope emission tomography. In the 1980s, MRI eclipsed the other modalities in many ways as the most informative medical imaging methodology. Besides these well-established techniques, computer-based mathematical methods are being explored in applications to other well-known methods, such as ultrasound and electroencephalography, as well as new techniques of optical imaging, impedance tomography, and magnetic source imaging. It is worth pointing out that, while the final images of many of these techniques bear many similarities to each other, the technologies involved in each are completely different and the parameters represented in the images are very different in character as well as in medical usefulness. In each case, rather different mathematical or statistical models are used, with different equations. One common thread is the paradigm of reconstruction from indirect measurements--this is the unifying theme of this report. The imaging methods used in biomedical applications that this report discusses include: (1) x-ray projection imaging; (2) x-ray computed tomography (CT); (3) magnetic resonance imaging (MRI) and magnetic resonance spectroscopy; (4) single photon emission computed tomography (SPECT); (5) positron emission tomography (PET); (6) ultrasonics; (7) electrical source imaging (ESI); (8) electrical impedance tomography (EIT); (9) magnetic source imaging (MSI); and (10) medical optical imaging