WorldWideScience

Sample records for accelerated similarity searching

  1. SW#db: GPU-Accelerated Exact Sequence Similarity Database Search.

    Matija Korpar

    Full Text Available In recent years we have witnessed a growth in sequencing yield, the number of samples sequenced, and as a result-the growth of publicly maintained sequence databases. The increase of data present all around has put high requirements on protein similarity search algorithms with two ever-opposite goals: how to keep the running times acceptable while maintaining a high-enough level of sensitivity. The most time consuming step of similarity search are the local alignments between query and database sequences. This step is usually performed using exact local alignment algorithms such as Smith-Waterman. Due to its quadratic time complexity, alignments of a query to the whole database are usually too slow. Therefore, the majority of the protein similarity search methods prior to doing the exact local alignment apply heuristics to reduce the number of possible candidate sequences in the database. However, there is still a need for the alignment of a query sequence to a reduced database. In this paper we present the SW#db tool and a library for fast exact similarity search. Although its running times, as a standalone tool, are comparable to the running times of BLAST, it is primarily intended to be used for exact local alignment phase in which the database of sequences has already been reduced. It uses both GPU and CPU parallelization and was 4-5 times faster than SSEARCH, 6-25 times faster than CUDASW++ and more than 20 times faster than SSW at the time of writing, using multiple queries on Swiss-prot and Uniref90 databases.

  2. Approximate similarity search

    Amato, Giuseppe

    2000-01-01

    Similarity searching is fundamental in various application areas. Recently it has attracted much attention in the database community because of the growing need to deal with large volume of data. Consequently, efficiency has become a matter of concern in design. Although much has been done to develop structures able to perform fast similarity search, results are still not satisfactory, and more research is needed. The performance of similarity search for complex features deteriorates and does...

  3. Multivariate Time Series Similarity Searching

    Jimin Wang; Yuelong Zhu; Shijin Li; Dingsheng Wan; Pengcheng Zhang

    2014-01-01

    Multivariate time series (MTS) datasets are very common in various financial, multimedia, and hydrological fields. In this paper, a dimension-combination method is proposed to search similar sequences for MTS. Firstly, the similarity of single-dimension series is calculated; then the overall similarity of the MTS is obtained by synthesizing each of the single-dimension similarity based on weighted BORDA voting method. The dimension-combination method could use the existing similarity searchin...

  4. Scaling Group Testing Similarity Search

    Iscen, Ahmet; Amsaleg, Laurent; Furon, Teddy

    2016-01-01

    The large dimensionality of modern image feature vectors, up to thousands of dimensions, is challenging the high dimensional indexing techniques. Traditional approaches fail at returning good quality results within a response time that is usable in practice. However, similarity search techniques inspired by the group testing framework have recently been proposed in an attempt to specifically defeat the curse of dimensionality. Yet, group testing does not scale and fails at indexing very large...

  5. Accelerated Profile HMM Searches.

    Sean R Eddy

    2011-10-01

    Full Text Available Profile hidden Markov models (profile HMMs and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the "multiple segment Viterbi" (MSV algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call "sparse rescaling". These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches.

  6. Semantically enabled image similarity search

    Casterline, May V.; Emerick, Timothy; Sadeghi, Kolia; Gosse, C. A.; Bartlett, Brent; Casey, Jason

    2015-05-01

    Georeferenced data of various modalities are increasingly available for intelligence and commercial use, however effectively exploiting these sources demands a unified data space capable of capturing the unique contribution of each input. This work presents a suite of software tools for representing geospatial vector data and overhead imagery in a shared high-dimension vector or embedding" space that supports fused learning and similarity search across dissimilar modalities. While the approach is suitable for fusing arbitrary input types, including free text, the present work exploits the obvious but computationally difficult relationship between GIS and overhead imagery. GIS is comprised of temporally-smoothed but information-limited content of a GIS, while overhead imagery provides an information-rich but temporally-limited perspective. This processing framework includes some important extensions of concepts in literature but, more critically, presents a means to accomplish them as a unified framework at scale on commodity cloud architectures.

  7. Biosequence Similarity Search on the Mercury System

    Krishnamurthy, Praveen; Buhler, Jeremy; Chamberlain, Roger; Franklin, Mark; Gyang, Kwame; Jacob, Arpith; Lancaster, Joseph

    2007-01-01

    Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high...

  8. Similarity Measures for Boolean Search Request Formulations.

    Radecki, Tadeusz

    1982-01-01

    Proposes a means for determining the similarity between search request formulations in online information retrieval systems, and discusses the use of similarity measures for clustering search formulations and document files in such systems. Experimental results using the proposed methods are presented in three tables. A reference list is provided.…

  9. Protein structural similarity search by Ramachandran codes

    Chang Chih-Hung; Huang Po-Jung; Lo Wei-Cheng; Lyu Ping-Chiang

    2007-01-01

    Abstract Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we ai...

  10. Protein structural similarity search by Ramachandran codes

    Chang Chih-Hung

    2007-08-01

    Full Text Available Abstract Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases. Results We propose a new linear encoding method, SARST (Structural similarity search Aided by Ramachandran Sequential Transformation. SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms. Conclusion As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era.

  11. Secure sketch search for document similarity

    Örencik, Cengiz; Orencik, Cengiz; Alewiwi, Mahmoud Khaled; SAVAŞ, Erkay; Savas, Erkay

    2015-01-01

    Document similarity search is an important problem that has many applications especially in outsourced data. With the wide spread of cloud computing, users tend to outsource their data to remote servers which are not necessarily trusted. This leads to the problem of protecting the privacy of sensitive data. We design and implement two secure similarity search schemes for textual documents utilizing locality sensitive hashing techniques for cosine similarity. While the first one provides very ...

  12. Efficient Authentication of Outsourced String Similarity Search

    Dong, Boxiang; Wang, Hui

    2016-01-01

    Cloud computing enables the outsourcing of big data analytics, where a third party server is responsible for data storage and processing. In this paper, we consider the outsourcing model that provides string similarity search as the service. In particular, given a similarity search query, the service provider returns all strings from the outsourced dataset that are similar to the query string. A major security concern of the outsourcing paradigm is to authenticate whether the service provider...

  13. Mobile P2P Fast Similarity Search

    Bocek, T; Hecht, F. V.; Hausheer, D; Hunt, E; Stiller, B.

    2009-01-01

    In informal data sharing environments, misspellings cause problems for data indexing and retrieval. This is even more pronounced in mobile environments, in which devices with limited input devices are used. In a mobile environment, similarity search algorithms for finding misspelled data need to account for limited CPU and bandwidth. This demo shows P2P fast similarity search (P2PFastSS) running on mobile phones and laptops that is tailored to uncertain data entry and use...

  14. Multiresolution Similarity Search in Image Databases

    Heczko, Martin; Hinneburg, Alexander; Keim, Daniel A.; Wawryniuk, Markus

    2004-01-01

    Typically searching image collections is based on features of the images. In most cases the features are based on the color histogram of the images. Similarity search based on color histograms is very efficient, but the quality of the search results is often rather poor. One of the reasons is that histogram-based systems only support a specific form of global similarity using the whole histogram as one vector. But there is more information in a histogram than the distribution of colors. This ...

  15. Representation Independent Proximity and Similarity Search

    Chodpathumwan, Yodsawalai; Aleyasin, Amirhossein; Termehchy, Arash; Sun, Yizhou

    2015-01-01

    Finding similar or strongly related entities in a graph database is a fundamental problem in data management and analytics with applications in similarity query processing, entity resolution, and pattern matching. Similarity search algorithms usually leverage the structural properties of the data graph to quantify the degree of similarity or relevance between entities. Nevertheless, the same information can be represented in many different structures and the structural properties observed ove...

  16. Web Search Results Summarization Using Similarity Assessment

    Sawant V.V.

    2014-06-01

    Full Text Available Now day’s internet has become part of our life, the WWW is most important service of internet because it allows presenting information such as document, imaging etc. The WWW grows rapidly and caters to a diversified levels and categories of users. For user specified results web search results are extracted. Millions of information pouring online, users has no time to surf the contents completely .Moreover the information available is repeated or duplicated in nature. This issue has created the necessity to restructure the search results that could yield results summarized. The proposed approach comprises of different feature extraction of web pages. Web page visual similarity assessment has been employed to address the problems in different fields including phishing, web archiving, web search engine etc. In this approach, initially by enters user query the number of search results get stored. The Earth Mover's Distance is used to assessment of web page visual similarity, in this technique take the web page as a low resolution image, create signature of that web page image with color and co-ordinate features .Calculate the distance between web pages by applying EMD method. Compute the Layout Similarity value by using tag comparison algorithm and template comparison algorithm. Textual similarity is computed by using cosine similarity, and hyperlink analysis is performed to compute outward links. The final similarity value is calculated by fusion of layout, text, hyperlink and EMD value. Once the similarity matrix is found clustering is employed with the help of connected component. Finally group of similar web pages i.e. summarized results get displayed to user. Experiment conducted to demonstrate the effectiveness of four methods to generate summarized result on different web pages and user queries also.

  17. SEAL: Spatio-Textual Similarity Search

    Fan, Ju; Zhou, Lizhu; Chen, Shanshan; Hu, Jun

    2012-01-01

    Location-based services (LBS) have become more and more ubiquitous recently. Existing methods focus on finding relevant points-of-interest (POIs) based on users' locations and query keywords. Nowadays, modern LBS applications generate a new kind of spatio-textual data, regions-of-interest (ROIs), containing region-based spatial information and textual description, e.g., mobile user profiles with active regions and interest tags. To satisfy search requirements on ROIs, we study a new research problem, called spatio-textual similarity search: Given a set of ROIs and a query ROI, we find the similar ROIs by considering spatial overlap and textual similarity. Spatio-textual similarity search has many important applications, e.g., social marketing in location-aware social networks. It calls for an efficient search method to support large scales of spatio-textual data in LBS systems. To this end, we introduce a filter-and-verification framework to compute the answers. In the filter step, we generate signatures for ...

  18. New similarity search based glioma grading

    MR-based differentiation between low- and high-grade gliomas is predominately based on contrast-enhanced T1-weighted images (CE-T1w). However, functional MR sequences as perfusion- and diffusion-weighted sequences can provide additional information on tumor grade. Here, we tested the potential of a recently developed similarity search based method that integrates information of CE-T1w and perfusion maps for non-invasive MR-based glioma grading. We prospectively included 37 untreated glioma patients (23 grade I/II, 14 grade III gliomas), in whom 3T MRI with FLAIR, pre- and post-contrast T1-weighted, and perfusion sequences was performed. Cerebral blood volume, cerebral blood flow, and mean transit time maps as well as CE-T1w images were used as input for the similarity search. Data sets were preprocessed and converted to four-dimensional Gaussian Mixture Models that considered correlations between the different MR sequences. For each patient, a so-called tumor feature vector (= probability-based classifier) was defined and used for grading. Biopsy was used as gold standard, and similarity based grading was compared to grading solely based on CE-T1w. Accuracy, sensitivity, and specificity of pure CE-T1w based glioma grading were 64.9%, 78.6%, and 56.5%, respectively. Similarity search based tumor grading allowed differentiation between low-grade (I or II) and high-grade (III) gliomas with an accuracy, sensitivity, and specificity of 83.8%, 78.6%, and 87.0%. Our findings indicate that integration of perfusion parameters and CE-T1w information in a semi-automatic similarity search based analysis improves the potential of MR-based glioma grading compared to CE-T1w data alone. (orig.)

  19. New similarity search based glioma grading

    Haegler, Katrin; Brueckmann, Hartmut; Linn, Jennifer [Ludwig-Maximilians-University of Munich, Department of Neuroradiology, Munich (Germany); Wiesmann, Martin; Freiherr, Jessica [RWTH Aachen University, Department of Neuroradiology, Aachen (Germany); Boehm, Christian [Ludwig-Maximilians-University of Munich, Department of Computer Science, Munich (Germany); Schnell, Oliver; Tonn, Joerg-Christian [Ludwig-Maximilians-University of Munich, Department of Neurosurgery, Munich (Germany)

    2012-08-15

    MR-based differentiation between low- and high-grade gliomas is predominately based on contrast-enhanced T1-weighted images (CE-T1w). However, functional MR sequences as perfusion- and diffusion-weighted sequences can provide additional information on tumor grade. Here, we tested the potential of a recently developed similarity search based method that integrates information of CE-T1w and perfusion maps for non-invasive MR-based glioma grading. We prospectively included 37 untreated glioma patients (23 grade I/II, 14 grade III gliomas), in whom 3T MRI with FLAIR, pre- and post-contrast T1-weighted, and perfusion sequences was performed. Cerebral blood volume, cerebral blood flow, and mean transit time maps as well as CE-T1w images were used as input for the similarity search. Data sets were preprocessed and converted to four-dimensional Gaussian Mixture Models that considered correlations between the different MR sequences. For each patient, a so-called tumor feature vector (= probability-based classifier) was defined and used for grading. Biopsy was used as gold standard, and similarity based grading was compared to grading solely based on CE-T1w. Accuracy, sensitivity, and specificity of pure CE-T1w based glioma grading were 64.9%, 78.6%, and 56.5%, respectively. Similarity search based tumor grading allowed differentiation between low-grade (I or II) and high-grade (III) gliomas with an accuracy, sensitivity, and specificity of 83.8%, 78.6%, and 87.0%. Our findings indicate that integration of perfusion parameters and CE-T1w information in a semi-automatic similarity search based analysis improves the potential of MR-based glioma grading compared to CE-T1w data alone. (orig.)

  20. Comparison of Two ``Document Similarity Search Engines''

    Poinçot, Phillipe; Lesteven, Soizick; Murtagh, Fionn

    We have developed and used the ``CDS document map'' based on neural networks (Kohonen maps) http://simbad.u-strasbg.fr/A+A/map.pl In this self-organizing map, documents are gradually clustered by subject themes. The tool is based on keywords associated with the documents. For one selected document, we locate it on the CDS document map and retrieve articles clustered in the same area. The second search engine, used by the ADS (NASA Astrophysics Data System http://cdsads.u-strasbg.fr http://adswww.harvard.edu http://ads.nao.ac.jp, has the capability to find all similar abstracts in the ADS database, with ``keyword request''. We have compared the results of the document similarity search engines, using the same set of documents. One example will be described and results will be discussed.

  1. Efficient Video Similarity Measurement and Search

    Cheung, S-C S

    2002-12-19

    The amount of information on the world wide web has grown enormously since its creation in 1990. Duplication of content is inevitable because there is no central management on the web. Studies have shown that many similar versions of the same text documents can be found throughout the web. This redundancy problem is more severe for multimedia content such as web video sequences, as they are often stored in multiple locations and different formats to facilitate downloading and streaming. Similar versions of the same video can also be found, unknown to content creators, when web users modify and republish original content using video editing tools. Identifying similar content can benefit many web applications and content owners. For example, it will reduce the number of similar answers to a web search and identify inappropriate use of copyright content. In this dissertation, they present a system architecture and corresponding algorithms to efficiently measure, search, and organize similar video sequences found on any large database such as the web.

  2. Earthquake detection through computationally efficient similarity search.

    Yoon, Clara E; O'Reilly, Ossian; Bergen, Karianne J; Beroza, Gregory C

    2015-12-01

    Seismology is experiencing rapid growth in the quantity of data, which has outpaced the development of processing algorithms. Earthquake detection-identification of seismic events in continuous data-is a fundamental operation for observational seismology. We developed an efficient method to detect earthquakes using waveform similarity that overcomes the disadvantages of existing detection methods. Our method, called Fingerprint And Similarity Thresholding (FAST), can analyze a week of continuous seismic waveform data in less than 2 hours, or 140 times faster than autocorrelation. FAST adapts a data mining algorithm, originally designed to identify similar audio clips within large databases; it first creates compact "fingerprints" of waveforms by extracting key discriminative features, then groups similar fingerprints together within a database to facilitate fast, scalable search for similar fingerprint pairs, and finally generates a list of earthquake detections. FAST detected most (21 of 24) cataloged earthquakes and 68 uncataloged earthquakes in 1 week of continuous data from a station located near the Calaveras Fault in central California, achieving detection performance comparable to that of autocorrelation, with some additional false detections. FAST is expected to realize its full potential when applied to extremely long duration data sets over a distributed network of seismic stations. The widespread application of FAST has the potential to aid in the discovery of unexpected seismic signals, improve seismic monitoring, and promote a greater understanding of a variety of earthquake processes. PMID:26665176

  3. Performance Evaluation and Optimization of Math-Similarity Search

    Zhang, Qun; Youssef, Abdou

    2015-01-01

    Similarity search in math is to find mathematical expressions that are similar to a user's query. We conceptualized the similarity factors between mathematical expressions, and proposed an approach to math similarity search (MSS) by defining metrics based on those similarity factors [11]. Our preliminary implementation indicated the advantage of MSS compared to non-similarity based search. In order to more effectively and efficiently search similar math expressions, MSS is further optimized. ...

  4. Self-Taught Hashing for Fast Similarity Search

    Zhang, Dell; Cai, Deng; Lu, Jinsong

    2010-01-01

    The ability of fast similarity search at large scale is of great importance to many Information Retrieval (IR) applications. A promising way to accelerate similarity search is semantic hashing which designs compact binary codes for a large number of documents so that semantically similar documents are mapped to similar codes (within a short Hamming distance). Although some recently proposed techniques are able to generate high-quality codes for documents known in advance, obtaining the codes for previously unseen documents remains to be a very challenging problem. In this paper, we emphasise this issue and propose a novel Self-Taught Hashing (STH) approach to semantic hashing: we first find the optimal $l$-bit binary codes for all documents in the given corpus via unsupervised learning, and then train $l$ classifiers via supervised learning to predict the $l$-bit code for any query document unseen before. Our experiments on three real-world text datasets show that the proposed approach using binarised Laplaci...

  5. Non-accelerator neutrino mass searches

    Zuber, K.

    2000-01-01

    The current status of non-accelerator based searches for effects of a non-vanishing neutrino mass is reviewed. Beside the direct kinematical methods this includes searches for magnetic moments and a discussion of the solar neutrino problem. Double beta decay is not included.

  6. Web Search Results Summarization Using Similarity Assessment

    Sawant V.V.; Takale S.A.

    2014-01-01

    Now day’s internet has become part of our life, the WWW is most important service of internet because it allows presenting information such as document, imaging etc. The WWW grows rapidly and caters to a diversified levels and categories of users. For user specified results web search results are extracted. Millions of information pouring online, users has no time to surf the contents completely .Moreover the information available is repeated or duplicated in nature. This issue has created th...

  7. Outsourced similarity search on metric data assets

    Yiu, Man Lung; Assent, Ira; Jensen, Christian Søndergaard;

    2012-01-01

    This paper considers a cloud computing setting in which similarity querying of metric data is outsourced to a service provider. The data is to be revealed only to trusted users, not to the service provider or anyone else. Users query the server for the most similar data objects to a query example...

  8. A Similarity Search Using Molecular Topological Graphs

    Yoshifumi Fukunishi

    2009-01-01

    Full Text Available A molecular similarity measure has been developed using molecular topological graphs and atomic partial charges. Two kinds of topological graphs were used. One is the ordinary adjacency matrix and the other is a matrix which represents the minimum path length between two atoms of the molecule. The ordinary adjacency matrix is suitable to compare the local structures of molecules such as functional groups, and the other matrix is suitable to compare the global structures of molecules. The combination of these two matrices gave a similarity measure. This method was applied to in silico drug screening, and the results showed that it was effective as a similarity measure.

  9. Query-dependent banding (QDB for faster RNA similarity searches.

    Eric P Nawrocki

    2007-03-01

    Full Text Available When searching sequence databases for RNAs, it is desirable to score both primary sequence and RNA secondary structure similarity. Covariance models (CMs are probabilistic models well-suited for RNA similarity search applications. However, the computational complexity of CM dynamic programming alignment algorithms has limited their practical application. Here we describe an acceleration method called query-dependent banding (QDB, which uses the probabilistic query CM to precalculate regions of the dynamic programming lattice that have negligible probability, independently of the target database. We have implemented QDB in the freely available Infernal software package. QDB reduces the average case time complexity of CM alignment from LN(2.4 to LN(1.3 for a query RNA of N residues and a target database of L residues, resulting in a 4-fold speedup for typical RNA queries. Combined with other improvements to Infernal, including informative mixture Dirichlet priors on model parameters, benchmarks also show increased sensitivity and specificity resulting from improved parameterization.

  10. Fast similarity search in peer-to-peer networks

    Bocek, T; Hunt, E; Hausheer, D; Stiller, B.

    2008-01-01

    Peer-to-peer (P2P) systems show numerous advantages over centralized systems, such as load balancing, scalability, and fault tolerance, and they require certain functionality, such as search, repair, and message and data transfer. In particular, structured P2P networks perform an exact search in logarithmic time proportional to the number of peers. However, keyword similarity search in a structured P2P network remains a challenge. Similarity search for service discovery can significantly impr...

  11. Outsourced similarity search on metric data assets

    Yiu, Man Lung

    2012-02-01

    This paper considers a cloud computing setting in which similarity querying of metric data is outsourced to a service provider. The data is to be revealed only to trusted users, not to the service provider or anyone else. Users query the server for the most similar data objects to a query example. Outsourcing offers the data owner scalability and a low-initial investment. The need for privacy may be due to the data being sensitive (e.g., in medicine), valuable (e.g., in astronomy), or otherwise confidential. Given this setting, the paper presents techniques that transform the data prior to supplying it to the service provider for similarity queries on the transformed data. Our techniques provide interesting trade-offs between query cost and accuracy. They are then further extended to offer an intuitive privacy guarantee. Empirical studies with real data demonstrate that the techniques are capable of offering privacy while enabling efficient and accurate processing of similarity queries.

  12. The Time Course of Similarity Effects in Visual Search

    Guest, Duncan; Lamberts, Koen

    2011-01-01

    It is well established that visual search becomes harder when the similarity between target and distractors is increased and the similarity between distractors is decreased. However, in models of visual search, similarity is typically treated as a static, time-invariant property of the relation between objects. Data from other perceptual tasks…

  13. Search for Dark Photons with Accelerators

    Merkel Harald

    2014-01-01

    Full Text Available A dark photon as the mediator of an interaction of the dark sector is a well motivated extension of the standard model. While possible dark matter particles are heavy and seem to be beyond the reach of current accelerators, the dark photon is not necessarily heavy and might have a mass in the range of existing accelerators. In recent years, an extensive experimental program at several accelerators for the search for dark photons were established. In this talk, recent results and progress in the determination of exclusion limits with accelerators is presented.

  14. A Similarity Search Using Molecular Topological Graphs

    2009-01-01

    A molecular similarity measure has been developed using molecular topological graphs and atomic partial charges. Two kinds of topological graphs were used. One is the ordinary adjacency matrix and the other is a matrix which represents the minimum path length between two atoms of the molecule. The ordinary adjacency matrix is suitable to compare the local structures of molecules such as functional groups, and the other matrix is suitable to compare the global structures of molecules. The comb...

  15. Learning Style Similarity for Searching Infographics

    Saleh, Babak; Dontcheva, Mira; Hertzmann, Aaron; Liu, Zhicheng

    2015-01-01

    Infographics are complex graphic designs integrating text, images, charts and sketches. Despite the increasing popularity of infographics and the rapid growth of online design portfolios, little research investigates how we can take advantage of these design resources. In this paper we present a method for measuring the style similarity between infographics. Based on human perception data collected from crowdsourced experiments, we use computer vision and machine learning algorithms to learn ...

  16. Visual similarity is stronger than semantic similarity in guiding visual search for numbers

    Godwin, H.J.; Hout, M.C.; Menneer, T.

    2014-01-01

    Using a visual search task, we explored how behavior is influenced by both visual and semantic information. We recorded participants’ eye movements as they searched for a single target number in a search array of single-digit numbers (0–9). We examined the probability of fixating the various distractors as a function of two key dimensions: the visual similarity between the target and each distractor, and the semantic similarity (i.e., the numerical distance) between the target and each distra...

  17. Fast and secure similarity search in high dimensional space

    Furon, Teddy; Jégou, Hervé; Amsaleg, Laurent; Mathon, Benjamin

    2013-01-01

    Similarity search in high dimensional space database is split into two worlds: i) fast, scalable, and approximate search algorithms which are not secure, and ii) search protocols based on secure computation which are not scalable. This paper presents a one-way privacy protocol that lies in between these two worlds. Approximate metrics for the cosine similarity allows speed. Elements of large random matrix theory provides security evidences if the size of the database is not too big with respe...

  18. Distributed Efficient Similarity Search Mechanism in Wireless Sensor Networks

    Khandakar Ahmed

    2015-03-01

    Full Text Available The Wireless Sensor Network similarity search problem has received considerable research attention due to sensor hardware imprecision and environmental parameter variations. Most of the state-of-the-art distributed data centric storage (DCS schemes lack optimization for similarity queries of events. In this paper, a DCS scheme with metric based similarity searching (DCSMSS is proposed. DCSMSS takes motivation from vector distance index, called iDistance, in order to transform the issue of similarity searching into the problem of an interval search in one dimension. In addition, a sector based distance routing algorithm is used to efficiently route messages. Extensive simulation results reveal that DCSMSS is highly efficient and significantly outperforms previous approaches in processing similarity search queries.

  19. Distributed efficient similarity search mechanism in wireless sensor networks.

    Ahmed, Khandakar; Gregory, Mark A

    2015-01-01

    The Wireless Sensor Network similarity search problem has received considerable research attention due to sensor hardware imprecision and environmental parameter variations. Most of the state-of-the-art distributed data centric storage (DCS) schemes lack optimization for similarity queries of events. In this paper, a DCS scheme with metric based similarity searching (DCSMSS) is proposed. DCSMSS takes motivation from vector distance index, called iDistance, in order to transform the issue of similarity searching into the problem of an interval search in one dimension. In addition, a sector based distance routing algorithm is used to efficiently route messages. Extensive simulation results reveal that DCSMSS is highly efficient and significantly outperforms previous approaches in processing similarity search queries. PMID:25751081

  20. Accelerating Neuroimage Registration through Parallel Computation of Similarity Metric.

    Yun-Gang Luo

    Full Text Available Neuroimage registration is crucial for brain morphometric analysis and treatment efficacy evaluation. However, existing advanced registration algorithms such as FLIRT and ANTs are not efficient enough for clinical use. In this paper, a GPU implementation of FLIRT with the correlation ratio (CR as the similarity metric and a GPU accelerated correlation coefficient (CC calculation for the symmetric diffeomorphic registration of ANTs have been developed. The comparison with their corresponding original tools shows that our accelerated algorithms can greatly outperform the original algorithm in terms of computational efficiency. This paper demonstrates the great potential of applying these registration tools in clinical applications.

  1. Distributed Efficient Similarity Search Mechanism in Wireless Sensor Networks

    Khandakar Ahmed; Gregory, Mark A.

    2015-01-01

    The Wireless Sensor Network similarity search problem has received considerable research attention due to sensor hardware imprecision and environmental parameter variations. Most of the state-of-the-art distributed data centric storage (DCS) schemes lack optimization for similarity queries of events. In this paper, a DCS scheme with metric based similarity searching (DCSMSS) is proposed. DCSMSS takes motivation from vector distance index, called iDistance, in order to transform the issue of s...

  2. Activity-relevant similarity values for fingerprints and implications for similarity searching

    Swarit Jasial; Ye Hu; Martin Vogt; Jürgen Bajorath

    2016-01-01

    A largely unsolved problem in chemoinformatics is the issue of how calculated compound similarity relates to activity similarity, which is central to many applications. In general, activity relationships are predicted from calculated similarity values. However, there is no solid scientific foundation to bridge between calculated molecular and observed activity similarity. Accordingly, the success rate of identifying new active compounds by similarity searching is limited. Although various att...

  3. How Google Web Search copes with very similar documents

    Mettrop, W.; Nieuwenhuysen, P.; Smulders, H.

    2006-01-01

    A significant portion of the computer files that carry documents, multimedia, programs etc. on the Web are identical or very similar to other files on the Web. How do search engines cope with this? Do they perform some kind of “deduplication”? How should users take into account that web search resul

  4. Effective and Efficient Similarity Search in Scientific Workflow Repositories

    Starlinger, Johannes; Cohen-Boulakia, Sarah; Khanna, Sanjeev; Davidson, Susan; Leser, Ulf

    2015-01-01

    Scientific workflows have become a valuable tool for large-scale data processing and analysis. This has led to the creation of specialized online repositories to facilitate worflkow sharing and reuse. Over time, these repositories have grown to sizes that call for advanced methods to support workflow discovery, in particular for similarity search. Effective similarity search requires both high quality algorithms for the comparison of scientific workflows and efficient strategies for indexing,...

  5. The search for new accelerator techniques

    The European Committee for Future Accelerators, ECFA, organized a Conference from 27-30 September under the title The Challenge of Ultra-high Energies'. The aims were to discuss possible new acceleration techniques and, if possible, to help identify the most promising and encourage further research on them. Appropriately enough this search for the new took place in the dignified setting of New College Oxford. The fact that New College is many centuries old should have helped put things in perspective

  6. Indexing schemes for similarity search: an illustrated paradigm

    Pestov, Vladimir; Stojmirovic, Aleksandar

    2002-01-01

    We suggest a variation of the Hellerstein--Koutsoupias--Papadimitriou indexability model for datasets equipped with a similarity measure, with the aim of better understanding the structure of indexing schemes for similarity-based search and the geometry of similarity workloads. This in particular provides a unified approach to a great variety of schemes used to index into metric spaces and facilitates their transfer to more general similarity measures such as quasi-metrics. We discuss links b...

  7. Efficient Subgraph Similarity Search on Large Probabilistic Graph Databases

    Yuan, Ye; Chen, Lei; Wang, Haixun

    2012-01-01

    Many studies have been conducted on seeking the efficient solution for subgraph similarity search over certain (deterministic) graphs due to its wide application in many fields, including bioinformatics, social network analysis, and Resource Description Framework (RDF) data management. All these works assume that the underlying data are certain. However, in reality, graphs are often noisy and uncertain due to various factors, such as errors in data extraction, inconsistencies in data integration, and privacy preserving purposes. Therefore, in this paper, we study subgraph similarity search on large probabilistic graph databases. Different from previous works assuming that edges in an uncertain graph are independent of each other, we study the uncertain graphs where edges' occurrences are correlated. We formally prove that subgraph similarity search over probabilistic graphs is #P-complete, thus, we employ a filter-and-verify framework to speed up the search. In the filtering phase,we develop tight lower and u...

  8. SEARCH PROFILES BASED ON USER TO CLUSTER SIMILARITY

    Ilija Subasic

    2007-12-01

    Full Text Available Privacy of web users' query search logs has, since last year's AOL dataset release, been treated as one of the central issues concerning privacy on the Internet, Therefore, the question of privacy preservation has also raised a lot of attention in different communities surrounding the search engines. Usage of clustering methods for providing low level contextual search, wriile retaining high privacy/utility is examined in this paper. By using only the user's cluster membership the search query terms could be no longer retained thus providing less privacy concerns both for the users and companies. The paper brings lightweight framework for combining query words, user similarities and clustering in order to provide a meaningful way of mining user searches while protecting their privacy. This differs from previous attempts for privacy preserving in the attempt to anonymize the queries instead of the users.

  9. Multiple search methods for similarity-based virtual screening: analysis of search overlap and precision

    Holliday John D; Kanoulas Evangelos; Malim Nurul; Willett Peter

    2011-01-01

    Abstract Background Data fusion methods are widely used in virtual screening, and make the implicit assumption that the more often a molecule is retrieved in multiple similarity searches, the more likely it is to be active. This paper tests the correctness of this assumption. Results Sets of 25 searches using either the same reference structure and 25 different similarity measures (similarity fusion) or 25 different reference structures and the same similarity measure (group fusion) show that...

  10. Improving spectral library search by redefining similarity measures.

    Garg, Ankita; Enright, Catherine G; Madden, Michael G

    2015-05-26

    Similarity plays a central role in spectral library search. The goal of spectral library search is to identify those spectra in a reference library of known materials that most closely match an unknown query spectrum, on the assumption that this will allow us to identify the main constituent(s) of the query spectrum. The similarity measures used for this task in software and the academic literature are almost exclusively metrics, meaning that the measures obey the three axioms of metrics: (1) minimality; (2) symmetry; (3) triangle inequality. Consequently, they implicitly assume that the query spectrum is drawn from the same distribution as that of the reference library. In this paper, we demonstrate that this assumption is not necessary in practical spectral library search and that in fact it is often violated in practice. Although the reference library may be constructed carefully, it is generally impossible to guarantee that all future query spectra will be drawn from the same distribution as the reference library. Before evaluating different similarity measures, we need to understand how they define the relationship between spectra. In spectral library search, we often aim to find the constituent(s) of a mixture. We propose that, rather than asking which reference library spectra are similar to the mixture, we should ask which of the reference library spectra are contained in the given query mixture. This question is inherently asymmetric. Therefore, we should adopt a nonmetric measure. To evaluate our hypothesis, we apply a nonmetric measure formulated by Tversky [Psychol. Rev. 1977, 84, 327-352] known as the Contrast Model and compare its performance to the well-known Jaccard similarity index metric on spectroscopic data sets. Our results show that the Tversky similarity measure yields better results than the Jaccard index. PMID:25902003

  11. A Visual Similarity-Based 3D Search Engine

    Lmaati, Elmustapha Ait; Oirrak, Ahmed El; M.N. Kaddioui

    2009-01-01

    Retrieval systems for 3D objects are required because 3D databases used around the web are growing. In this paper, we propose a visual similarity based search engine for 3D objects. The system is based on a new representation of 3D objects given by a 3D closed curve that captures all information about the surface of the 3D object. We propose a new 3D descriptor, which is a combination of three signatures of this new representation, and we implement it in our interactive web based search engin...

  12. RAPSearch: a fast protein similarity search tool for short reads

    Choi Jeong-Hyeon

    2011-05-01

    Full Text Available Abstract Background Next Generation Sequencing (NGS is producing enormous corpuses of short DNA reads, affecting emerging fields like metagenomics. Protein similarity search--a key step to achieve annotation of protein-coding genes in these short reads, and identification of their biological functions--faces daunting challenges because of the very sizes of the short read datasets. Results We developed a fast protein similarity search tool RAPSearch that utilizes a reduced amino acid alphabet and suffix array to detect seeds of flexible length. For short reads (translated in 6 frames we tested, RAPSearch achieved ~20-90 times speedup as compared to BLASTX. RAPSearch missed only a small fraction (~1.3-3.2% of BLASTX similarity hits, but it also discovered additional homologous proteins (~0.3-2.1% that BLASTX missed. By contrast, BLAT, a tool that is even slightly faster than RAPSearch, had significant loss of sensitivity as compared to RAPSearch and BLAST. Conclusions RAPSearch is implemented as open-source software and is accessible at http://omics.informatics.indiana.edu/mg/RAPSearch. It enables faster protein similarity search. The application of RAPSearch in metageomics has also been demonstrated.

  13. Online multiple kernel similarity learning for visual search.

    Xia, Hao; Hoi, Steven C H; Jin, Rong; Zhao, Peilin

    2014-03-01

    Recent years have witnessed a number of studies on distance metric learning to improve visual similarity search in content-based image retrieval (CBIR). Despite their successes, most existing methods on distance metric learning are limited in two aspects. First, they usually assume the target proximity function follows the family of Mahalanobis distances, which limits their capacity of measuring similarity of complex patterns in real applications. Second, they often cannot effectively handle the similarity measure of multimodal data that may originate from multiple resources. To overcome these limitations, this paper investigates an online kernel similarity learning framework for learning kernel-based proximity functions which goes beyond the conventional linear distance metric learning approaches. Based on the framework, we propose a novel online multiple kernel similarity (OMKS) learning method which learns a flexible nonlinear proximity function with multiple kernels to improve visual similarity search in CBIR. We evaluate the proposed technique for CBIR on a variety of image data sets in which encouraging results show that OMKS outperforms the state-of-the-art techniques significantly. PMID:24457509

  14. Similarity preserving snippet-based visualization of web search results.

    Gomez-Nieto, Erick; San Roman, Frizzi; Pagliosa, Paulo; Casaca, Wallace; Helou, Elias S; de Oliveira, Maria Cristina F; Nonato, Luis Gustavo

    2014-03-01

    Internet users are very familiar with the results of a search query displayed as a ranked list of snippets. Each textual snippet shows a content summary of the referred document (or webpage) and a link to it. This display has many advantages, for example, it affords easy navigation and is straightforward to interpret. Nonetheless, any user of search engines could possibly report some experience of disappointment with this metaphor. Indeed, it has limitations in particular situations, as it fails to provide an overview of the document collection retrieved. Moreover, depending on the nature of the query--for example, it may be too general, or ambiguous, or ill expressed--the desired information may be poorly ranked, or results may contemplate varied topics. Several search tasks would be easier if users were shown an overview of the returned documents, organized so as to reflect how related they are, content wise. We propose a visualization technique to display the results of web queries aimed at overcoming such limitations. It combines the neighborhood preservation capability of multidimensional projections with the familiar snippet-based representation by employing a multidimensional projection to derive two-dimensional layouts of the query search results that preserve text similarity relations, or neighborhoods. Similarity is computed by applying the cosine similarity over a "bag-of-words" vector representation of collection built from the snippets. If the snippets are displayed directly according to the derived layout, they will overlap considerably, producing a poor visualization. We overcome this problem by defining an energy functional that considers both the overlapping among snippets and the preservation of the neighborhood structure as given in the projected layout. Minimizing this energy functional provides a neighborhood preserving two-dimensional arrangement of the textual snippets with minimum overlap. The resulting visualization conveys both a global

  15. On optimizing distance-based similarity search for biological databases.

    Mao, Rui; Xu, Weijia; Ramakrishnan, Smriti; Nuckolls, Glen; Miranker, Daniel P

    2005-01-01

    Similarity search leveraging distance-based index structures is increasingly being used for both multimedia and biological database applications. We consider distance-based indexing for three important biological data types, protein k-mers with the metric PAM model, DNA k-mers with Hamming distance and peptide fragmentation spectra with a pseudo-metric derived from cosine distance. To date, the primary driver of this research has been multimedia applications, where similarity functions are often Euclidean norms on high dimensional feature vectors. We develop results showing that the character of these biological workloads is different from multimedia workloads. In particular, they are not intrinsically very high dimensional, and deserving different optimization heuristics. Based on MVP-trees, we develop a pivot selection heuristic seeking centers and show it outperforms the most widely used corner seeking heuristic. Similarly, we develop a data partitioning approach sensitive to the actual data distribution in lieu of median splits. PMID:16447992

  16. Computing Semantic Similarity Measure Between Words Using Web Search Engine

    Pushpa C N

    2013-05-01

    Full Text Available Semantic Similarity measures between words plays an important role in information retrieval, natural language processing and in various tasks on the web. In this paper, we have proposed a Modified Pattern Extraction Algorithm to compute th e supervised semantic similarity measure between the words by combining both page count meth od and web snippets method. Four association measures are used to find semantic simi larity between words in page count method using web search engines. We use a Sequential Minim al Optimization (SMO support vector machines (SVM to find the optimal combination of p age counts-based similarity scores and top-ranking patterns from the web snippets method. The SVM is trained to classify synonymous word-pairs and non-synonymous word-pairs. The propo sed Modified Pattern Extraction Algorithm outperforms by 89.8 percent of correlatio n value.

  17. On Fuzzy vs. Metric Similarity Search in Complex Databases

    Eckhardt, Alan; Skopal, T.; Vojtáš, Peter

    Berlin: Springer, 2009 - ( And reasen, T.; Yager, R.; Bulskov, H.; Christiansen, H.; Larsen, H.), s. 64-75. (Lecture Notes in Artificial Intelligence . 5822). ISBN 978-3-642-04956-9. ISSN 0302-9743. [FQAS 2009. International Conference on Flexible Query Answering Systems /8./. Roskilde (DK), 26.10.2009-28.10.2009] R&D Projects: GA AV ČR 1ET100300517; GA ČR GD201/09/H057 Grant ostatní: GA ČR(CZ) GA201/09/0683 Institutional research plan: CEZ:AV0Z10300504 Keywords : fuzzy operators * non-metric search * similarity search * indexing Subject RIV: IN - Informatics, Computer Science

  18. SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

    Lefkowitz Elliot J

    2004-10-01

    Full Text Available Abstract Background Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. Results We describe the implementation of SS-Wrapper (Similarity Search Wrapper, a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST that provides a complementary solution for BLAST searches when the database is too large to fit into

  19. SHOP: scaffold hopping by GRID-based similarity searches

    Bergmann, Rikke; Linusson, Anna; Zamora, Ismael

    2007-01-01

    A new GRID-based method for scaffold hopping (SHOP) is presented. In a fully automatic manner, scaffolds were identified in a database based on three types of 3D-descriptors. SHOP's ability to recover scaffolds was assessed and validated by searching a database spiked with fragments of known...... scaffolds were in the 31 top-ranked scaffolds. SHOP also identified new scaffolds with substantially different chemotypes from the queries. Docking analysis indicated that the new scaffolds would have similar binding modes to those of the respective query scaffolds observed in X-ray structures. The...

  20. Quick and easy implementation of approximate similarity search with Lucene

    Amato, Giuseppe; Bolettieri, Paolo; Gennaro, Claudio; Rabitti, Fausto

    2013-01-01

    Similarity search technique has been proved to be an effective way for retrieving multimedia content. However, as the amount of available multimedia data increases, the cost of developing from scratch a robust and scalable system with content-based image retrieval facilities is quite prohibitive. In this paper, we propose to exploit an approach that allows us to convert low level features into a textual form. In this way, we are able to easily set up a retrieval system on top of the Lucene se...

  1. Rank-Based Similarity Search: Reducing the Dimensional Dependence.

    Houle, Michael E; Nett, Michael

    2015-01-01

    This paper introduces a data structure for k-NN search, the Rank Cover Tree (RCT), whose pruning tests rely solely on the comparison of similarity values; other properties of the underlying space, such as the triangle inequality, are not employed. Objects are selected according to their ranks with respect to the query object, allowing much tighter control on the overall execution costs. A formal theoretical analysis shows that with very high probability, the RCT returns a correct query result in time that depends very competitively on a measure of the intrinsic dimensionality of the data set. The experimental results for the RCT show that non-metric pruning strategies for similarity search can be practical even when the representational dimension of the data is extremely high. They also show that the RCT is capable of meeting or exceeding the level of performance of state-of-the-art methods that make use of metric pruning or other selection tests involving numerical constraints on distance values. PMID:26353214

  2. Activity-relevant similarity values for fingerprints and implications for similarity searching [version 1; referees: 3 approved

    Swarit Jasial

    2016-04-01

    Full Text Available A largely unsolved problem in chemoinformatics is the issue of how calculated compound similarity relates to activity similarity, which is central to many applications. In general, activity relationships are predicted from calculated similarity values. However, there is no solid scientific foundation to bridge between calculated molecular and observed activity similarity. Accordingly, the success rate of identifying new active compounds by similarity searching is limited. Although various attempts have been made to establish relationships between calculated fingerprint similarity values and biological activities, none of these has yielded generally applicable rules for similarity searching. In this study, we have addressed the question of molecular versus activity similarity in a more fundamental way. First, we have evaluated if activity-relevant similarity value ranges could in principle be identified for standard fingerprints and distinguished from similarity resulting from random compound comparisons. Then, we have analyzed if activity-relevant similarity values could be used to guide typical similarity search calculations aiming to identify active compounds in databases. It was found that activity-relevant similarity values can be identified as a characteristic feature of fingerprints. However, it was also shown that such values cannot be reliably used as thresholds for practical similarity search calculations. In addition, the analysis presented herein helped to rationalize differences in fingerprint search performance.

  3. Future short-baseline sterile neutrino searches with accelerators

    A number of experimental anomalies in neutrino oscillation physics point to the existence of at least one light sterile neutrino. This hypothesis can be precisely tested using neutrinos from reactors, radioactive isotopes, and particle accelerators. The focus of these proceedings is on future dedicated short-baseline sterile neutrino searches using accelerators

  4. Activity-relevant similarity values for fingerprints and implications for similarity searching [version 2; referees: 3 approved

    Swarit Jasial; Ye Hu; Martin Vogt; Jürgen Bajorath

    2016-01-01

    A largely unsolved problem in chemoinformatics is the issue of how calculated compound similarity relates to activity similarity, which is central to many applications. In general, activity relationships are predicted from calculated similarity values. However, there is no solid scientific foundation to bridge between calculated molecular and observed activity similarity. Accordingly, the success rate of identifying new active compounds by similarity searching is limited. Although various att...

  5. Similarity between Grover's quantum search algorithm and classical two-body collisions

    Zhang, Jingfu; Lu, Zhiheng

    2001-01-01

    By studying the attribute of the inversion about average operation in quantum searching algorithm, we find the similarity between the quantum searching and the course of two rigid bodies'collision. Some related questions are discussed from this similarity.

  6. Dark Matter Searches at Accelerator Facilities

    Dutta, Bhaskar

    2014-01-01

    About 80 percent of the matter content of the universe is dark matter. However, the particle origin of dark matter is yet to be established. Many extensions of the Standard Model (SM) contain candidates of dark matter. The search for the particle origin is currently ongoing at the large hadron collider (LHC). In this review, I will summarize the different search strategies for this elusive particle.

  7. Cosmic ray acceleration search in Supernova Remnants

    Giordano, Francesco; Di Venere, Leonardo [Dipartimento di Fisica M. Merlin dell' Università e del Politecnico di Bari, I-70126 Bari (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Bari, I-70126 Bari (Italy)

    2014-11-15

    Galactic Supernova Remnants (SNRs) are among the best candidates as source of cosmic rays due to energetics, observed rate of explosion and as possible sites where the Fermi mechanisms naturally plays a key role. Evidence of hadronic acceleration processes taking place in SNRs are being collected with the Fermi-LAT, whose sensitivity in the range 100MeV–100GeV is crucial for disentangling possible hadronic contribution from inverse Compton or bremsstrahlung leptonic component. A survey of the detected SNRs will be given, focusing the attention on the role of the environment and the evolution stage of the SNR in the interpretation of the observed γ-ray spectra.

  8. Cosmic ray acceleration search in Supernova Remnants

    Galactic Supernova Remnants (SNRs) are among the best candidates as source of cosmic rays due to energetics, observed rate of explosion and as possible sites where the Fermi mechanisms naturally plays a key role. Evidence of hadronic acceleration processes taking place in SNRs are being collected with the Fermi-LAT, whose sensitivity in the range 100MeV–100GeV is crucial for disentangling possible hadronic contribution from inverse Compton or bremsstrahlung leptonic component. A survey of the detected SNRs will be given, focusing the attention on the role of the environment and the evolution stage of the SNR in the interpretation of the observed γ-ray spectra

  9. Astrophysical search strategies for accelerator blind dark matter

    Wells, James D.

    1998-01-01

    A weakly interacting dark-matter particle may be difficult to discover at an accelerator because it either (1) is too massive, (2) has no standard-model gauge interactions, or (3) is almost degenerate with other states. In each of these cases, searches for annihilation products in the Galactic halo are useful probes of dark-matter properties. Using the example of supersymmetric dark matter, I discuss how astrophysical searches for dark matter may provide discovery and mass information inacces...

  10. Gene expression module-based chemical function similarity search

    Li, Yun; Hao, Pei; Zheng, Siyuan; Tu, Kang; Fan, Haiwei; Zhu, Ruixin; Ding, Guohui; Dong, Changzheng; Wang, Chuan; Li, Xuan; Thiesen, H.-J.; Chen, Y. Eugene; Jiang, HuaLiang; Liu, Lei; Li, Yixue

    2008-01-01

    Investigation of biological processes using selective chemical interventions is generally applied in biomedical research and drug discovery. Many studies of this kind make use of gene expression experiments to explore cellular responses to chemical interventions. Recently, some research groups constructed libraries of chemical related expression profiles, and introduced similarity comparison into chemical induced transcriptome analysis. Resembling sequence similarity alignment, expression pat...

  11. Cognitive Residues of Similarity: 'After-Effects' of Similarity Computations in Visual Search

    O'Toole, Stephanie; Keane, Mark T.

    2013-01-01

    What are the 'cognitive after-effects' of making a similarity judgement? What, cognitively, is left behind and what effect might these residues have on subsequent processing? In this paper, we probe for such after-effects using a visual searcht ask, performed after a task in which pictures of real-world objects were compared. So, target objects were first presented in a comparison task (e.g., rate the similarity of this object to another) thus, presumably, modifying some of their features bef...

  12. G-Hash: Towards Fast Kernel-based Similarity Search in Large Graph Databases

    Wang, Xiaohong; Smalter, Aaron; Huan, Jun; Lushington, Gerald H.

    2009-01-01

    Structured data including sets, sequences, trees and graphs, pose significant challenges to fundamental aspects of data management such as efficient storage, indexing, and similarity search. With the fast accumulation of graph databases, similarity search in graph databases has emerged as an important research topic. Graph similarity search has applications in a wide range of domains including cheminformatics, bioinformatics, sensor network management, social network management, and XML docum...

  13. Ranking and clustering of search results: Analysis of Similarity graph

    Shevchuk, Ksenia Alexander

    2008-01-01

    Evaluate the clustering of the similarity matrix and confirm that it is high. Compare the ranking results of the eigenvector ranking and the Link Popularity ranking and confirm for the high clustered graph the correlation between those is larger than for the low clustered graph.

  14. Density-based similarity measures for content based search

    Hush, Don R [Los Alamos National Laboratory; Porter, Reid B [Los Alamos National Laboratory; Ruggiero, Christy E [Los Alamos National Laboratory

    2009-01-01

    We consider the query by multiple example problem where the goal is to identify database samples whose content is similar to a coUection of query samples. To assess the similarity we use a relative content density which quantifies the relative concentration of the query distribution to the database distribution. If the database distribution is a mixture of the query distribution and a background distribution then it can be shown that database samples whose relative content density is greater than a particular threshold {rho} are more likely to have been generated by the query distribution than the background distribution. We describe an algorithm for predicting samples with relative content density greater than {rho} that is computationally efficient and possesses strong performance guarantees. We also show empirical results for applications in computer network monitoring and image segmentation.

  15. Feasibility of new particle search at future light source accelerators

    Various types of accelerators are proposed as a future light source. Especially those design which can produce high peak power at high repetition rate utilizing energy recovery scheme are interesting also for searching a new particle which couples with photons. We estimated sensitivity of axion search with future XFEL-O, EUV-FEL, and LCSS-γ machines. It shows experiment at these machines can extend the parameter space. We also checked the feasibility of FEL output power assumed in this discussion. (author)

  16. Perceptual Grouping in Haptic Search: The Influence of Proximity, Similarity, and Good Continuation

    Overvliet, Krista E.; Krampe, Ralf Th.; Wagemans, Johan

    2012-01-01

    We conducted a haptic search experiment to investigate the influence of the Gestalt principles of proximity, similarity, and good continuation. We expected faster search when the distractors could be grouped. We chose edges at different orientations as stimuli because they are processed similarly in the haptic and visual modality. We therefore…

  17. Improving image similarity search effectiveness in a multimedia content management system

    Amato, Giuseppe; Falchi, Fabrizio; Gennaro, Claudio; Rabitti, Fausto; Savino, Pasquale; Stanchev, Peter

    2004-01-01

    In this paper, a technique for making more effective the similarity search process of images in a Multimedia Content Management System is proposed. The content-based retrieval process integrates the search on different multimedia components, linked in XML structures. Depending on the specific characteristics of an image data set, some features can be more effective than others when performing similarity search. Starting from this observation, we propose a technique that predicts the effective...

  18. On a Probabilistic Approach to Determining the Similarity between Boolean Search Request Formulations.

    Radecki, Tadeusz

    1982-01-01

    Presents and discusses the results of research into similarity measures for search request formulations which employ Boolean combinations of index terms. The use of a weighting mechanism to indicate the importance of attributes in a search formulation is described. A 16-item reference list is included. (JL)

  19. Comparative study on Authenticated Sub Graph Similarity Search in Outsourced Graph Database

    N. D. Dhamale; Prof. S. R. Durugkar

    2015-01-01

    Today security is very important in the database system. Advanced database systems face a great challenge raised by the emergence of massive, complex structural data in bioinformatics, chem-informatics, and many other applications. Since exact matching is often too restrictive, similarity search of complex structures becomes a vital operation that must be supported efficiently. The Subgraph similarity search is used in graph databases to retrieve graphs whose subgraphs...

  20. Effects of Part-based Similarity on Visual Search: The Frankenbear Experiment

    Alexander, Robert G.; Zelinsky, Gregory J.

    2012-01-01

    Do the target-distractor and distractor-distractor similarity relationships known to exist for simple stimuli extend to real-world objects, and are these effects expressed in search guidance or target verification? Parts of photorealistic distractors were replaced with target parts to create four levels of target-distractor similarity under heterogenous and homogenous conditions. We found that increasing target-distractor similarity and decreasing distractor-distractor similarity impaired sea...

  1. A Theoretical Framework for Defining Similarity Measures for Boolean Search Request Formulations, Including Some Experimental Results.

    Radecki, Tadeusz

    1985-01-01

    Reports research results into a methodology for determining similarity between queries characterized by Boolean search request formulations and discusses similarity measures for Boolean combinations of index terms. Rationale behind these measures is outlined, and conditions ensuring their equivalence are identified. Results of an experiment…

  2. SAPIR - Executing complex similarity queries over multi layer P2P search structures

    Falchi, Fabrizio; Batko, Michal

    2009-01-01

    This deliverable reports the activities conducted within Task 5.4 "Executing complex similarity queries over multi layer P2P search structures" of the SAPIR project. In particular the deliverable discusses complex similarity queries issues and the implementation of the query processing over the P2P indexing. The document is accompanied by a zip file containing the javadoc for MUFIN.

  3. MEASURING THE PERFORMANCE OF SIMILARITY PROPAGATION IN AN SEMANTIC SEARCH ENGINE

    S. K. Jayanthi

    2013-10-01

    Full Text Available In the current scenario, web page result personalization is playing a vital role. Nearly 80 % of the users expect the best results in the first page itself without having any persistence to browse longer in URL mode. This research work focuses on two main themes: Semantic web search through online and Domain based search through offline. The first part is to find an effective method which allows grouping similar results together using BookShelf Data Structure and organizing the various clusters. The second one is focused on the academic domain based search through offline. This paper focuses on finding documents which are similar and how Vector space can be used to solve it. So more weightage is given for the principles and working methodology of similarity propagation. Cosine similarity measure is used for finding the relevancy among the documents.

  4. Comparative study on Authenticated Sub Graph Similarity Search in Outsourced Graph Database

    N. D. Dhamale

    2015-11-01

    Full Text Available Today security is very important in the database system. Advanced database systems face a great challenge raised by the emergence of massive, complex structural data in bioinformatics, chem-informatics, and many other applications. Since exact matching is often too restrictive, similarity search of complex structures becomes a vital operation that must be supported efficiently. The Subgraph similarity search is used in graph databases to retrieve graphs whose subgraphs are similar to a given query graph. It has been proven successful in a wide range of applications including bioinformatics and chem-informatics, etc. Due to the cost of providing efficient similarity search services on everincreasing graph data, database outsourcing is apparently an appealing solution to database owners. In this paper, we are studying on authentication techniques that follow the popular filtering-and-verification framework. An authentication-friendly metric index called GMTree. Specifically, we transform the similarity search into a search in a graph metric space and derive small verification objects (VOs to-be-transmitted to query clients. To further optimize GMTree, we are studying on a sampling-based pivot selection method and an authenticated version of MCS computation.

  5. Efficient Retrieval of Images for Search Engine by Visual Similarity and Re Ranking

    Viswa S S

    2013-06-01

    Full Text Available Nowadays, web scale image search engines (e.g. Google Image Search, Microsoft Live Image Search rely almost purely on surrounding text features. Users type keywords in hope of finding a certain type of images. The search engine returns thousands of images ranked by the text keywords extracted from the surrounding text. However, many of returned images are noisy, disorganized, or irrelevant. Even Google and Microsoft have no Visual Information for searching of images. Using visual information to re rank and improve text based image search results is the idea. This improves the precision of the text based image search ranking by incorporating the information conveyed by the visual modality. The typical assumption that the top- images in the text-based search result are equally relevant is relaxed by linking the relevance of the images to their initial rank positions. Then, a number of images from the initial search result are employed as the prototypes that serve to visually represent the query and that are subsequently used to construct meta re rankers .i.e. The most relevant images are found by visual similarity and the average scores are calculated. By applying different meta re rankers to an image from the initial result, re ranking scores are generated, which are then used to find the new rank position for an image in the re ranked search result. Human supervision is introduced to learn the model weights offline, prior to the online re ranking process. While model learning requires manual labelling of the results for a few queries, the resulting model is query independent and therefore applicable to any other query. The experimental results on a representative web image search dataset comprising 353 queries demonstrate that the proposed method outperforms the existing supervised and unsupervised Re ranking approaches. Moreover, it improves the performance over the text-based image search engine by more than 25.48%.

  6. Improving protein structure similarity searches using domain boundaries based on conserved sequence information

    Madej Tom; Wang Yanli; Thompson Kenneth; Bryant Stephen H

    2009-01-01

    Abstract Background The identification of protein domains plays an important role in protein structure comparison. Domain query size and composition are critical to structure similarity search algorithms such as the Vector Alignment Search Tool (VAST), the method employed for computing related protein structures in NCBI Entrez system. Currently, domains identified on the basis of structural compactness are used for VAST computations. In this study, we have investigated how alternative definit...

  7. A comparison of field-based similarity searching methods: CatShape, FBSS, and ROCS.

    Moffat, Kirstin; Gillet, Valerie J; Whittle, Martin; Bravi, Gianpaolo; Leach, Andrew R

    2008-04-01

    Three field-based similarity methods are compared in retrospective virtual screening experiments. The methods are the CatShape module of CATALYST, ROCS, and an in-house program developed at the University of Sheffield called FBSS. The programs are used in both rigid and flexible searches carried out in the MDL Drug Data Report. UNITY 2D fingerprints are also used to provide a comparison with a more traditional approach to similarity searching, and similarity based on simple whole-molecule properties is used to provide a baseline for the more sophisticated searches. Overall, UNITY 2D fingerprints and ROCS with the chemical force field option gave comparable performance and were superior to the shape-only 3D methods. When the flexible methods were compared with the rigid methods, it was generally found that the flexible methods gave slightly better results than their respective rigid methods; however, the increased performance did not justify the additional computational cost required. PMID:18351728

  8. Accelerated Search for Gaussian Generator Based on Triple Prime Integers

    Boris S. Verkhovsky

    2009-01-01

    Full Text Available Problem statement: Modern cryptographic algorithms are based on complexity of two problems: Integer factorization of real integers and a Discrete Logarithm Problem (DLP. Approach: The latter problem is even more complicated in the domain of complex integers, where Public Key Cryptosystems (PKC had an advantage over analogous encryption-decryption protocols in arithmetic of real integers modulo p: The former PKC have quadratic cycles of order O (p2 while the latter PKC had linear cycles of order O(p. Results: An accelerated non-deterministic search algorithm for a primitive root (generator in a domain of complex integers modulo triple prime p was provided in this study. It showed the properties of triple primes, the frequencies of their occurrence on a specified interval and analyzed the efficiency of the proposed algorithm. Conclusion: Numerous computer experiments and their analysis indicated that three trials were sufficient on average to find a Gaussian generator.

  9. Global search acceleration in the nested optimization scheme

    Grishagin, Vladimir A.; Israfilov, Ruslan A.

    2016-06-01

    Multidimensional unconstrained global optimization problem with objective function under Lipschitz condition is considered. For solving this problem the dimensionality reduction approach on the base of the nested optimization scheme is used. This scheme reduces initial multidimensional problem to a family of one-dimensional subproblems being Lipschitzian as well and thus allows applying univariate methods for the execution of multidimensional optimization. For two well-known one-dimensional methods of Lipschitz optimization the modifications providing the acceleration of the search process in the situation when the objective function is continuously differentiable in a vicinity of the global minimum are considered and compared. Results of computational experiments on conventional test class of multiextremal functions confirm efficiency of the modified methods.

  10. Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity

    Petitjean Michel

    2009-08-01

    Full Text Available Abstract Background Virtual screening methods are now well established as effective to identify hit and lead candidates and are fully integrated in most drug discovery programs. Ligand-based approaches make use of physico-chemical, structural and energetics properties of known active compounds to search large chemical libraries for related and novel chemotypes. While 2D-similarity search tools are known to be fast and efficient, the use of 3D-similarity search methods can be very valuable to many research projects as integration of "3D knowledge" can facilitate the identification of not only related molecules but also of chemicals possessing distant scaffolds as compared to the query and therefore be more inclined to scaffolds hopping. To date, very few methods performing this task are easily available to the scientific community. Results We introduce a new approach (LigCSRre to the 3D ligand similarity search of drug candidates. It combines a 3D maximum common substructure search algorithm independent on atom order with a tunable description of atomic compatibilities to prune the search and increase its physico-chemical relevance. We show, on 47 experimentally validated active compounds across five protein targets having different specificities, that for single compound search, the approach is able to recover on average 52% of the co-actives in the top 1% of the ranked list which is better than gold standards of the field. Moreover, the combination of several runs on a single protein target using different query active compounds shows a remarkable improvement in enrichment. Such Results demonstrate LigCSRre as a valuable tool for ligand-based screening. Conclusion LigCSRre constitutes a new efficient and generic approach to the 3D similarity screening of small compounds, whose flexible design opens the door to many enhancements. The program is freely available to the academics for non-profit research at: http://bioserv.rpbs.univ-paris-diderot.fr/LigCSRre.html.

  11. Accelerated search for materials with targeted properties by adaptive design

    Xue, Dezhen; Balachandran, Prasanna V.; Hogden, John; Theiler, James; Xue, Deqing; Lookman, Turab

    2016-04-01

    Finding new materials with targeted properties has traditionally been guided by intuition, and trial and error. With increasing chemical complexity, the combinatorial possibilities are too large for an Edisonian approach to be practical. Here we show how an adaptive design strategy, tightly coupled with experiments, can accelerate the discovery process by sequentially identifying the next experiments or calculations, to effectively navigate the complex search space. Our strategy uses inference and global optimization to balance the trade-off between exploitation and exploration of the search space. We demonstrate this by finding very low thermal hysteresis (ΔT) NiTi-based shape memory alloys, with Ti50.0Ni46.7Cu0.8Fe2.3Pd0.2 possessing the smallest ΔT (1.84 K). We synthesize and characterize 36 predicted compositions (9 feedback loops) from a potential space of ~800,000 compositions. Of these, 14 had smaller ΔT than any of the 22 in the original data set.

  12. Similarity-based search of model organism, disease and drug effect phenotypes

    Hoehndorf, Robert

    2015-02-19

    Background: Semantic similarity measures over phenotype ontologies have been demonstrated to provide a powerful approach for the analysis of model organism phenotypes, the discovery of animal models of human disease, novel pathways, gene functions, druggable therapeutic targets, and determination of pathogenicity. Results: We have developed PhenomeNET 2, a system that enables similarity-based searches over a large repository of phenotypes in real-time. It can be used to identify strains of model organisms that are phenotypically similar to human patients, diseases that are phenotypically similar to model organism phenotypes, or drug effect profiles that are similar to the phenotypes observed in a patient or model organism. PhenomeNET 2 is available at http://aber-owl.net/phenomenet. Conclusions: Phenotype-similarity searches can provide a powerful tool for the discovery and investigation of molecular mechanisms underlying an observed phenotypic manifestation. PhenomeNET 2 facilitates user-defined similarity searches and allows researchers to analyze their data within a large repository of human, mouse and rat phenotypes.

  13. An efficient similarity search based on indexing in large DNA databases.

    Jeong, In-Seon; Park, Kyoung-Wook; Kang, Seung-Ho; Lim, Hyeong-Seok

    2010-04-01

    Index-based search algorithms are an important part of a genomic search, and how to construct indices is the key to an index-based search algorithm to compute similarities between two DNA sequences. In this paper, we propose an efficient query processing method that uses special transformations to construct an index. It uses small storage and it rapidly finds the similarity between two sequences in a DNA sequence database. At first, a sequence is partitioned into equal length windows. We select the likely subsequences by computing Hamming distance to query sequence. The algorithm then transforms the subsequences in each window into a multidimensional vector space by indexing the frequencies of the characters, including the positional information of the characters in the subsequences. The result of our experiments shows that the algorithm has faster run time than other heuristic algorithms based on index structure. Also, the algorithm is as accurate as those heuristic algorithms. PMID:20418167

  14. Twin Similarities in Holland Types as Shown by Scores on the Self-Directed Search

    Chauvin, Ida; McDaniel, Janelle R.; Miller, Mark J.; King, James M.; Eddlemon, Ondie L. M.

    2012-01-01

    This study examined the degree of similarity between scores on the Self-Directed Search from one set of identical twins. Predictably, a high congruence score was found. Results from a biographical sheet are discussed as well as implications of the results for career counselors.

  15. Similarity and heterogeneity effects in visual search are mediated by "segmentability".

    Utochkin, Igor S; Yurevich, Maria A

    2016-07-01

    The heterogeneity of our visual environment typically reduces the speed with which a singleton target can be found. Visual search theories explain this phenomenon via nontarget similarities and dissimilarities that affect grouping, perceptual noise, and so forth. In this study, we show that increasing the heterogeneity of a display can facilitate rather than inhibit visual search for size and orientation singletons when heterogeneous features smoothly fill the transition between highly distinguishable nontargets. We suggest that this smooth transition reduces the "segmentability" of dissimilar items to otherwise separate subsets, causing the visual system to treat them as a near-homogenous set standing apart from a singleton. (PsycINFO Database Record PMID:26784002

  16. Manifold Learning for Multivariate Variable-Length Sequences With an Application to Similarity Search.

    Ho, Shen-Shyang; Dai, Peng; Rudzicz, Frank

    2016-06-01

    Multivariate variable-length sequence data are becoming ubiquitous with the technological advancement in mobile devices and sensor networks. Such data are difficult to compare, visualize, and analyze due to the nonmetric nature of data sequence similarity measures. In this paper, we propose a general manifold learning framework for arbitrary-length multivariate data sequences driven by similarity/distance (parameter) learning in both the original data sequence space and the learned manifold. Our proposed algorithm transforms the data sequences in a nonmetric data sequence space into feature vectors in a manifold that preserves the data sequence space structure. In particular, the feature vectors in the manifold representing similar data sequences remain close to one another and far from the feature points corresponding to dissimilar data sequences. To achieve this objective, we assume a semisupervised setting where we have knowledge about whether some of data sequences are similar or dissimilar, called the instance-level constraints. Using this information, one learns the similarity measure for the data sequence space and the distance measures for the manifold. Moreover, we describe an approach to handle the similarity search problem given user-defined instance level constraints in the learned manifold using a consensus voting scheme. Experimental results on both synthetic data and real tropical cyclone sequence data are presented to demonstrate the feasibility of our manifold learning framework and the robustness of performing similarity search in the learned manifold. PMID:25781959

  17. Accelerated optimization problem search using Bose-Einstein condensation

    We investigate a computational device that harnesses the effects of Bose-Einstein condensation to accelerate the speed of finding the solution of optimization problems. Many computationally difficult problems, including NP-complete problems, can be formulated as a ground state search problem. In a Bose-Einstein condensate, below the critical temperature, bosonic particles have a natural tendency to accumulate in the ground state. Furthermore, the speed of attaining this configuration is enhanced as a result of final state stimulation. We propose a physical device that incorporates these basic properties of bosons into the optimization problem, such that an optimized solution is found by a simple cooling of the physical temperature of the device. Using a semiclassical model to calculate the equilibration time for reaching the ground state, we found that this can be sped up by a factor of N, where N is the boson number per site. This allows for the annealing times for reaching a particular error to be systematically decreased by increasing the boson number per site. (paper)

  18. Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia

    Ertl, Peter; Patiny, Luc; Sander, Thomas; Rufener, Christian; Zasso, Michaël

    2015-01-01

    Background Wikipedia, the world’s largest and most popular encyclopedia is an indispensable source of chemistry information. It contains among others also entries for over 15,000 chemicals including metabolites, drugs, agrochemicals and industrial chemicals. To provide an easy access to this wealth of information we decided to develop a substructure and similarity search tool for chemical structures referenced in Wikipedia. Results We extracted chemical structures from entries in Wikipedia an...

  19. Target enhanced 2D similarity search by using explicit biological activity annotations and profiles

    Yu, Xiang; Geer, Lewis Y.; Han, Lianyi; Bryant, Stephen H

    2015-01-01

    Background The enriched biological activity information of compounds in large and freely-accessible chemical databases like the PubChem Bioassay Database has become a powerful research resource for the scientific research community. Currently, 2D fingerprint based conventional similarity search (CSS) is the most common widely used approach for database screening, but it does not typically incorporate the relative importance of fingerprint bits to biological activity. Results In this study, a ...

  20. Protein similarity search with subset seeds on a dedicated reconfigurable hardware

    Peterlongo, Pierre; Noé, Laurent; Lavenier, Dominique; Georges, Gilles; Jacques, Julien; Kucherov, Gregory; Giraud, Mathieu

    2007-01-01

    Genome sequencing of numerous species raises the need of complete genome comparison with precise and fast similarity searches. Today, advanced seed-based techniques (spaced seeds, multiple seeds, subset seeds) provide better sensitivity/specificity ratios. We present an implementation of such a seed-based technique onto parallel specialized hardware embedding reconfigurable architecture (FPGA), where the FPGA is tightly connected to large capacity Flash memories. This parallel system allows l...

  1. Efficient Similarity Search Using the Earth Mover's Distance for Large Multimedia Databases

    Assent, Ira; Wichterich, Marc; Meisen, Tobias;

    2008-01-01

    Multimedia similarity search in large databases requires efficient query processing. The Earth mover's distance, introduced in computer vision, is successfully used as a similarity model in a number of small-scale applications. Its computational complexity hindered its adoption in large multimedia...... databases. We enable directly indexing the Earth mover's distance in structures such as the R-tree and the VA-file by providing the accurate 'MinDist' function to any bounding rectangle in the index. We exploit the computational structure of the new MinDist to derive a new lower bound for the EMD Min...

  2. Database searching for compounds with similar biological activity using short binary bit string representations of molecules.

    Xue, L; Godden, J W; Bajorath, J

    1999-01-01

    In an effort to identify biologically active molecules in compound databases, we have investigated similarity searching using short binary bit strings with a maximum of 54 bit positions. These "minifingerprints" (MFPs) were designed to account for the presence or absence of structural fragments and/or aromatic character, flexibility, and hydrogen-bonding capacity of molecules. MFP design was based on an analysis of distributions of molecular descriptors and structural fragments in two large compound collections. The performance of different MFPs and a reference fingerprint was tested by systematic "one-against-all" similarity searches of molecules in a database containing 364 compounds with different biological activities. For each fingerprint, the most effective similarity cutoff value was determined. An MFP accounting for only 32 structural fragments showed less than 2% false positive similarity matches and correctly assigned on average approximately 40% of the compounds with the same biological activity to a query molecule. Inclusion of three numerical two-dimensional (2D) molecular descriptors increased the performance by 15%. This MFP performed better than a complex 2D fingerprint. At a similarity cutoff value of 0.85, the 2D fingerprint totally eliminated false positives but recognized less than 10% of the compounds within the same activity class. PMID:10529986

  3. WEB SEARCH ENGINE BASED SEMANTIC SIMILARITY MEASURE BETWEEN WORDS USING PATTERN RETRIEVAL ALGORITHM

    Pushpa C N

    2013-02-01

    Full Text Available Semantic Similarity measures plays an important role in information retrieval, natural language processing and various tasks on web such as relation extraction, community mining, document clustering, and automatic meta-data extraction. In this paper, we have proposed a Pattern Retrieval Algorithm [PRA] to compute the semantic similarity measure between the words by combining both page count method and web snippets method. Four association measures are used to find semantic similarity between words in page count method using web search engines. We use a Sequential Minimal Optimization (SMO support vector machines (SVM to find the optimal combination of page counts-based similarity scores and top-ranking patterns from the web snippets method. The SVM is trained to classify synonymous word-pairs and nonsynonymous word-pairs. The proposed approach aims to improve the Correlation values, Precision, Recall, and F-measures, compared to the existing methods. The proposed algorithm outperforms by 89.8 % of correlation value.

  4. Similarity-regulation of OS-EM for accelerated SPECT reconstruction

    Vaissier, P. E. B.; Beekman, F. J.; Goorden, M. C.

    2016-06-01

    Ordered subsets expectation maximization (OS-EM) is widely used to accelerate image reconstruction in single photon emission computed tomography (SPECT). Speedup of OS-EM over maximum likelihood expectation maximization (ML-EM) is close to the number of subsets used. Although a high number of subsets can shorten reconstruction times significantly, it can also cause severe image artifacts such as improper erasure of reconstructed activity if projections contain few counts. We recently showed that such artifacts can be prevented by using a count-regulated OS-EM (CR-OS-EM) algorithm which automatically adapts the number of subsets for each voxel based on the estimated number of counts that the voxel contributed to the projections. While CR-OS-EM reached high speed-up over ML-EM in high-activity regions of images, speed in low-activity regions could still be very slow. In this work we propose similarity-regulated OS-EM (SR-OS-EM) as a much faster alternative to CR-OS-EM. SR-OS-EM also automatically and locally adapts the number of subsets, but it uses a different criterion for subset regulation: the number of subsets that is used for updating an individual voxel depends on how similar the reconstruction algorithm would update the estimated activity in that voxel with different subsets. Reconstructions of an image quality phantom and in vivo scans show that SR-OS-EM retains all of the favorable properties of CR-OS-EM, while reconstruction speed can be up to an order of magnitude higher in low-activity regions. Moreover our results suggest that SR-OS-EM can be operated with identical reconstruction parameters (including the number of iterations) for a wide range of count levels, which can be an additional advantage from a user perspective since users would only have to post-filter an image to present it at an appropriate noise level.

  5. Accelerating chemical database searching using graphics processing units.

    Liu, Pu; Agrafiotis, Dimitris K; Rassokhin, Dmitrii N; Yang, Eric

    2011-08-22

    The utility of chemoinformatics systems depends on the accurate computer representation and efficient manipulation of chemical compounds. In such systems, a small molecule is often digitized as a large fingerprint vector, where each element indicates the presence/absence or the number of occurrences of a particular structural feature. Since in theory the number of unique features can be exceedingly large, these fingerprint vectors are usually folded into much shorter ones using hashing and modulo operations, allowing fast "in-memory" manipulation and comparison of molecules. There is increasing evidence that lossless fingerprints can substantially improve retrieval performance in chemical database searching (substructure or similarity), which have led to the development of several lossless fingerprint compression algorithms. However, any gains in storage and retrieval afforded by compression need to be weighed against the extra computational burden required for decompression before these fingerprints can be compared. Here we demonstrate that graphics processing units (GPU) can greatly alleviate this problem, enabling the practical application of lossless fingerprints on large databases. More specifically, we show that, with the help of a ~$500 ordinary video card, the entire PubChem database of ~32 million compounds can be searched in ~0.2-2 s on average, which is 2 orders of magnitude faster than a conventional CPU. If multiple query patterns are processed in batch, the speedup is even more dramatic (less than 0.02-0.2 s/query for 1000 queries). In the present study, we use the Elias gamma compression algorithm, which results in a compression ratio as high as 0.097. PMID:21696144

  6. Accelerator searches for new physics in the context of dark matter

    Lowette, Steven

    2016-05-01

    A review is given of the current status of searches for dark matter at accelerators. Particular emphasis is put on generic searches for direct production of dark matter at the LHC during its first run, and on the recent developments for the interpretation of the results, where the models using an effective field theory approach are now being complemented with more generic interpretations in the context of simplified models. Furthermore, results are reported briefly for searches for dark matter at the LHC in the context of supersymmetry, as well as for non-LHC accelerator searches.

  7. Semantic similarity measures in the biomedical domain by leveraging a web search engine.

    Hsieh, Sheau-Ling; Chang, Wen-Yung; Chen, Chi-Huang; Weng, Yung-Ching

    2013-07-01

    Various researches in web related semantic similarity measures have been deployed. However, measuring semantic similarity between two terms remains a challenging task. The traditional ontology-based methodologies have a limitation that both concepts must be resided in the same ontology tree(s). Unfortunately, in practice, the assumption is not always applicable. On the other hand, if the corpus is sufficiently adequate, the corpus-based methodologies can overcome the limitation. Now, the web is a continuous and enormous growth corpus. Therefore, a method of estimating semantic similarity is proposed via exploiting the page counts of two biomedical concepts returned by Google AJAX web search engine. The features are extracted as the co-occurrence patterns of two given terms P and Q, by querying P, Q, as well as P AND Q, and the web search hit counts of the defined lexico-syntactic patterns. These similarity scores of different patterns are evaluated, by adapting support vector machines for classification, to leverage the robustness of semantic similarity measures. Experimental results validating against two datasets: dataset 1 provided by A. Hliaoutakis; dataset 2 provided by T. Pedersen, are presented and discussed. In dataset 1, the proposed approach achieves the best correlation coefficient (0.802) under SNOMED-CT. In dataset 2, the proposed method obtains the best correlation coefficient (SNOMED-CT: 0.705; MeSH: 0.723) with physician scores comparing with measures of other methods. However, the correlation coefficients (SNOMED-CT: 0.496; MeSH: 0.539) with coder scores received opposite outcomes. In conclusion, the semantic similarity findings of the proposed method are close to those of physicians' ratings. Furthermore, the study provides a cornerstone investigation for extracting fully relevant information from digitizing, free-text medical records in the National Taiwan University Hospital database. PMID:25055314

  8. Accelerated Simplified Swarm Optimization with Exploitation Search Scheme for Data Clustering.

    Wei-Chang Yeh

    Full Text Available Data clustering is commonly employed in many disciplines. The aim of clustering is to partition a set of data into clusters, in which objects within the same cluster are similar and dissimilar to other objects that belong to different clusters. Over the past decade, the evolutionary algorithm has been commonly used to solve clustering problems. This study presents a novel algorithm based on simplified swarm optimization, an emerging population-based stochastic optimization approach with the advantages of simplicity, efficiency, and flexibility. This approach combines variable vibrating search (VVS and rapid centralized strategy (RCS in dealing with clustering problem. VVS is an exploitation search scheme that can refine the quality of solutions by searching the extreme points nearby the global best position. RCS is developed to accelerate the convergence rate of the algorithm by using the arithmetic average. To empirically evaluate the performance of the proposed algorithm, experiments are examined using 12 benchmark datasets, and corresponding results are compared with recent works. Results of statistical analysis indicate that the proposed algorithm is competitive in terms of the quality of solutions.

  9. Costly Search with Adverse Selection: Solicitation Curse vs. Accelerating Blessing

    Marilyn Pease; Kyungmin Kim

    2014-01-01

    We study the effects of endogenizing search intensity in sequential search models of trading under adverse selection. Ceteris paribus, the low-type seller obtains more surplus from search and, therefore, searches more intensively than the high-type seller. This has two ramifications for trade. On the one hand, a seller who successfully finds a buyer is more likely to be the low type (solicitation curse). On the other hand, since the low-type seller leaves the market even faster than the high-...

  10. Sequence heterogeneity accelerates protein search for targets on DNA

    The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity, and chemical composition in the protein search dynamics. Using a discrete-state stochastic approach with a first-passage events analysis, which takes into account the most relevant physical-chemical processes, a full analytical description of the search dynamics is obtained. It is found that, contrary to existing views, the protein search is generally faster on DNA with more heterogeneous sequences. In addition, the search dynamics might be affected by the chemical composition near the target site. The physical origins of these phenomena are discussed. Our results suggest that biological processes might be effectively regulated by modifying chemical composition, symmetry, and heterogeneity of a genome

  11. Sequence heterogeneity accelerates protein search for targets on DNA

    Shvets, Alexey A.; Kolomeisky, Anatoly B., E-mail: tolya@rice.edu [Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005 (United States)

    2015-12-28

    The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity, and chemical composition in the protein search dynamics. Using a discrete-state stochastic approach with a first-passage events analysis, which takes into account the most relevant physical-chemical processes, a full analytical description of the search dynamics is obtained. It is found that, contrary to existing views, the protein search is generally faster on DNA with more heterogeneous sequences. In addition, the search dynamics might be affected by the chemical composition near the target site. The physical origins of these phenomena are discussed. Our results suggest that biological processes might be effectively regulated by modifying chemical composition, symmetry, and heterogeneity of a genome.

  12. A search for integrable four-dimensional nonlinear accelerator lattices

    Nagaitsev, S

    2012-01-01

    Integrable nonlinear motion in accelerators has the potential to introduce a large betatron tune spread to suppress instabilities and to mitigate the effects of space charge and magnetic field errors. To create such an accelerator lattice one has to find magnetic and/or electric field combinations leading to a stable integrable motion. This paper presents families of lattices with one invariant where bounded motion can be easily created in large volumes of the phase space. In addition, it presents two examples of integrable nonlinear accelerator lattices, realizable with longitudinal-coordinate-dependent magnetic or electric fields with the stable nonlinear motion, which can be solved in terms of separable variables.

  13. On a criterion of similarity of the plasma accelerators of the stationary plasma jet engine type

    One examined operation of ATON stationary plasma jet engine with various working gases. Applying criterion of similarity one selected the optimal operation of engine using krypton. Paper presents comparison integral parameters of engine operated by krypton and xenon. It is shown that when using various working media engine operates under similar modes at similar values of similarity criterion

  14. A search for integrable four-dimensional nonlinear accelerator lattices

    Nagaitsev, S.; Danilov, V.

    2012-01-01

    Integrable nonlinear motion in accelerators has the potential to introduce a large betatron tune spread to suppress instabilities and to mitigate the effects of space charge and magnetic field errors. To create such an accelerator lattice one has to find magnetic and/or electric field combinations leading to a stable integrable motion. This paper presents families of lattices with one invariant where bounded motion can be easily created in large volumes of the phase space. In addition, it pre...

  15. Complementarity of Indirect and Accelerator Dark Matter Searches

    G. Bertone; Cerdeño, D. G.; Fornasa, M.; L. Pieri; Ruiz de Austri, R.; Trotta, R.

    2011-01-01

    Even if supersymmetric particles are found at the Large Hadron Collider (LHC), it will be difficult to prove that they constitute the bulk of the dark matter (DM) in the Universe using LHC data alone. We study the complementarity of LHC and DM indirect searches, working out explicitly the reconstruction of the DM properties for a specific benchmark model in the coannihilation region of a 24-parameters supersymmetric model. Combining mock high-luminosity LHC data with presentday null searches ...

  16. GHOSTM: a GPU-accelerated homology search tool for metagenomics.

    Shuji Suzuki

    Full Text Available BACKGROUND: A large number of sensitive homology searches are required for mapping DNA sequence fragments to known protein sequences in public and private databases during metagenomic analysis. BLAST is currently used for this purpose, but its calculation speed is insufficient, especially for analyzing the large quantities of sequence data obtained from a next-generation sequencer. However, faster search tools, such as BLAT, do not have sufficient search sensitivity for metagenomic analysis. Thus, a sensitive and efficient homology search tool is in high demand for this type of analysis. METHODOLOGY/PRINCIPAL FINDINGS: We developed a new, highly efficient homology search algorithm suitable for graphics processing unit (GPU calculations that was implemented as a GPU system that we called GHOSTM. The system first searches for candidate alignment positions for a sequence from the database using pre-calculated indexes and then calculates local alignments around the candidate positions before calculating alignment scores. We implemented both of these processes on GPUs. The system achieved calculation speeds that were 130 and 407 times faster than BLAST with 1 GPU and 4 GPUs, respectively. The system also showed higher search sensitivity and had a calculation speed that was 4 and 15 times faster than BLAT with 1 GPU and 4 GPUs. CONCLUSIONS: We developed a GPU-optimized algorithm to perform sensitive sequence homology searches and implemented the system as GHOSTM. Currently, sequencing technology continues to improve, and sequencers are increasingly producing larger and larger quantities of data. This explosion of sequence data makes computational analysis with contemporary tools more difficult. We developed GHOSTM, which is a cost-efficient tool, and offer this tool as a potential solution to this problem.

  17. Accelerating dark-matter axion searches with quantum measurement technology

    Zheng, Huaixiu; Silveri, Matti; Brierley, R. T.; Girvin, S. M.; Lehnert, K. W.

    2016-01-01

    The axion particle, a consequence of an elegant hypothesis that resolves the strong-CP problem of quantum chromodynamics, is a plausible origin for cosmological dark matter. In searches for axionic dark matter that detect the conversion of axions to microwave photons, the quantum noise associated with microwave vacuum fluctuations will soon limit the rate at which parameter space is searched. Here we show that this noise can be partially overcome either by squeezing the quantum vacuum using r...

  18. Searching the protein structure database for ligand-binding site similarities using CPASS v.2

    Caprez Adam

    2011-01-01

    Full Text Available Abstract Background A recent analysis of protein sequences deposited in the NCBI RefSeq database indicates that ~8.5 million protein sequences are encoded in prokaryotic and eukaryotic genomes, where ~30% are explicitly annotated as "hypothetical" or "uncharacterized" protein. Our Comparison of Protein Active-Site Structures (CPASS v.2 database and software compares the sequence and structural characteristics of experimentally determined ligand binding sites to infer a functional relationship in the absence of global sequence or structure similarity. CPASS is an important component of our Functional Annotation Screening Technology by NMR (FAST-NMR protocol and has been successfully applied to aid the annotation of a number of proteins of unknown function. Findings We report a major upgrade to our CPASS software and database that significantly improves its broad utility. CPASS v.2 is designed with a layered architecture to increase flexibility and portability that also enables job distribution over the Open Science Grid (OSG to increase speed. Similarly, the CPASS interface was enhanced to provide more user flexibility in submitting a CPASS query. CPASS v.2 now allows for both automatic and manual definition of ligand-binding sites and permits pair-wise, one versus all, one versus list, or list versus list comparisons. Solvent accessible surface area, ligand root-mean square difference, and Cβ distances have been incorporated into the CPASS similarity function to improve the quality of the results. The CPASS database has also been updated. Conclusions CPASS v.2 is more than an order of magnitude faster than the original implementation, and allows for multiple simultaneous job submissions. Similarly, the CPASS database of ligand-defined binding sites has increased in size by ~ 38%, dramatically increasing the likelihood of a positive search result. The modification to the CPASS similarity function is effective in reducing CPASS similarity scores

  19. Gene network homology in prokaryotes using a similarity search approach: queries of quorum sensing signal transduction.

    David N Quan

    Full Text Available Bacterial cell-cell communication is mediated by small signaling molecules known as autoinducers. Importantly, autoinducer-2 (AI-2 is synthesized via the enzyme LuxS in over 80 species, some of which mediate their pathogenicity by recognizing and transducing this signal in a cell density dependent manner. AI-2 mediated phenotypes are not well understood however, as the means for signal transduction appears varied among species, while AI-2 synthesis processes appear conserved. Approaches to reveal the recognition pathways of AI-2 will shed light on pathogenicity as we believe recognition of the signal is likely as important, if not more, than the signal synthesis. LMNAST (Local Modular Network Alignment Similarity Tool uses a local similarity search heuristic to study gene order, generating homology hits for the genomic arrangement of a query gene sequence. We develop and apply this tool for the E. coli lac and LuxS regulated (Lsr systems. Lsr is of great interest as it mediates AI-2 uptake and processing. Both test searches generated results that were subsequently analyzed through a number of different lenses, each with its own level of granularity, from a binary phylogenetic representation down to trackback plots that preserve genomic organizational information. Through a survey of these results, we demonstrate the identification of orthologs, paralogs, hitchhiking genes, gene loss, gene rearrangement within an operon context, and also horizontal gene transfer (HGT. We found a variety of operon structures that are consistent with our hypothesis that the signal can be perceived and transduced by homologous protein complexes, while their regulation may be key to defining subsequent phenotypic behavior.

  20. Efficient Retrieval of Images for Search Engine by Visual Similarity and Re Ranking

    Viswa S S

    2013-01-01

    Nowadays, web scale image search engines (e.g. Google Image Search, Microsoft Live Image Search) rely almost purely on surrounding text features. Users type keywords in hope of finding a certain type of images. The search engine returns thousands of images ranked by the text keywords extracted from the surrounding text. However, many of returned images are noisy, disorganized, or irrelevant. Even Google and Microsoft have no Visual Information for searching of images. Using visual information...

  1. PHOG-BLAST – a new generation tool for fast similarity search of protein families

    Mironov Andrey A

    2006-06-01

    Full Text Available Abstract Background The need to compare protein profiles frequently arises in various protein research areas: comparison of protein families, domain searches, resolution of orthology and paralogy. The existing fast algorithms can only compare a protein sequence with a protein sequence and a profile with a sequence. Algorithms to compare profiles use dynamic programming and complex scoring functions. Results We developed a new algorithm called PHOG-BLAST for fast similarity search of profiles. This algorithm uses profile discretization to convert a profile to a finite alphabet and utilizes hashing for fast search. To determine the optimal alphabet, we analyzed columns in reliable multiple alignments and obtained column clusters in the 20-dimensional profile space by applying a special clustering procedure. We show that the clustering procedure works best if its parameters are chosen so that 20 profile clusters are obtained which can be interpreted as ancestral amino acid residues. With these clusters, only less than 2% of columns in multiple alignments are out of clusters. We tested the performance of PHOG-BLAST vs. PSI-BLAST on three well-known databases of multiple alignments: COG, PFAM and BALIBASE. On the COG database both algorithms showed the same performance, on PFAM and BALIBASE PHOG-BLAST was much superior to PSI-BLAST. PHOG-BLAST required 10–20 times less computer memory and computation time than PSI-BLAST. Conclusion Since PHOG-BLAST can compare multiple alignments of protein families, it can be used in different areas of comparative proteomics and protein evolution. For example, PHOG-BLAST helped to build the PHOG database of phylogenetic orthologous groups. An essential step in building this database was comparing protein complements of different species and orthologous groups of different taxons on a personal computer in reasonable time. When it is applied to detect weak similarity between protein families, PHOG-BLAST is less

  2. Accelerating dark-matter axion searches with quantum measurement technology

    Zheng, Huaixiu; Brierley, R T; Girvin, S M; Lehnert, K W

    2016-01-01

    The axion particle, a consequence of an elegant hypothesis that resolves the strong-CP problem of quantum chromodynamics, is a plausible origin for cosmological dark matter. In searches for axionic dark matter that detect the conversion of axions to microwave photons, the quantum noise associated with microwave vacuum fluctuations will soon limit the rate at which parameter space is searched. Here we show that this noise can be partially overcome either by squeezing the quantum vacuum using recently developed Josephson parametric devices, or by using superconducting qubits to count microwave photons.

  3. Breast cancer stories on the internet: improving search facilities to help patients find stories of similar others

    Overberg, Regina Ingrid

    2013-01-01

    The primary aim of this thesis is to gain insight into which search facilities for spontaneously published stories facilitate breast cancer patients in finding stories by other patients in a similar situation. According to the narrative approach, social comparison theory, and social cognitive theory, reading stories about similar others may have the most positive impact. The research followed a user-centred design: users of search facilities (i.e., patients who want to read stories written by...

  4. Identification of protein biochemical functions by similarity search using the molecular surface database eF-site

    Kinoshita, Kengo; Nakamura, Haruki

    2003-01-01

    The identification of protein biochemical functions based on their three-dimensional structures is strongly required in the post-genome-sequencing era. We have developed a new method to identify and predict protein biochemical functions using the similarity information of molecular surface geometries and electrostatic potentials on the surfaces. Our prediction system consists of a similarity search method based on a clique search algorithm and the molecular surface database eF-site (electrost...

  5. PSimScan: algorithm and utility for fast protein similarity search.

    Anna Kaznadzey

    Full Text Available In the era of metagenomics and diagnostics sequencing, the importance of protein comparison methods of boosted performance cannot be overstated. Here we present PSimScan (Protein Similarity Scanner, a flexible open source protein similarity search tool which provides a significant gain in speed compared to BLASTP at the price of controlled sensitivity loss. The PSimScan algorithm introduces a number of novel performance optimization methods that can be further used by the community to improve the speed and lower hardware requirements of bioinformatics software. The optimization starts at the lookup table construction, then the initial lookup table-based hits are passed through a pipeline of filtering and aggregation routines of increasing computational complexity. The first step in this pipeline is a novel algorithm that builds and selects 'similarity zones' aggregated from neighboring matches on small arrays of adjacent diagonals. PSimScan performs 5 to 100 times faster than the standard NCBI BLASTP, depending on chosen parameters, and runs on commodity hardware. Its sensitivity and selectivity at the slowest settings are comparable to the NCBI BLASTP's and decrease with the increase of speed, yet stay at the levels reasonable for many tasks. PSimScan is most advantageous when used on large collections of query sequences. Comparing the entire proteome of Streptocuccus pneumoniae (2,042 proteins to the NCBI's non-redundant protein database of 16,971,855 records takes 6.5 hours on a moderately powerful PC, while the same task with the NCBI BLASTP takes over 66 hours. We describe innovations in the PSimScan algorithm in considerable detail to encourage bioinformaticians to improve on the tool and to use the innovations in their own software development.

  6. The Cost of Search for Multiple Targets: Effects of Practice and Target Similarity

    Menneer, Tamaryn; Cave, Kyle R.; Donnelly, Nick

    2009-01-01

    With the use of X-ray images, performance in the simultaneous search for two target categories was compared with performance in two independent searches, one for each category. In all cases, displays contained one target at most. Dual-target search, for both categories simultaneously, produced a cost in accuracy, although the magnitude of this…

  7. Application of Group Theory of the Similarity Solutions of the Power law Fluids Flow Past a Suddenly Accelerating Plate

    Krishna Lal

    1970-01-01

    Full Text Available The motion of a power law fluid past a suddenly accelerated wall which moves with a constant velocity U (t parallel to the wall has been considered for the similarity analysis. Recently this problem has been discussed and two possible group of transformation have been used by T.Y. Na/sup 1/. In this paper the third possible transformation has been found. The variation of the wall velocity U (t with time, t, has been worked out.

  8. Acceleration of stable interface structure searching using a kriging approach

    Kiyohara, Shin; Oda, Hiromi; Tsuda, Koji; Mizoguchi, Teruyasu

    2016-04-01

    Crystalline interfaces have a tremendous impact on the properties of materials. Determination of the atomic structure of the interface is crucial for a comprehensive understanding of the interface properties. Despite this importance, extensive calculation is necessary to determine even one interface structure. In this study, we apply a technique called kriging, borrowed from geostatistics, to accelerate the determination of the interface structure. The atomic structure of simplified coincidence-site lattice interfaces were determined using the kriging approach. Our approach successfully determined the most stable interface structure with an efficiency almost 2 orders of magnitude better than the traditional “brute force” approach.

  9. Early Visual Tagging: Effects of Target-Distractor Similarity and Old Age on Search, Subitization, and Counting

    Watson, Derrick G.; Maylor, Elizabeth A.; Allen, Gareth E. J.; Bruce, Lucy A. M.

    2007-01-01

    Three experiments examined the effects of target-distractor (T-D) similarity and old age on the efficiency of searching for single targets and enumerating multiple targets. Experiment 1 showed that increasing T-D similarity selectively reduced the efficiency of enumerating small (less than 4) numerosities (subitizing) but had little effect on…

  10. Application of 3D Zernike descriptors to shape-based ligand similarity searching

    Venkatraman Vishwesh

    2009-12-01

    Full Text Available Abstract Background The identification of promising drug leads from a large database of compounds is an important step in the preliminary stages of drug design. Although shape is known to play a key role in the molecular recognition process, its application to virtual screening poses significant hurdles both in terms of the encoding scheme and speed. Results In this study, we have examined the efficacy of the alignment independent three-dimensional Zernike descriptor (3DZD for fast shape based similarity searching. Performance of this approach was compared with several other methods including the statistical moments based ultrafast shape recognition scheme (USR and SIMCOMP, a graph matching algorithm that compares atom environments. Three benchmark datasets are used to thoroughly test the methods in terms of their ability for molecular classification, retrieval rate, and performance under the situation that simulates actual virtual screening tasks over a large pharmaceutical database. The 3DZD performed better than or comparable to the other methods examined, depending on the datasets and evaluation metrics used. Reasons for the success and the failure of the shape based methods for specific cases are investigated. Based on the results for the three datasets, general conclusions are drawn with regard to their efficiency and applicability. Conclusion The 3DZD has unique ability for fast comparison of three-dimensional shape of compounds. Examples analyzed illustrate the advantages and the room for improvements for the 3DZD.

  11. Development of methods for beam angle optimization for IMRT using an accelerated exhaustive search strategy

    Purpose: The purpose of this article is to explore the use of the accelerated exhaustive search strategy for developing and validating methods for optimizing beam orientations for intensity-modulated radiation therapy (IMRT). Combining beam-angle optimization (BAO) with intensity distribution optimization is expected to improve the quality of IMRT treatment plans. However, BAO is one of the most difficult problems to solve adequately because of the huge hyperspace of possible beam configurations (e.g., selecting 7 of 36 uniformly spaced coplanar beams would require the intercomparison of 8,347,680 IMRT plans). Methods and materials: An 'influence vector' (IV) approximation technique for high-speed estimation of IMRT dose distributions was used in combination with a fast gradient search algorithm (Newton's method) for IMRT optimization. In the IV approximation, it is assumed that the change in intensity of a ray (or bixel) proportionately changes dose along the ray. Evidence is presented that the IV approximation is valid for BAO. The scatter contribution at points away from the ray is accounted for fully in IMRT optimization after the optimum beam orientation has been determined. IVs for all candidate beam angles are generated before the start of optimization. For all subsets of beams selected from a given pool of beams (e.g., 5 of 24 uniformly spaced beams), the distribution of planning scores for the best and the worst plans, optimum angle distributions, dose distributions, and dose-volume histograms (DVH) were analyzed for one prostate and two lung cancer cases. The results of the exhaustive search technique were used to develop a 'multiresolution' search strategy. In this approach, a smaller number of beams (e.g., three) is first used to explore the hyperspace of solutions to determine the most preferred and the least preferred directions. The results of such exploration are then used as a starting point for determining an optimum configuration comprising a

  12. Search for Galactic cosmic ray accelerators with the combined IceCube+AMANDA detector

    The IceCube neutrino observatory instruments a volume of 1 cubic km of the Antarctic ice with 5160 photomultiplier tubes (PMTs) aligned on 86 strings with the goal to detect astrophysical sources of high energy neutrinos. During the construction phase from 2004 until 2011, the detector has been growing each year and data was collected in each configuration. In the season 2008/2009, 40 strings of IceCube were operated. In addition, the predecessor of IceCube, AMANDA, acted as an integrated part of the detector. With its denser spacing of PMTs, AMANDA improved the effective area below 10 TeV and acted as a first generation low energy extension of IceCube. We present a search for astrophysical sources of neutrinos in the Milky Way with the combined detector consisting of 40 strings of IceCube plus AMANDA. Potential Galactic cosmic ray accelerators are characterized by their proximity in comparison to other objects such as AGN but their energy spectra show exponential cut-offs. In transparent sources, high energy neutrinos will follow similar soft or cut-off spectra. This strongly motivates a low energy optimized analysis with IceCube. Several test including a scan of the Galactic Plane and a dedicated analysis for the Cygnus region are presented. No neutrino signal has been observed and upper limits are reported.

  13. Massively Multi-core Acceleration of a Document-Similarity Classifier to Detect Web Attacks

    Ulmer, C; Gokhale, M; Top, P; Gallagher, B; Eliassi-Rad, T

    2010-01-14

    This paper describes our approach to adapting a text document similarity classifier based on the Term Frequency Inverse Document Frequency (TFIDF) metric to two massively multi-core hardware platforms. The TFIDF classifier is used to detect web attacks in HTTP data. In our parallel hardware approaches, we design streaming, real time classifiers by simplifying the sequential algorithm and manipulating the classifier's model to allow decision information to be represented compactly. Parallel implementations on the Tilera 64-core System on Chip and the Xilinx Virtex 5-LX FPGA are presented. For the Tilera, we employ a reduced state machine to recognize dictionary terms without requiring explicit tokenization, and achieve throughput of 37MB/s at slightly reduced accuracy. For the FPGA, we have developed a set of software tools to help automate the process of converting training data to synthesizable hardware and to provide a means of trading off between accuracy and resource utilization. The Xilinx Virtex 5-LX implementation requires 0.2% of the memory used by the original algorithm. At 166MB/s (80X the software) the hardware implementation is able to achieve Gigabit network throughput at the same accuracy as the original algorithm.

  14. Efficient Retrieval of Images for Search Engine by Visual Similarity and Re Ranking

    Viswa S S

    2013-06-01

    Full Text Available Nowadays, web scale image search engines (e.g.Google Image Search, Microsoft Live ImageSearch rely almost purely on surrounding textfeatures. Users type keywords in hope of finding acertain type of images. The search engine returnsthousands of images ranked by the text keywordsextracted from the surrounding text. However,many of returned images are noisy, disorganized, orirrelevant. Even Google and Microsoft have noVisual Information for searching of images. Usingvisual information to re rank and improve textbased image search results is the idea. Thisimproves the precision of the text based imagesearch ranking by incorporating the informationconveyed by the visual modality.The typicalassumption that the top-images in the text-basedsearch result are equally relevant is relaxed bylinking the relevance of the images to their initialrank positions. Then, a number of images from theinitial search result are employed as the prototypesthat serve to visually represent the query and thatare subsequently used to construct meta re rankers.i.e. The most relevant images are found by visualsimilarity and the average scores are calculated. Byapplying different meta re rankers to an image fromthe initial result, re ranking scores are generated,which are then used to find the new rank positionfor an image in the re ranked search result.Humansupervision is introduced to learn the model weightsoffline, prior to the online re ranking process. Whilemodel learning requires manual labelling of theresults for a few queries, the resulting model isquery independent and therefore applicable to anyother query. The experimental results on arepresentative web image search dataset comprising353 queries demonstrate that the proposed methodoutperforms the existing supervised andunsupervised Re ranking approaches. Moreover, itimproves the performance over the text-based imagesearch engine by morethan 25.48%

  15. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

    Zhao, Yongan; Tang, Haixu; Ye, Yuzhen

    2011-01-01

    Summary: With the wide application of next-generation sequencing (NGS) techniques, fast tools for protein similarity search that scale well to large query datasets and large databases are highly desirable. In a previous work, we developed RAPSearch, an algorithm that achieved a ~20–90-fold speedup relative to BLAST while still achieving similar levels of sensitivity for short protein fragments derived from NGS data. RAPSearch, however, requires a substantial memory footprint to identify align...

  16. Breast cancer stories on the internet : improving search facilities to help patients find stories of similar others

    Overberg, Regina Ingrid

    2013-01-01

    The primary aim of this thesis is to gain insight into which search facilities for spontaneously published stories facilitate breast cancer patients in finding stories by other patients in a similar situation. According to the narrative approach, social comparison theory, and social cognitive theory

  17. Search for doubly-charged negative ions via accelerator mass spectrometry

    The Argonne FN tandem accelerator in conjunction with an Enge split-pole magnetic spectrograph has been used as a highly sensitive mass spectrometer to search for doubly charged negative ions of 11B, 12C and 16O. No evidence for the formation of these ions in an inverted sputter source and the subsequent acceleration in the tandem has been found. The following limits for the ratio of doubly-charged to singly-charged ions were measured: X--/X- -15, 11B; -15, 12C; -14, 16O. A relatively abundant formation of the short lived, metastable He- ion in the sputter source has been observed

  18. BlastMultAl, a Blast Extension for Similarity Searching with Alignment Graphs

    Nicodème, Pierre

    1996-01-01

    We describe a new method of processing similarity queries of a proteic multiple alignment with a set (database) of protein sequences, or similarity queries of a protein sequence with a set of protein alignments. We use a representation of multiple alignments as alignment-graphs. Comparisons with different classical methods is made. This new method allows the detection of subtle similarities which are not found by the other methods. It has direct applications for similarities querying with the...

  19. SHOP: receptor-based scaffold hopping by GRID-based similarity searches

    Bergmann, Rikke; Liljefors, Tommy; Sørensen, Morten D;

    2009-01-01

    find known active CDK2 scaffolds in a database. Additionally, SHOP was used for suggesting new inhibitors of p38 MAP kinase. Four p38 complexes were used to perform six scaffold searches. Several new scaffolds were suggested, and the resulting compounds were successfully docked into the query proteins....

  20. Finding and Reusing Learning Materials with Multimedia Similarity Search and Social Networks

    Little, Suzanne; Ferguson, Rebecca; Ruger, Stefan

    2012-01-01

    The authors describe how content-based multimedia search technologies can be used to help learners find new materials and learning pathways by identifying semantic relationships between educational resources in a social learning network. This helps users--both learners and educators--to explore and find material to support their learning aims.…

  1. FSim: A Novel Functional Similarity Search Algorithm and Tool for Discovering Functionally Related Gene Products

    2014-01-01

    Background. During the analysis of genomics data, it is often required to quantify the functional similarity of genes and their products based on the annotation information from gene ontology (GO) with hierarchical structure. A flexible and user-friendly way to estimate the functional similarity of genes utilizing GO annotation is therefore highly desired. Results. We proposed a novel algorithm using a level coefficient-weighted model to measure the functional similarity of gene products base...

  2. Acceleration Method of Neighbor Search with GRAPE and Morton-ordering

    Saitoh, T. R.; J. Koda

    2003-01-01

    We describe a new method to accelerate neighbor searches on GRAPE, i.e. a special purpose hardware that efficiently calculates gravitational forces and potentials in $N$-body simulations. In addition to the gravitational calculations, GRAPE simultaneously constructs the lists of neighbor particles that are necessary for Smoothed Particle Hydrodynamics (SPH). However, data transfer of the neighbor lists from GRAPE to the host computer is time consuming, and can be a bottleneck. In fact, the da...

  3. Improving GPU-accelerated Adaptive IDW Interpolation Algorithm Using Fast kNN Search

    Mei, Gang; Xu, Nengxiong; Xu, Liangliang

    2016-01-01

    This paper presents an efficient parallel Adaptive Inverse Distance Weighting (AIDW) interpolation algorithm on modern Graphics Processing Unit (GPU). The presented algorithm is an improvement of our previous GPU-accelerated AIDW algorithm by adopting fast k-Nearest Neighbors (kNN) search. In AIDW, it needs to find several nearest neighboring data points for each interpolated point to adaptively determine the power parameter; and then the desired prediction value of the interpolated point is ...

  4. Efficient EMD-based Similarity Search in Multimedia Databases via Flexible Dimensionality Reduction

    Wichterich, Marc; Assent, Ira; Philipp, Kranen;

    2008-01-01

    The Earth Mover's Distance (EMD) was developed in computer vision as a flexible similarity model that utilizes similarities in feature space to define a high quality similarity measure in feature representation space. It has been successfully adopted in a multitude of applications with low to...... dimensionality reduction techniques for the EMD in a filter-and-refine architecture for efficient lossless retrieval. Thorough experimental evaluation on real world data sets demonstrates a substantial reduction of the number of expensive high-dimensional EMD computations and thus remarkably faster response...

  5. A Commodity Information Search Model of E-Commerce Search Engine Based on Semantic Similarity and Multi-Attribute Decision Method

    Ziming Zeng

    2010-01-01

    The paper presented an intelligent commodity information search model, which integrates semantic retrieval andmulti-attribute decision method. First, semantic similarity is computed by constructing semantic vector-space, inorder to realize the semantic consistency between retrieved result and customer’s query. Besides, TOPSISmethod is also utilized to construct the comparison mechanism of commodity by calculating the utility value ofeach retrieved commodity. Finally, the experiment is conduct...

  6. Proposal for a Similar Question Search System on a Q&A Site

    Katsutoshi Kanamori

    2014-06-01

    Full Text Available There is a service to help Internet users obtain answers to specific questions when they visit a Q&A site. A Q&A site is very useful for the Internet user, but posted questions are often not answered immediately. This delay in answering occurs because in most cases another site user is answering the question manually. In this study, we propose a system that can present a question that is similar to a question posted by a user. An advantage of this system is that a user can refer to an answer to a similar question. This research measures the similarity of a candidate question based on word and dependency parsing. In an experiment, we examined the effectiveness of the proposed system for questions actually posted on the Q&A site. The result indicates that the system can show the questioner the answer to a similar question. However, the system still has a number of aspects that should be improved.

  7. Managing Biomedical Image Metadata for Search and Retrieval of Similar Images

    Korenblum, Daniel; Rubin, Daniel; Napel, Sandy; Cesar RODRIGUEZ; Beaulieu, Chris

    2010-01-01

    Radiology images are generally disconnected from the metadata describing their contents, such as imaging observations (“semantic” metadata), which are usually described in text reports that are not directly linked to the images. We developed a system, the Biomedical Image Metadata Manager (BIMM) to (1) address the problem of managing biomedical image metadata and (2) facilitate the retrieval of similar images using semantic feature metadata. Our approach allows radiologists, researchers, and ...

  8. Application of kernel functions for accurate similarity search in large chemical databases

    2010-01-01

    Background Similaritysearch in chemical structure databases is an important problem with many applications in chemical genomics, drug design, and efficient chemical probe screening among others. It is widely believed that structure based methods provide an efficient way to do the query. Recently various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful in constructing accurate predictive and classification models, graph kernel functions...

  9. Integrating structure- and ligand-based virtual screening: comparison of individual, parallel, and fused molecular docking and similarity search calculations on multiple targets.

    Tan, Lu; Geppert, Hanna; Sisay, Mihiret T; Gütschow, Michael; Bajorath, Jürgen

    2008-10-01

    Similarity searching is often used to preselect compounds for docking, thereby decreasing the size of screening databases. However, integrated structure- and ligand-based screening schemes are rare at present. Docking and similarity search calculations using 2D fingerprints were carried out in a comparative manner on nine target enzymes, for which significant numbers of diverse inhibitors could be obtained. In the absence of knowledge-based docking constraints and target-directed parameter optimisation, fingerprint searching displayed a clear preference over docking calculations. Alternative combinations of docking and similarity search results were investigated and found to further increase compound recall of individual methods in a number of instances. When the results of similarity searching and docking were combined, parallel selection of candidate compounds from individual rankings was generally superior to rank fusion. We suggest that complementary results from docking and similarity searching can be captured by integrated compound selection schemes. PMID:18651695

  10. HBLAST: Parallelised sequence similarity--A Hadoop MapReducable basic local alignment search tool.

    O'Driscoll, Aisling; Belogrudov, Vladislav; Carroll, John; Kropp, Kai; Walsh, Paul; Ghazal, Peter; Sleator, Roy D

    2015-04-01

    The recent exponential growth of genomic databases has resulted in the common task of sequence alignment becoming one of the major bottlenecks in the field of computational biology. It is typical for these large datasets and complex computations to require cost prohibitive High Performance Computing (HPC) to function. As such, parallelised solutions have been proposed but many exhibit scalability limitations and are incapable of effectively processing "Big Data" - the name attributed to datasets that are extremely large, complex and require rapid processing. The Hadoop framework, comprised of distributed storage and a parallelised programming framework known as MapReduce, is specifically designed to work with such datasets but it is not trivial to efficiently redesign and implement bioinformatics algorithms according to this paradigm. The parallelisation strategy of "divide and conquer" for alignment algorithms can be applied to both data sets and input query sequences. However, scalability is still an issue due to memory constraints or large databases, with very large database segmentation leading to additional performance decline. Herein, we present Hadoop Blast (HBlast), a parallelised BLAST algorithm that proposes a flexible method to partition both databases and input query sequences using "virtual partitioning". HBlast presents improved scalability over existing solutions and well balanced computational work load while keeping database segmentation and recompilation to a minimum. Enhanced BLAST search performance on cheap memory constrained hardware has significant implications for in field clinical diagnostic testing; enabling faster and more accurate identification of pathogenic DNA in human blood or tissue samples. PMID:25625550

  11. Search for doubly-charged negative ions via accelerator mass spectrometry

    Kutschera, W.; Frekers, D.; Pardo, R.; Rehm, K.E.; Smither, R.K.; Yntema, J.L.

    1983-01-01

    The Argonne FN tandem accelerator in conjunction with an Enge split-pole magnetic spectrograph has been used as a highly sensitive mass spectrometer to search for doubly charged negative ions of /sup 11/B, /sup 12/C and /sup 16/O. No evidence for the formation of these ions in an inverted sputter source and the subsequent acceleration in the tandem has been found. The following limits for the ratio of doubly-charged to singly-charged ions were measured: X/sup - -//X/sup -/ < 1 x 10/sup -15/, /sup 11/B; < 2 x 10/sup -15/, /sup 12/C; < 2 x 10/sup -14/, /sup 16/O. A relatively abundant formation of the short lived, metastable He/sup -/ ion in the sputter source has been observed.

  12. Efficient SAT engines for concise logics: Accelerating proof search for zero-one linear constraint systems

    Fränzle, Martin; Herde, Christian

    We investigate the problem of generalizing acceleration techniques as found in recent satisfiability engines for conjunctive normal forms (CNFs) to linear constraint systems over the Booleans. The rationale behind this research is that rewriting the propositional formulae occurring in e.g. bounded...... model checking (BMC) [Biere, Cimatti,Zhu, 1999] to CNF requires a blowup in either the formula size (worst-case exponential) or in the number of propositional variables (linear, thus yielding a worst-case exponential blow-up of the search space). We demonstrate that acceleration techniques like....... Despite the more expressive input language, the performance of our prototype implementation comes surprisingly close to that of state-of-the-art CNF-SAT engines like ZChaff [Moskewicz e.a., 2001]. First experiments with bounded model-construction problems show that the overhead in the satisfiability...

  13. Searching for magnetic monopoles trapped in accelerator material at the Large Hadron Collider

    Joergensen, M. Dam; De Roeck, A; Hächler, H. -P.; Hirt, A.; Katre, A.; Mermod, P.; D. Milstead; Sloan, T.

    2012-01-01

    If produced in high energy particle collisions at the LHC, magnetic monopoles could stop in material surrounding the interaction points. Obsolete parts of the beam pipe near the CMS interaction region, which were exposed to the products of pp and heavy ion collisions, were analysed using a SQUID-based magnetometer. The purpose of this work is to quantify the performance of the magnetometer in the context of a monopole search using a small set of samples of accelerator material ahead of the 20...

  14. Searching for magnetic monopoles trapped in accelerator material at the Large Hadron Collider

    Joergensen, M Dam; Hächler, H -P; Hirt, A; Katre, A; Mermod, P; Milstead, D; Sloan, T

    2012-01-01

    If produced in high energy particle collisions at the LHC, magnetic monopoles could stop in material surrounding the interaction points. Obsolete parts of the beam pipe near the CMS interaction region, which were exposed to the products of pp and heavy ion collisions, were analysed using a SQUID-based magnetometer. The purpose of this work is to quantify the performance of the magnetometer in the context of a monopole search using a small set of samples of accelerator material ahead of the 2013 shutdown.

  15. Web Similarity

    Cohen, Andrew; Vitányi, Paul

    2015-01-01

    Normalized web distance (NWD) is a similarity or normalized semantic distance based on the World Wide Web or any other large electronic database, for instance Wikipedia, and a search engine that returns reliable aggregate page counts. For sets of search terms the NWD gives a similarity on a scale from 0 (identical) to 1 (completely different). The NWD approximates the similarity according to all (upper semi)computable properties. We develop the theory and give applications. The derivation of ...

  16. Geometry navigation acceleration based on automatic neighbor search and oriented bounding box in Monte Carlo simulation

    Geometry navigation plays the most fundamental role in Monte Carlo particle transport simulation. It's mainly responsible for locating a particle inside which geometry volume it is and computing the distance to the volume boundary along the certain particle trajectory during each particle history. Geometry navigation directly affects the run-time performance of the Monte Carlo particle transport simulation, especially for large scale complicated systems. Two geometry acceleration algorithms, the automatic neighbor search algorithm and the oriented bounding box algorithm, are presented for improving geometry navigation performance. The algorithms have been implemented in the Super Monte Carlo Calculation Program for Nuclear and Radiation Process (SuperMC) version 2.0. The FDS-II and ITER benchmark models have been tested to highlight the efficiency gains that can be achieved by using the acceleration algorithms. The exact gains may be problem dependent, but testing results showed that runtime of Monte Carlo simulation can be considerably reduced 50%∼60% with the proposed acceleration algorithms. (author)

  17. SimSearch : a new variant of dynamic programming based on distance series for optimal and near-optimal similarity discovery in biological sequences

    Sérgio DEUSDADO; Carvalho, Paulo

    2009-01-01

    In this paper, we propose SimSearch, an algorithm implementing a new variant of dynamic programming based on distance series for optimal and near-optimal similarity discovery in biological sequences. The initial phase of SimSearch is devoted to fulfil the binary similarity matrices by signalling the distances between occurrences of the same symbol. The scoring scheme is further applied, when analysed the maximal extension of the pattern. Employing bit parallelism to analyse the global similar...

  18. Accelerator

    The invention claims equipment for stabilizing the position of the front covers of the accelerator chamber in cyclic accelerators which significantly increases accelerator reliability. For stabilizing, it uses hydraulic cushions placed between the electromagnet pole pieces and the front chamber covers. The top and the bottom cushions are hydraulically connected. The cushions are disconnected and removed from the hydraulic line using valves. (J.P.)

  19. Improving performance of content-based image retrieval schemes in searching for similar breast mass regions: an assessment

    This study aims to assess three methods commonly used in content-based image retrieval (CBIR) schemes and investigate the approaches to improve scheme performance. A reference database involving 3000 regions of interest (ROIs) was established. Among them, 400 ROIs were randomly selected to form a testing dataset. Three methods, namely mutual information, Pearson's correlation and a multi-feature-based k-nearest neighbor (KNN) algorithm, were applied to search for the 15 'the most similar' reference ROIs to each testing ROI. The clinical relevance and visual similarity of searching results were evaluated using the areas under receiver operating characteristic (ROC) curves (AZ) and average mean square difference (MSD) of the mass boundary spiculation level ratings between testing and selected ROIs, respectively. The results showed that the AZ values were 0.893 ± 0.009, 0.606 ± 0.021 and 0.699 ± 0.026 for the use of KNN, mutual information and Pearson's correlation, respectively. The AZ values increased to 0.724 ± 0.017 and 0.787 ± 0.016 for mutual information and Pearson's correlation when using ROIs with the size adaptively adjusted based on actual mass size. The corresponding MSD values were 2.107 ± 0.718, 2.301 ± 0.733 and 2.298 ± 0.743. The study demonstrates that due to the diversity of medical images, CBIR schemes using multiple image features and mass size-based ROIs can achieve significantly improved performance.

  20. Accelerating and separating mixed beams of ions with similar charge to mass ratio in the CERN ps complex

    This paper reports that sulphur 32 ions were accelerated by the CERN machines to a world record energy of 6.4 TeV. An Electron Cyclotron Resonance source produces sulphur ions as a 5 per cent contamination of an oxygen ion beam. As their charge-to-mass ratios differ by only 5.4 E-4, the two species are not distinguishable by the downstream accelerators (RFQ, Linac 1, PSB), though measurable in a specially equipped spectrometer line. In this way, enough current is available for controlled acceleration at low beta in the PSB. However, at phase transition energy in the PS - about 6 GeV/nucleon (GeV/u) - this synchrotron becomes an extremely fine spectrometer, with sulphur 16+ ions being driven inwards, and oxygen 8+ outwards. This can be used for separating the beams by manipulating the low-level radio-frequency system at transition, so that either oxygen or sulphur is selected. Indeed, the SPS could be fed with a fairly intense oxygen beam for setting-up, and later with some 2E7 sulphur ions per PS cycle. The required RF manipulations, the present understanding on beam dynamics at transition, as well as diagnostic techniques for determining the amount of sulphur are presented

  1. Ultra-short laser-accelerated proton pulses have similar DNA-damaging effectiveness but produce less immediate nitroxidative stress than conventional proton beams.

    Raschke, S; Spickermann, S; Toncian, T; Swantusch, M; Boeker, J; Giesen, U; Iliakis, G; Willi, O; Boege, F

    2016-01-01

    Ultra-short proton pulses originating from laser-plasma accelerators can provide instantaneous dose rates at least 10(7)-fold in excess of conventional, continuous proton beams. The impact of such extremely high proton dose rates on A549 human lung cancer cells was compared with conventionally accelerated protons and 90 keV X-rays. Between 0.2 and 2 Gy, the yield of DNA double strand breaks (foci of phosphorylated histone H2AX) was not significantly different between the two proton sources or proton irradiation and X-rays. Protein nitroxidation after 1 h judged by 3-nitrotyrosine generation was 2.5 and 5-fold higher in response to conventionally accelerated protons compared to laser-driven protons and X-rays, respectively. This difference was significant (p < 0.01) between 0.25 and 1 Gy. In conclusion, ultra-short proton pulses originating from laser-plasma accelerators have a similar DNA damaging potential as conventional proton beams, while inducing less immediate nitroxidative stress, which probably entails a distinct therapeutic potential. PMID:27578260

  2. Similar muscles contribute to horizontal and vertical acceleration of center of mass in forward and backward walking: implications for neural control.

    Jansen, Karen; De Groote, Friedl; Massaad, Firas; Meyns, Pieter; Duysens, Jacques; Jonkers, Ilse

    2012-06-01

    Leg kinematics during backward walking (BW) are very similar to the time-reversed kinematics during forward walking (FW). This suggests that the underlying muscle activation pattern could originate from a simple time reversal, as well. Experimental electromyography studies have confirmed that this is the case for some muscles. Furthermore, it has been hypothesized that muscles showing a time reversal should also exhibit a reversal in function [from accelerating the body center of mass (COM) to decelerating]. However, this has not yet been verified in simulation studies. In the present study, forward simulations were used to study the effects of muscles on the acceleration of COM in FW and BW. We found that a reversal in function was indeed present in the muscle control of the horizontal movement of COM (e.g., tibialis anterior and gastrocnemius). In contrast, muscles' antigravity contributions maintained their function for both directions of movement. An important outcome of the present study is therefore that similar muscles can be used to achieve opposite functional demands at the level of control of the COM when walking direction is reversed. However, some muscles showed direction-specific contributions (i.e., dorsiflexors). We concluded that the changes in muscle contributions imply that a simple time reversal would be insufficient to produce BW from FW. We therefore propose that BW utilizes extra elements, presumably supraspinal, in addition to a common spinal drive. These additions are needed for propulsion and require a partial reconfiguration of lower level common networks. PMID:22423005

  3. Developing Molecular Interaction Database and Searching for Similar Pathways (MOLECULAR BIOLOGY AND INFORMATION-Biological Information Science)

    Kawashima, Shuichi; Katayama, Toshiaki; Kanehisa, Minoru

    1998-01-01

    We have developed a database named BRITE, which contains knowledge of interacting molecules and/or genes concering cell cycle and early development. Here, we report an overview of the database and the method of automatic search for functionally common sub-pathways between two biological pathways in BRITE.

  4. Topology-based document similarity search algorithm%一种基于文档拓扑的相似性搜索算法

    杨艳; 朱戈; 范文彬

    2011-01-01

    Searching for similar documents from the large number of documents quickly and efficiently is an important and time-consuming problem.The existing algorithms first find the candidate document set, and then sort them based on a document related evaluation to identify the most relevant ones.A topology-based document similarity search algorithm--Hub-Nis put forward, and the document similarity search problem is transformed into graph search problem, applying the pruning techniques, reducing the scope of scanned documents, and significantly improving retrieval efficiency.lt proves to be effective and feasible through experiment.%从海量文档中快速有效地搜索到相似文档是一个重要且耗时的问题.现有的文档相似性搜索算法是先找出候选文档集,再对候选文档进行相关性排序,找出最相关的文档.提出了一种基于文档拓扑的相似性搜索算法-Hub-N,将文档相似性搜索问题转化为图搜索问题,应用相应的剪枝技术,缩小了扫描文档的范围,提高了搜索效率.通过实验验证了算法的有效性和可行性.

  5. Novel DOCK clique driven 3D similarity database search tools for molecule shape matching and beyond: adding flexibility to the search for ligand kin.

    Good, Andrew C

    2007-10-01

    With readily available CPU power and copious disk storage, it is now possible to undertake rapid comparison of 3D properties derived from explicit ligand overlay experiments. With this in mind, shape software tools originally devised in the 1990s are revisited, modified and applied to the problem of ligand database shape comparison. The utility of Connolly surface data is highlighted using the program MAKESITE, which leverages surface normal data to a create ligand shape cast. This cast is applied directly within DOCK, allowing the program to be used unmodified as a shape searching tool. In addition, DOCK has undergone multiple modifications to create a dedicated ligand shape comparison tool KIN. Scoring has been altered to incorporate the original incarnation of Gaussian function derived shape description based on STO-3G atomic electron density. In addition, a tabu-like search refinement has been added to increase search speed by removing redundant starting orientations produced during clique matching. The ability to use exclusion regions, again based on Gaussian shape overlap, has also been integrated into the scoring function. The use of both DOCK with MAKESITE and KIN in database screening mode is illustrated using a published ligand shape virtual screening template. The advantages of using a clique-driven search paradigm are highlighted, including shape optimization within a pharmacophore constrained framework, and easy incorporation of additional scoring function modifications. The potential for further development of such methods is also discussed. PMID:17482856

  6. Search for reducing methodology of acceleration aging time in reversed sequential application of heat and radiation using numerical computational program

    Two consecutive numerical calculations on degradation of polymeric insulations under thermal and radiation environment are carried out to simulate so-called reversal sequential acceleration test. The calculation is aiming at searching the test conditions which provide material damage equivalent to the case of simultaneous exposure of heat and radiation. The total aging time in reversal sequential method becomes the shortest if all amount of target degradation is assigned to radiation process with the strongest allowable dose rate. If the total time becomes shorter than this using the heating process, radiation process in any dose rate conditions would prolong the testing time. (author)

  7. PHASE-RESOLVED INFRARED SPECTROSCOPY AND PHOTOMETRY OF V1500 CYGNI, AND A SEARCH FOR SIMILAR OLD CLASSICAL NOVAE

    We present phase-resolved near-infrared photometry and spectroscopy of the classical nova (CN) V1500 Cyg to explore whether cyclotron emission is present in this system. While the spectroscopy do not indicate the presence of discrete cyclotron harmonic emission, the light curves suggest that a sizable fraction of its near-infrared fluxes are due to this component. The light curves of V1500 Cyg appear to remain dominated by emission from the heated face of the secondary star in this system. We have used infrared spectroscopy and photometry to search for other potential magnetic systems among old CNe. We have found that the infrared light curves of V1974 Cyg superficially resemble those of V1500 Cyg, suggesting a highly irradiated companion. The old novae V446 Her and QV Vul have light curves with large amplitude variations like those seen in polars, suggesting they might have magnetic primaries. We extract photometry for 79 old novae from the Two Micron All Sky Survey Point Source Catalog and use those data to derive the mean, un-reddened infrared colors of quiescent novae. We also extract WISE data for these objects and find that 45 of them were detected. Surprisingly, a number of these systems were detected in the WISE 22 μm band. While two of those objects produced significant dust shells (V705 Cas and V445 Pup), the others did not. It appears that line emission from their ionized ejected shells is the most likely explanation for those detections

  8. Accelerator facilities probing the physics of scales: the 12 GeV upgrade of CEBAF in search of 'Quark Confinement'

    We will identify the various accelerator-based US facilities in operation and/or planned for exploring Nuclear/Particle Physics at different scales from the multibody Nucleon-Nucleon Force. Rare Nuclear Isotopes and Nuclear Astrophysics on one hand through facilities probing 'Hadronic Physics' deep inside a nucleon (such as the search for 'pentaquark' and strange matter) to colliders in search of 'new states' of nuclear matter (such as the 'quark-gluon plasma' or 'strongly interacting nuclear liquid'). In particular, we will explore in some depth the science behind the 'GlueX' experiment planned in Hall D of Jefferson Lab's upgraded 12 GeV Continuous Electron Beam Accelerator Facility (CEBAF). There, coherent Bremsstrahlung photons of 9 GeV energy, obtained from a continuous string of 12 GeV electrons stopped by a diamond crystal, will be used to photoexcite 'exotic' mesons where the degree of freedom of the strong gluonic force binding the quark-antiquark pair is excited. A careful partial wave analysis eliminating the vibrational and rotational 'quark' degrees of freedom of the 'di-quark' molecule and an analysis of the forbidden J'PC' quantum states will reveal the signal of new truly 'exotic' quantum states with pure gluonic information. The exotic meson spectroscopy will allow 'mapping the strong force' that confines quarks as a 'function of distance between quarks', with the search for a possible ultimate 'glueball' state within reach. The experiment will firmly establish QCD experimentally in the nonperturbative 'confinement regime', complementing the perturbative QCD established firmly in the regime of 'asymptotic freedom', recognized via the Nobel Prize in 2004. (author)

  9. Search for magnetic fields in particle-accelerating colliding-wind binaries

    Neiner, C.; Grunhut, J.; Leroy, B; De Becker, Michaël; Rauw, Grégor

    2014-01-01

    Some colliding-wind massive binaries, called particle-accelerating colliding-wind binaries (PACWB), exhibit synchrotron radio emission, which is assumed to be generated by a stellar magnetic field. However, no measurement of magnetic fields in these stars has ever been performed. We aim at quantifying the possible stellar magnetic fields present in PACWB to provide constraints for models. We gathered 21 high-resolution spectropolarimetric observations of 9 PACWB available in the ESPaDOnS, Nar...

  10. Tempest: Accelerated MS/MS Database Search Software for Heterogeneous Computing Platforms.

    Adamo, Mark E; Gerber, Scott A

    2016-01-01

    MS/MS database search algorithms derive a set of candidate peptide sequences from in silico digest of a protein sequence database, and compute theoretical fragmentation patterns to match these candidates against observed MS/MS spectra. The original Tempest publication described these operations mapped to a CPU-GPU model, in which the CPU (central processing unit) generates peptide candidates that are asynchronously sent to a discrete GPU (graphics processing unit) to be scored against experimental spectra in parallel. The current version of Tempest expands this model, incorporating OpenCL to offer seamless parallelization across multicore CPUs, GPUs, integrated graphics chips, and general-purpose coprocessors. Three protocols describe how to configure and run a Tempest search, including discussion of how to leverage Tempest's unique feature set to produce optimal results. © 2016 by John Wiley & Sons, Inc. PMID:27603022

  11. Throughput Analysis for a High-Performance FPGA-Accelerated Real-Time Search Application

    Wim Vanderbauwhede

    2012-01-01

    Full Text Available We propose an FPGA design for the relevancy computation part of a high-throughput real-time search application. The application matches terms in a stream of documents against a static profile, held in off-chip memory. We present a mathematical analysis of the throughput of the application and apply it to the problem of scaling the Bloom filter used to discard nonmatches.

  12. QAR数据多维子序列的相似性搜索%Similarity search for multidimensional QAR data subsequence

    杨慧; 张国振

    2013-01-01

    High dimensionality of QAR and the uncertain relevance among them which make the method to do the similarity search for time series in the low dimensionality are no longer applicable in such situation. Taking into account the specificity of the civil aviation industry, with the similarity search for QAR to ascertain the plane faults requires a special definition of the similarity. In this paper, expertise and analytic hierarchy process algorithm are combined to be used to calculate the weightiness of different dimensionalities for the plane fault. It translates the QAR data with the symbolic method, and then builds a k-d tree index, which makes it possible to do the similarity search on multidimensional QAR data subsequences. Shape and distance are used toghther to define similarity. The high precision and the low cost are proved by the experiments in this paper.%QAR数据的高维度以及维度之间不确定的相互关联性,使得原有低维空间上度量时间序列的相似性的方法不再适用,另一方面由于民航行业的特殊性,利用QAR数据进行相似性搜索来确定飞行故障,对相似性的定义也有特殊的要求.通过专家经验结合一种层次分析算法来确定飞行故障所关联的属性维度的重要性,对QAR数据的多维子序列进行符号化表示,并利用k-d树的特殊性质建立索引,使QAR数据多维子序列的快速相似性搜索成为可能,结合形状和距离对相似性进行定义和度量,实验证明查找速度快,准确度较为满意.

  13. SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity.

    Yang, Yuedong; Zhan, Jian; Zhou, Yaoqi

    2016-07-01

    Structure-based virtual screening usually involves docking of a library of chemical compounds onto the functional pocket of the target receptor so as to discover novel classes of ligands. However, the overall success rate remains low and screening a large library is computationally intensive. An alternative to this "ab initio" approach is virtual screening by binding homology search. In this approach, potential ligands are predicted based on similar interaction pairs (similarity in receptors and ligands). SPOT-Ligand is an approach that integrates ligand similarity by Tanimoto coefficient and receptor similarity by protein structure alignment program SPalign. The method was found to yield a consistent performance in DUD and DUD-E docking benchmarks even if model structures were employed. It improves over docking methods (DOCK6 and AUTODOCK Vina) and has a performance comparable to or better than other binding-homology methods (FINDsite and PoLi) with higher computational efficiency. The server is available at http://sparks-lab.org. © 2016 Wiley Periodicals, Inc. PMID:27074979

  14. Accelerated equilibrium core composition search using a new MCNP-based simulator

    MocDown is a new Monte Carlo depletion and recycling simulator which couples neutron transport with MCNP and transmutation with ORIGEN. This modular approach to depletion allows for flexible operation by incorporating the accelerated progression of a complex fuel processing scheme towards equilibrium and by allowing for the online coupling of thermo-fluids feedback. MocDown also accounts for the variation of decay heat with fuel isotopics evolution. In typical cases, MocDown requires just over a day to find the equilibrium core composition for a multi-recycling fuel cycle, with a self-consistent thermo-fluids solution-a task that required between one and two weeks using previous Monte Carlo-based approaches. (authors)

  15. Accelerated equilibrium core composition search using a new MCNP-based simulator

    Seifried, Jeffrey E.; Gorman, Phillip M.; Vujic, Jasmina L.; Greenspan, Ehud

    2014-06-01

    MocDown is a new Monte Carlo depletion and recycling simulator which couples neutron transport with MCNP and transmutation with ORIGEN. This modular approach to depletion allows for flexible operation by incorporating the accelerated progression of a complex fuel processing scheme towards equilibrium and by allowing for the online coupling of thermo-fluids feedback. MocDown also accounts for the variation of decay heat with fuel isotopics evolution. In typical cases, MocDown requires just over a day to find the equilibrium core composition for a multi-recycling fuel cycle, with a self-consistent thermo-fluids solution-a task that required between one and two weeks using previous Monte Carlo-based approaches.

  16. Accelerator mass spectrometry of actinides and the search for superheavy elements

    In the 1960s nuclear shell model calculations indicated an increased stability of superheavy closed-shell nuclides beyond any known species. This region was quickly nicknamed island of stability', and half-lives up to 109 years were predicted for some nuclides. Assuming their presence in the Early Solar System, the predicted half-lives would be sufficiently long to find traces of these nuclides in natural materials today. Within the last decades numerous experiments - utilizing different measurement techniques - were conducted to detect superheavy elements (SHEs) in nature - all with negative results. Appreciable technical progress in Accelerator Mass Spectrometry (AMS) within recent years triggered new attempts to find SHEs in natural materials. AMS is considered to be the 'technique of choice' for the detection of long-lived radionuclides at ultra-low abundances. The outstanding selectivity of AMS allowed the investigation of chemically untreated natural samples, preventing a priori an unintended separation of SHEs in chemical preparations, which are required for other measurement techniques. For the first time the 'Vienna Environmental Research Accelerator' (VERA) facility was set up for AMS measurements in the mass range of A = 288-300 amu. Altogether 30 nuclides in the vicinity of the 'island of stability' were investigated. Sample material extracted from natural ores containing Pb or Bi and nuggets of Pt and Au was used in these measurements. Since no unambiguous events were detected, upper limits for the abundance of those nuclides within the sample matrix in the range of 10-12 to 10-15 (relative to the carrier matrix atoms) could be established. When the SHE project started at VERA, the detection of a long-lived superheavy ion species with A = 292 in thorium was reported by the group of Marinov et al. in Jerusalem performed by means of inductively coupled plasma sector field mass spectrometry (ICPSF-MS). The group also reported on the detection of four long

  17. Similarity Search in Document Collections

    Jordanov, Dimitar Dimitrov

    2009-01-01

    Hlavním cílem této práce je odhadnout výkonnost volně šířeni balík  Sémantický Vektory a třída MoreLikeThis z balíku Apache Lucene. Tato práce nabízí porovnání těchto dvou přístupů a zavádí metody, které mohou vést ke zlepšení kvality vyhledávání.

  18. Search for magnetic fields in particle-accelerating colliding-wind binaries

    Neiner, C; Leroy, B; De Becker, M; Rauw, G

    2014-01-01

    Some colliding-wind massive binaries, called particle-accelerating colliding-wind binaries (PACWB), exhibit synchrotron radio emission, which is assumed to be generated by a stellar magnetic field. However, no measurement of magnetic fields in these stars has ever been performed. We aim at quantifying the possible stellar magnetic fields present in PACWB to provide constraints for models. We gathered 21 high-resolution spectropolarimetric observations of 9 PACWB available in the ESPaDOnS, Narval and HarpsPol archives. We analysed these observations with the Least Squares Deconvolution method. We separated the binary spectral components when possible. No magnetic signature is detected in any of the 9 PACWB stars and all longitudinal field measurements are compatible with 0 G. We derived the upper field strength of a possible field that could have remained hidden in the noise of the data. While the data are not very constraining for some stars, for several stars we could derive an upper limit of the polar field...

  19. Search for magnetic fields in particle-accelerating colliding-wind binaries

    Neiner, C.; Grunhut, J.; Leroy, B.; De Becker, M.; Rauw, G.

    2015-03-01

    Context. Some colliding-wind massive binaries, called particle-accelerating colliding-wind binaries (PACWB), exhibit synchrotron radio emission, which is assumed to be generated by a stellar magnetic field. However, no measurement of magnetic fields in these stars has ever been performed. Aims: We aim at quantifying the possible stellar magnetic fields present in PACWB to provide constraints for models. Methods: We gathered 21 high-resolution spectropolarimetric observations of 9 PACWB available in the ESPaDOnS, Narval and HarpsPol archives. We analysed these observations with the least squares deconvolution method. We separated the binary spectral components when possible. Results: No magnetic signature is detected in any of the 9 PACWB stars and all longitudinal field measurements are compatible with 0 G. We derived the upper field strength of a possible field that could have remained hidden in the noise of the data. While the data are not very constraining for some stars, for several stars we could derive an upper limit of the polar field strength of the order of 200 G. Conclusions: We can therefore exclude the presence of strong or moderate stellar magnetic fields in PACWB, typical of the ones present in magnetic massive stars. Weak magnetic fields could however be present in these objects. These observational results provide the first quantitative constraints for future models of PACWB. Based on archival observations obtained at the Télescope Bernard Lyot (USR5026) operated by the Observatoire Midi-Pyrénées, Université de Toulouse (Paul Sabatier), Centre National de la Recherche Scientifique (CNRS) of France, at the Canada-France-Hawaii Telescope (CFHT) operated by the National Research Council of Canada, the Institut National des Sciences de l'Univers of the CNRS of France, and the University of Hawaii, and at the European Southern Observatory (ESO), Chile.

  20. Design of a bioactive small molecule that targets the myotonic dystrophy type 1 RNA via an RNA motif-ligand database and chemical similarity searching.

    Parkesh, Raman; Childs-Disney, Jessica L; Nakamori, Masayuki; Kumar, Amit; Wang, Eric; Wang, Thomas; Hoskins, Jason; Tran, Tuan; Housman, David; Thornton, Charles A; Disney, Matthew D

    2012-03-14

    Myotonic dystrophy type 1 (DM1) is a triplet repeating disorder caused by expanded CTG repeats in the 3'-untranslated region of the dystrophia myotonica protein kinase (DMPK) gene. The transcribed repeats fold into an RNA hairpin with multiple copies of a 5'CUG/3'GUC motif that binds the RNA splicing regulator muscleblind-like 1 protein (MBNL1). Sequestration of MBNL1 by expanded r(CUG) repeats causes splicing defects in a subset of pre-mRNAs including the insulin receptor, the muscle-specific chloride ion channel, sarco(endo)plasmic reticulum Ca(2+) ATPase 1, and cardiac troponin T. Based on these observations, the development of small-molecule ligands that target specifically expanded DM1 repeats could be of use as therapeutics. In the present study, chemical similarity searching was employed to improve the efficacy of pentamidine and Hoechst 33258 ligands that have been shown previously to target the DM1 triplet repeat. A series of in vitro inhibitors of the RNA-protein complex were identified with low micromolar IC(50)'s, which are >20-fold more potent than the query compounds. Importantly, a bis-benzimidazole identified from the Hoechst query improves DM1-associated pre-mRNA splicing defects in cell and mouse models of DM1 (when dosed with 1 mM and 100 mg/kg, respectively). Since Hoechst 33258 was identified as a DM1 binder through analysis of an RNA motif-ligand database, these studies suggest that lead ligands targeting RNA with improved biological activity can be identified by using a synergistic approach that combines analysis of known RNA-ligand interactions with chemical similarity searching. PMID:22300544

  1. Improving Limit Surface Search Algorithms in RAVEN Using Acceleration Schemes: Level II Milestone

    Alfonsi, Andrea [Idaho National Laboratory (INL), Idaho Falls, ID (United States); Rabiti, Cristian [Idaho National Laboratory (INL), Idaho Falls, ID (United States); Mandelli, Diego [Idaho National Laboratory (INL), Idaho Falls, ID (United States); Cogliati, Joshua Joseph [Idaho National Laboratory (INL), Idaho Falls, ID (United States); Sen, Ramazan Sonat [Idaho National Laboratory (INL), Idaho Falls, ID (United States); Smith, Curtis Lee [Idaho National Laboratory (INL), Idaho Falls, ID (United States)

    2015-07-01

    , subject of the analysis. These methodologies are named, in the RAVEN environment, adaptive sampling strategies. These methodologies infer system responses from surrogate models constructed from already existing samples (produced using high fidelity simulations) and suggest the most relevant location (coordinate in the input space) of the next sampling point to be explored in the uncertain/parametric domain. When using those methodologies, it is possible to understand features of the system response with a small number of carefully selected samples. This report focuses on the development and improvement of the limit surface search. The limit surface is an important concept in system reliability analysis. Without going into the details, which will be covered later in the report, the limit surface could be briefly described as an hyper-surface in the system uncertainty/parametric space separating the regions leading to a prescribed system outcome. For example, if the uncertainty/parametric space is the one generated by the reactor power level and the duration of the batteries, the system is a nuclear power plant and the system outcome discriminating variable is the clad failure in a station blackout scenario, then the limit surface separates the combinations of reactor power level and battery duration that lead to clad failure from the ones that do not.

  2. Improving Limit Surface Search Algorithms in RAVEN Using Acceleration Schemes: Level II Milestone

    system, subject of the analysis. These methodologies are named, in the RAVEN environment, adaptive sampling strategies. These methodologies infer system responses from surrogate models constructed from already existing samples (produced using high fidelity simulations) and suggest the most relevant location (coordinate in the input space) of the next sampling point to be explored in the uncertain/parametric domain. When using those methodologies, it is possible to understand features of the system response with a small number of carefully selected samples. This report focuses on the development and improvement of the limit surface search. The limit surface is an important concept in system reliability analysis. Without going into the details, which will be covered later in the report, the limit surface could be briefly described as an hyper-surface in the system uncertainty/parametric space separating the regions leading to a prescribed system outcome. For example, if the uncertainty/parametric space is the one generated by the reactor power level and the duration of the batteries, the system is a nuclear power plant and the system outcome discriminating variable is the clad failure in a station blackout scenario, then the limit surface separates the combinations of reactor power level and battery duration that lead to clad failure from the ones that do not.

  3. Compression-based similarity

    Vitányi, Paul

    2011-01-01

    First we consider pair-wise distances for literal objects consisting of finite binary files. These files are taken to contain all of their meaning, like genomes or books. The distances are based on compression of the objects concerned, normalized, and can be viewed as similarity distances. Second, we consider pair-wise distances between names of objects, like "red" or "christianity." In this case the distances are based on searches of the Internet. Such a search can be performed by any search...

  4. Current trends in non-accelerator particle physics: 1, Neutrino mass and oscillation. 2, High energy neutrino astrophysics. 3, Detection of dark matter. 4, Search for strange quark matter. 5, Magnetic monopole searches

    This report is a compilation of papers reflecting current trends in non-accelerator particle physics, corresponding to talks that its author was invited to present at the Workshop on Tibet Cosmic Ray Experiment and Related Physics Topics held in Beijing, China, April 4--13, 1995. The papers are entitled 'Neutrino Mass and Oscillation', 'High Energy Neutrino Astrophysics', 'Detection of Dark Matter', 'Search for Strange Quark Matter', and 'Magnetic Monopole Searches'. The report is introduced by a survey of the field and a brief description of each of the author's papers

  5. Current trends in non-accelerator particle physics: 1, Neutrino mass and oscillation. 2, High energy neutrino astrophysics. 3, Detection of dark matter. 4, Search for strange quark matter. 5, Magnetic monopole searches

    He, Yudong [California Univ., Berkeley, CA (United States)]|[Lawrence Berkeley Lab., CA (United States)

    1995-07-01

    This report is a compilation of papers reflecting current trends in non-accelerator particle physics, corresponding to talks that its author was invited to present at the Workshop on Tibet Cosmic Ray Experiment and Related Physics Topics held in Beijing, China, April 4--13, 1995. The papers are entitled `Neutrino Mass and Oscillation`, `High Energy Neutrino Astrophysics`, `Detection of Dark Matter`, `Search for Strange Quark Matter`, and `Magnetic Monopole Searches`. The report is introduced by a survey of the field and a brief description of each of the author`s papers.

  6. Neural circuits of eye movements during performance of the visual exploration task, which is similar to the responsive search score task, in schizophrenia patients and normal subjects

    Abnormal exploratory eye movements have been studied as a biological marker for schizophrenia. Using functional MRI (fMRI), we investigated brain activations of 12 healthy and 8 schizophrenic subjects during performance of a visual exploration task that is similar to the responsive search score task to clarify the neural basis of the abnormal exploratory eye movement. Performance data, such as the number of eye movements, the reaction time, and the percentage of correct answers showed no significant differences between the two groups. Only the normal subjects showed activations at the bilateral thalamus and the left anterior medial frontal cortex during the visual exploration tasks. In contrast, only the schizophrenic subjects showed activations at the right anterior cingulate gyms during the same tasks. The activation at the different locations between the two groups, the left anterior medial frontal cortex in normal subjects and the right anterior cingulate gyrus in schizophrenia subjects, was explained by the feature of the visual tasks. Hypoactivation at the bilateral thalamus supports a dysfunctional filtering theory of schizophrenia. (author)

  7. Gesture Recognition from Data Streams of Human Motion Sensor Using Accelerated PSO Swarm Search Feature Selection Algorithm

    Simon Fong

    2015-01-01

    Full Text Available Human motion sensing technology gains tremendous popularity nowadays with practical applications such as video surveillance for security, hand signing, and smart-home and gaming. These applications capture human motions in real-time from video sensors, the data patterns are nonstationary and ever changing. While the hardware technology of such motion sensing devices as well as their data collection process become relatively mature, the computational challenge lies in the real-time analysis of these live feeds. In this paper we argue that traditional data mining methods run short of accurately analyzing the human activity patterns from the sensor data stream. The shortcoming is due to the algorithmic design which is not adaptive to the dynamic changes in the dynamic gesture motions. The successor of these algorithms which is known as data stream mining is evaluated versus traditional data mining, through a case of gesture recognition over motion data by using Microsoft Kinect sensors. Three different subjects were asked to read three comic strips and to tell the stories in front of the sensor. The data stream contains coordinates of articulation points and various positions of the parts of the human body corresponding to the actions that the user performs. In particular, a novel technique of feature selection using swarm search and accelerated PSO is proposed for enabling fast preprocessing for inducing an improved classification model in real-time. Superior result is shown in the experiment that runs on this empirical data stream. The contribution of this paper is on a comparative study between using traditional and data stream mining algorithms and incorporation of the novel improved feature selection technique with a scenario where different gesture patterns are to be recognized from streaming sensor data.

  8. Textual Spatial Cosine Similarity

    Crocetti, Giancarlo

    2015-01-01

    When dealing with document similarity many methods exist today, like cosine similarity. More complex methods are also available based on the semantic analysis of textual information, which are computationally expensive and rarely used in the real time feeding of content as in enterprise-wide search environments. To address these real-time constraints, we developed a new measure of document similarity called Textual Spatial Cosine Similarity, which is able to detect similitude at the semantic ...

  9. Similarity Search in Data Stream with Adaptive Segmental Approximations%基于适应性分段估计的数据流相似性搜索

    吴枫; 仲妍; 吴泉源; 贾焰; 杨树强

    2009-01-01

    Similarity search has attracted many researchers from various communities (real-time stock quotes, network security, sensor networks). Due to the infinite, continuous, fast and real-time properties of the data from these communities, a method is needed for online similarity search in data stream. This paper first proposes the lower bound function LB_seg_WF_(global) for DTW (dynamic time warping) in the presence of global warping constraints and LB_seg_WF for DTW without global warping constraints, which are not applied to any index structures. They are segmented DTW techniques, and can be applied to sequences and queries of varying lengths in data stream. Next, several tighter lower bounds are proposed to improve the approximate degree of the LB_seg_WF_(global) and LB_seg_WF. Finally, to deal with the possible continuously non-effective problem of LB_seg_WF_(global) or LB_seg_WF in data stream, it is believed that lower-bound LB_WF_(global) (in the presence of global warping constraints) and lower-bound LB_WF, upper-bound UB_WF (without global warping constraints) can fast estimate DTW and hence reduce a lot of redundant computations by incrementally computing. The theoretical analysis and statistical experiments confirm the validity of the proposed methods.%相似性搜索在股票交易行情、网络安全、传感器网络等众多领域应用广泛.由于这些领域中产生的数据具有无限的、连续的、快速的、实时的特性,所以需要适合数据流上的在线相似性搜索算法.首先,在具有或不具有全局约束条件下,分别提出了没有索引结构的DTW(dynamic time warping)下限函数LB_seg_WF_(global)和LB_seg_WF,它们是一种分段DTW技术,能够处理数据流上的非等长序列间在线相似性匹配问题.然后,为了进一步提高LB_seg_WF_(global)和LB_seg_WF的近似程度,提出了一系列的改进方法.最后,针对流上使用LB_seg_WF_(global)或LB_seg_WF可能会出现连续失效的情况,分别提

  10. Concept Search

    Giunchiglia, Fausto; Kharkevich, Uladzimir; Zaihrayeu, Ilya

    2008-01-01

    In this paper we present a novel approach, called Concept Search, which extends syntactic search, i.e., search based on the computation of string similarity between words, with semantic search, i.e., search based on the computation of semantic relations between concepts. The key idea of Concept Search is to operate on complex concepts and to maximally exploit the semantic information available, reducing to syntactic search only when necessary, i.e., when no semantic information is available. ...

  11. Modal Similarity

    Vigo , Dr. Ronaldo

    2009-01-01

    Just as Boolean rules define Boolean categories, the Boolean operators define higher-order Boolean categories referred to as modal categories. We examine the similarity order between these categories and the standard category of logical identity (i.e. the modal category defined by the biconditional or equivalence operator). Our goal is 4-fold: first, to introduce a similarity measure for determining this similarity order; second, to show that such a measure is a good predictor of the similari...

  12. CUDAMPF: a multi-tiered parallel framework for accelerating protein sequence search in HMMER on CUDA-enabled GPU

    Jiang, Hanyu; Ganesan, Narayan

    2016-01-01

    Background HMMER software suite is widely used for analysis of homologous protein and nucleotide sequences with high sensitivity. The latest version of hmmsearch in HMMER 3.x, utilizes heuristic-pipeline which consists of MSV/SSV (Multiple/Single ungapped Segment Viterbi) stage, P7Viterbi stage and the Forward scoring stage to accelerate homology detection. Since the latest version is highly optimized for performance on modern multi-core CPUs with SSE capabilities, only a few acceleration att...

  13. Combination of 2D/3D Ligand-Based Similarity Search in Rapid Virtual Screening from Multimillion Compound Repositories. Selection and Biological Evaluation of Potential PDE4 and PDE5 Inhibitors

    Krisztina Dobi

    2014-05-01

    Full Text Available Rapid in silico selection of target focused libraries from commercial repositories is an attractive and cost effective approach. If structures of active compounds are available rapid 2D similarity search can be performed on multimillion compound databases but the generated library requires further focusing by various 2D/3D chemoinformatics tools. We report here a combination of the 2D approach with a ligand-based 3D method (Screen3D which applies flexible matching to align reference and target compounds in a dynamic manner and thus to assess their structural and conformational similarity. In the first case study we compared the 2D and 3D similarity scores on an existing dataset derived from the biological evaluation of a PDE5 focused library. Based on the obtained similarity metrices a fusion score was proposed. The fusion score was applied to refine the 2D similarity search in a second case study where we aimed at selecting and evaluating a PDE4B focused library. The application of this fused 2D/3D similarity measure led to an increase of the hit rate from 8.5% (1st round, 47% inhibition at 10 µM to 28.5% (2nd round at 50% inhibition at 10 µM and the best two hits had 53 nM inhibitory activities.

  14. Accelerators and Dinosaurs

    Turner, Michael Stanley

    2003-01-01

    Using naturally occuring particles on which to research might have made accelerators become extinct. But in fact, results from astrophysics have made accelerator physics even more important. Not only are accelerators used in hospitals but they are also being used to understand nature's inner workings by searching for Higgs bosons, CP violation, neutrino mass and dark matter (2 pages)

  15. Cognitive residues of similarity

    OToole, Stephanie; Keane, Mark T.

    2013-01-01

    What are the cognitive after-effects of making a similarity judgement? What, cognitively, is left behind and what effect might these residues have on subsequent processing? In this paper, we probe for such after-effects using a visual search task, performed after a task in which pictures of real-world objects were compared. So, target objects were first presented in a comparison task (e.g., rate the similarity of this object to another) thus, presumably, modifying some of their features befor...

  16. Accelerated Cure Project for Multiple Sclerosis

    ... main content Accelerating research toward a cure for multiple sclerosis Home Contact Us Search form Search Connect Volunteer ... is to accelerate efforts toward a cure for multiple sclerosis by rapidly advancing research that determines its causes ...

  17. Search for major genes with progeny test data to accelerate the development of genetically superior loblolly pine

    NCSU

    2003-12-30

    This research project is to develop a novel approach that fully utilized the current breeding materials and genetic test information available from the NCSU-Industry Cooperative Tree Improvement Program to identify major genes that are segregating for growth and disease resistance in loblolly pine. If major genes can be identified in the existing breeding population, they can be utilized directly in the conventional loblolly pine breeding program. With the putative genotypes of parents identified, tree breeders can make effective decisions on management of breeding populations and operational deployment of genetically superior trees. Forest productivity will be significantly enhanced if genetically superior genotypes with major genes for economically important traits could be deployed in an operational plantation program. The overall objective of the project is to develop genetic model and analytical methods for major gene detection with progeny test data and accelerate the development of genetically superior loblolly pine. Specifically, there are three main tasks: (1) Develop genetic models for major gene detection and implement statistical methods and develop computer software for screening progeny test data; (2) Confirm major gene segregation with molecular markers; and (3) Develop strategies for using major genes for tree breeding.

  18. GPU-Accelerated Text Mining

    Cui, Xiaohui [ORNL; Mueller, Frank [North Carolina State University; Zhang, Yongpeng [ORNL; Potok, Thomas E [ORNL

    2009-01-01

    Accelerating hardware devices represent a novel promise for improving the performance for many problem domains but it is not clear for which domains what accelerators are suitable. While there is no room in general-purpose processor design to significantly increase the processor frequency, developers are instead resorting to multi-core chips duplicating conventional computing capabilities on a single die. Yet, accelerators offer more radical designs with a much higher level of parallelism and novel programming environments. This present work assesses the viability of text mining on CUDA. Text mining is one of the key concepts that has become prominent as an effective means to index the Internet, but its applications range beyond this scope and extend to providing document similarity metrics, the subject of this work. We have developed and optimized text search algorithms for GPUs to exploit their potential for massive data processing. We discuss the algorithmic challenges of parallelization for text search problems on GPUs and demonstrate the potential of these devices in experiments by reporting significant speedups. Our study may be one of the first to assess more complex text search problems for suitability for GPU devices, and it may also be one of the first to exploit and report on atomic instruction usage that have recently become available in NVIDIA devices.

  19. GPU-Accelerated Text Mining

    Accelerating hardware devices represent a novel promise for improving the performance for many problem domains but it is not clear for which domains what accelerators are suitable. While there is no room in general-purpose processor design to significantly increase the processor frequency, developers are instead resorting to multi-core chips duplicating conventional computing capabilities on a single die. Yet, accelerators offer more radical designs with a much higher level of parallelism and novel programming environments. This present work assesses the viability of text mining on CUDA. Text mining is one of the key concepts that has become prominent as an effective means to index the Internet, but its applications range beyond this scope and extend to providing document similarity metrics, the subject of this work. We have developed and optimized text search algorithms for GPUs to exploit their potential for massive data processing. We discuss the algorithmic challenges of parallelization for text search problems on GPUs and demonstrate the potential of these devices in experiments by reporting significant speedups. Our study may be one of the first to assess more complex text search problems for suitability for GPU devices, and it may also be one of the first to exploit and report on atomic instruction usage that have recently become available in NVIDIA devices

  20. Gene functional similarity search tool (GFSST)

    Russo James J; Sheng Huitao; Zhang Jinghui; Zhang Peisen; Osborne Brian; Buetow Kenneth

    2006-01-01

    Abstract Background With the completion of the genome sequences of human, mouse, and other species and the advent of high throughput functional genomic research technologies such as biomicroarray chips, more and more genes and their products have been discovered and their functions have begun to be understood. Increasing amounts of data about genes, gene products and their functions have been stored in databases. To facilitate selection of candidate genes for gene-disease research, genetic as...

  1. Personalized Search

    AUTHOR|(SzGeCERN)749939

    2015-01-01

    As the volume of electronically available information grows, relevant items become harder to find. This work presents an approach to personalizing search results in scientific publication databases. This work focuses on re-ranking search results from existing search engines like Solr or ElasticSearch. This work also includes the development of Obelix, a new recommendation system used to re-rank search results. The project was proposed and performed at CERN, using the scientific publications available on the CERN Document Server (CDS). This work experiments with re-ranking using offline and online evaluation of users and documents in CDS. The experiments conclude that the personalized search result outperform both latest first and word similarity in terms of click position in the search result for global search in CDS.

  2. A measurement of hadron production cross sections for the simulation of accelerator neutrino beams and a search for muon-neutrino to electron-neutrino oscillations in the delta m**2 about equals 1-eV**2 region

    Schmitz, David W.; /Columbia U.

    2008-01-01

    A measurement of hadron production cross-sections for the simulation of accelerator neutrino beams and a search for muon neutrino to electron neutrino oscillations in the {Delta}m{sup 2} {approx} 1 eV{sup 2} region. This dissertation presents measurements from two different high energy physics experiments with a very strong connection: the Hadron Production (HARP) experiment located at CERN in Geneva, Switzerland, and the Mini Booster Neutrino Experiment (Mini-BooNE) located at Fermilab in Batavia, Illinois.

  3. The search for evidence of particle acceleration at SN 1987A in MeV to PeV γ rays

    Young supernova remnants may be bright sources of energetic photons and neutrinos, which are produced by collisions of particles accelerated inside the remnant. The new supernova 1987A has led to renewed interest in the subject, with several papers discussing the possibility of observing high-energy neutrinos and photons from this supernova. This paper reviews the prospects for production of observable signatures of particle acceleration in SN1987A and their potential implications for energetic processes inside young, Type II supernovae. The bolometric light curve of SN1987A can place a strong upper limit on the power from a source other than the energy released in the radioactive decay chain of 56Ni → 56CO → 56Fe. This in turn limits the amount of power from a central source, such as a pulsar, that might accelerate particles. However, it is still possible that acceleration may be occurring in SN1987A at detectable levels

  4. Applying ligands profiling using multiple extended electron distribution based field templates and feature trees similarity searching in the discovery of new generation of urea-based antineoplastic kinase inhibitors.

    Eman M Dokla

    Full Text Available This study provides a comprehensive computational procedure for the discovery of novel urea-based antineoplastic kinase inhibitors while focusing on diversification of both chemotype and selectivity pattern. It presents a systematic structural analysis of the different binding motifs of urea-based kinase inhibitors and the corresponding configurations of the kinase enzymes. The computational model depends on simultaneous application of two protocols. The first protocol applies multiple consecutive validated virtual screening filters including SMARTS, support vector-machine model (ROC = 0.98, Bayesian model (ROC = 0.86 and structure-based pharmacophore filters based on urea-based kinase inhibitors complexes retrieved from literature. This is followed by hits profiling against different extended electron distribution (XED based field templates representing different kinase targets. The second protocol enables cancericidal activity verification by using the algorithm of feature trees (Ftrees similarity searching against NCI database. Being a proof-of-concept study, this combined procedure was experimentally validated by its utilization in developing a novel series of urea-based derivatives of strong anticancer activity. This new series is based on 3-benzylbenzo[d]thiazol-2(3H-one scaffold which has interesting chemical feasibility and wide diversification capability. Antineoplastic activity of this series was assayed in vitro against NCI 60 tumor-cell lines showing very strong inhibition of GI(50 as low as 0.9 uM. Additionally, its mechanism was unleashed using KINEX™ protein kinase microarray-based small molecule inhibitor profiling platform and cell cycle analysis showing a peculiar selectivity pattern against Zap70, c-src, Mink1, csk and MeKK2 kinases. Interestingly, it showed activity on syk kinase confirming the recent studies finding of the high activity of diphenyl urea containing compounds against this kinase. Allover, the new series

  5. A Denoising Autoencoder that Guides Stochastic Search

    Churchill, Alexander W.; Sigtia, Siddharth; Fernando, Chrisantha

    2014-01-01

    An algorithm is described that adaptively learns a non-linear mutation distribution. It works by training a denoising autoencoder (DA) online at each generation of a genetic algorithm to reconstruct a slowly decaying memory of the best genotypes so far. A compressed hidden layer forces the autoencoder to learn hidden features in the training set that can be used to accelerate search on novel problems with similar structure. Its output neurons define a probability distribution that we sample f...

  6. Can Accelerators Accelerate Learning?

    The 'Young Talented' education program developed by the Brazilian State Funding Agency (FAPERJ)[1] makes it possible for high-schools students from public high schools to perform activities in scientific laboratories. In the Atomic and Molecular Physics Laboratory at Federal University of Rio de Janeiro (UFRJ), the students are confronted with modern research tools like the 1.7 MV ion accelerator. Being a user-friendly machine, the accelerator is easily manageable by the students, who can perform simple hands-on activities, stimulating interest in physics, and getting the students close to modern laboratory techniques.

  7. Accelerated simulated tempering

    We propose a new stochastic global optimization method by accelerating the simulated tempering scheme with random walks executed on a temperature ladder with various transition step sizes. By suitably choosing the length of the transition steps, the accelerated scheme enables the search process to execute large jumps and escape entrapment in local minima, while retaining the capability to explore local details, whenever warranted. Our simulations confirm the expected improvements and show that the accelerated simulated tempering scheme has a much faster convergence to the target distribution than Geyer and Thompson's simulated tempering algorithm and exhibits accuracy comparable to the simulated annealing method

  8. Accelerated simulated tempering

    Li, Yaohang; Protopopescu, Vladimir A.; Gorin, Andrey

    2004-08-01

    We propose a new stochastic global optimization method by accelerating the simulated tempering scheme with random walks executed on a temperature ladder with various transition step sizes. By suitably choosing the length of the transition steps, the accelerated scheme enables the search process to execute large jumps and escape entrapment in local minima, while retaining the capability to explore local details, whenever warranted. Our simulations confirm the expected improvements and show that the accelerated simulated tempering scheme has a much faster convergence to the target distribution than Geyer and Thompson's simulated tempering algorithm and exhibits accuracy comparable to the simulated annealing method.

  9. Particle accelerator; the Universe machine

    Yurkewicz, Katie

    2008-01-01

    "In summer 2008, scientists will switch on one of the largest machines in the world to search for the smallest of particle. CERN's Large Hadron Collider particle accelerator has the potential to chagne our understanding of the Universe."

  10. Plasma accelerators

    Recently attention has focused on charged particle acceleration in a plasma by a fast, large amplitude, longitudinal electron plasma wave. The plasma beat wave and plasma wakefield accelerators are two efficient ways of producing ultra-high accelerating gradients. Starting with the plasma beat wave accelerator (PBWA) and laser wakefield accelerator (LWFA) schemes and the plasma wakefield accelerator (PWFA) steady progress has been made in theory, simulations and experiments. Computations are presented for the study of LWFA. (author)

  11. Memory support for desktop search

    Chen, Yi; Kelly, Liadh; Jones, Gareth J.F.

    2010-01-01

    The user's memory plays a very important role in desktop search. A search query with insufficiently or inaccurately recalled information may make the search dramatically less effective. In this paper, we discuss three approaches to support user’s memory during desktop search. These include extended types of well remembered search options, the use of past search queries and results, and search from similar items. We will also introduce our search system which incorporates these featur...

  12. Linear Accelerators

    Vretenar, M

    2014-01-01

    The main features of radio-frequency linear accelerators are introduced, reviewing the different types of accelerating structures and presenting the main characteristics aspects of linac beam dynamics.

  13. Studies of accelerated compact toruses

    In an earlier publication we considered acceleration of plasma rings (Compact Torus). Several possible accelerator configurations were suggested and the possibility of focusing the accelerated rings was discussed. In this paper we consider one scheme, acceleration of a ring between coaxial electrodes by a B/sub theta/ field as in a coaxial rail-gun. If the electrodes are conical, a ring accelerated towards the apex of the cone undergoes self-similar compression (focusing) during acceleration. Because the allowable acceleration force, F/sub a/ = kappaU/sub m//R where (kappa -2, the accelerating distance for conical electrodes is considerably shortened over that required for coaxial electrodes. In either case, however, since the accelerating flux can expand as the ring moves, most of the accelerating field energy can be converted into kinetic energy of the ring leading to high efficiency

  14. Fast Structural Search in Phylogenetic Databases

    William H. Piel

    2005-01-01

    Full Text Available As the size of phylogenetic databases grows, the need for efficiently searching these databases arises. Thanks to previous and ongoing research, searching by attribute value and by text has become commonplace in these databases. However, searching by topological or physical structure, especially for large databases and especially for approximate matches, is still an art. We propose structural search techniques that, given a query or pattern tree P and a database of phylogenies D, find trees in D that are sufficiently close to P . The “closeness” is a measure of the topological relationships in P that are found to be the same or similar in a tree D in D. We develop a filtering technique that accelerates searches and present algorithms for rooted and unrooted trees where the trees can be weighted or unweighted. Experimental results on comparing the similarity measure with existing tree metrics and on evaluating the efficiency of the search techniques demonstrate that the proposed approach is promising

  15. Custom Search Engines: Tools & Tips

    Notess, Greg R.

    2008-01-01

    Few have the resources to build a Google or Yahoo! from scratch. Yet anyone can build a search engine based on a subset of the large search engines' databases. Use Google Custom Search Engine or Yahoo! Search Builder or any of the other similar programs to create a vertical search engine targeting sites of interest to users. The basic steps to…

  16. Search for optimal 2D and 3D wave launching configurations for the largest acceleration of charged particles in a magnetized plasma, resonant moments method

    Optimal two-dimensional, three-dimensional wave launching configurations are proposed for enhanced acceleration of charged particles in magnetized plasmas. A primary wave is launched obliquely with respect to the magnetic field and a secondary, low amplitude, wave is launched perpendicularly. The effect of both the launching angle of the primary wave, and the presence of the secondary wave is investigated. Theoretical predictions of the highest performances of the three-dimensional configurations are proposed using a Resonance Moments Method (RMM) based on estimates for the moments of the velocity distribution function calculated inside the resonance layers (RL). They suggest the existence of an optimal angle corresponding to non parallel launching. Direct statistical simulations show that it is possible to rise the mean electron velocity up to the order of magnitude as compared to the primary wave launching alone. It is a quite promising result because the amplitude of the secondary wave is ten times lower than the one of the first wave. The parameters used are related to magnetic plasma fusion experiments in electron cyclotron resonance heating and electron acceleration in planetary ionospheres and magnetospheres. (authors)

  17. Future accelerators (?)

    I describe the future accelerator facilities that are currently foreseen for electroweak scale physics, neutrino physics, and nuclear structure. I will explore the physics justification for these machines, and suggest how the case for future accelerators can be made

  18. Future accelerators (?)

    John Womersley

    2003-08-21

    I describe the future accelerator facilities that are currently foreseen for electroweak scale physics, neutrino physics, and nuclear structure. I will explore the physics justification for these machines, and suggest how the case for future accelerators can be made.

  19. Perceptual grouping by similarity of surface roughness in haptics: the influence of task difficulty.

    Van Aarsen, V; Overvliet, K E

    2016-08-01

    We investigated grouping by similarity of surface roughness in the context of task difficulty. We hypothesized that grouping yields a larger benefit at higher levels of task complexity, because efficient processing is more helpful when more cognitive resources are needed to execute a task. Participants searched for a patch of a different roughness as compared to the distractors in two strips of similar or dissimilar roughness values. We reasoned that if the distractors could be grouped based on similar roughness values, exploration time would be shorter and fewer errors would occur. To manipulate task complexity, we varied task difficulty (high target saliency equalling low task difficulty), and we varied the fingers used to explore the display (two fingers of one hand being more cognitive demanding than two fingers of opposite hands). We found much better performance in the easy condition as compared to the difficult condition (in both error rates and mean search slopes). Moreover, we found a larger effect for the similarity manipulation in the difficult condition as compared to the easy condition. Within the difficult condition, we found a larger effect for the one-hand condition as compared to the two-hand condition. These results show that haptic search is accelerated by the use of grouping by similarity of surface roughness, especially when the task is relatively complex. We conclude that the effect of perceptual grouping is more prominent when more cognitive resources are needed to perform a task. PMID:27010724

  20. Accelerating Value Creation with Accelerators

    Jonsson, Eythor Ivar

    2015-01-01

    accelerator programs. Microsoft runs accelerators in seven different countries. Accelerators have grown out of the infancy stage and are now an accepted approach to develop new ventures based on cutting-edge technology like the internet of things, mobile technology, big data and virtual reality. It is also......Accelerators can help to accelerate value creation. Accelerators are short-term programs that have the objective of creating innovative and fast growing ventures. They have gained attraction as larger corporations like Microsoft, Barclays bank and Nordea bank have initiated and sponsored...

  1. Plasma based accelerators

    Caldwell, Allen [Max-Planck-Institut fuer Physik, Muenchen (Germany)

    2015-05-01

    The concept of laser-induced plasma wakefields as a technique to accelerate charged particles was introduced 35 years ago as a means to go beyond the accelerating gradients possible with metallic cavities supporting radio frequency electromagnetic fields. Significant developments in laser technology have made possible the pulse intensity needed to realize this concept, and rapid progress is now underway in the realization of laser-driven plasma wakefield acceleration. It has also been realized that similar accelerating gradients can be produced by particle beams propagating in plasmas, and experimental programs have also been undertaken to study this possibility. Positive results have been achieved with electron-driven plasma wakefields, and a demonstration experiment with proton-driven wakefields is under construction at CERN. The concepts behind these different schemes and their pros and cons are described, as well as the experimental results achieved. An outlook for future practical uses of plasma based accelerators will also be given.

  2. Fresnel diffraction patterns as accelerating beams

    Zhang, Yiqi; Belić, Milivoj R.; Zheng, Huaibin; Wu, Zhenkun; Li, Yuanyuan; Lu, Keqing; Zhang, Yanpeng

    2013-01-01

    We demonstrate that beams originating from Fresnel diffraction patterns are self-accelerating in free space. In addition to accelerating and self-healing, they also exhibit parabolic deceleration property, which is in stark contrast to other accelerating beams. We find that the trajectory of Fresnel paraxial accelerating beams is similar to that of nonparaxial Weber beams. Decelerating and accelerating regions are separated by a critical propagation distance, at which no acceleration is prese...

  3. Designing reliability into accelerators

    Future accelerators will have to provide a high degree of reliability. Quality must be designed in right from the beginning and must remain a central theme throughout the project. The problem is similar to the problems facing US industry today, and examples of the successful application of quality engineering will be given. Different aspects of an accelerator project will be addressed: Concept, Design, Motivation, Management Techniques, and Fault Diagnosis. The importance of creating and maintaining a coherent team will be stressed

  4. Persistent Homology and Partial Similarity of Shapes

    Di Fabio, Barbara; Landi, Claudia

    2011-01-01

    The ability to perform shape retrieval based not only on full similarity, but also partial similarity is a key property for any content-based search engine. We prove that persistence diagrams can reveal a partial similarity between two shapes by showing a common subset of points. This can be explained using the Mayer-Vietoris formulas that we develop for ordinary, relative and extended persistent homology. An experiment outlines the potential of persistence diagrams as shape descriptors in re...

  5. Are Defect Profile Similarity Criteria Different Than Velocity Profile Similarity Criteria for the Turbulent Boundary Layer?

    Weyburne, David

    2015-01-01

    The use of the defect profile instead of the experimentally observed velocity profile for the search for similarity parameters has become firmly imbedded in the turbulent boundary layer literature. However, a search of the literature reveals that there are no theoretical reasons for this defect profile preference over the more traditional velocity profile. In the report herein, we use the flow governing equation approach to develop similarity criteria for the two profiles. Results show that t...

  6. The baryonic self similarity of dark matter

    Alard, C., E-mail: alard@iap.fr [Institut d' Astrophysique de Paris, 98bis boulevard Arago, F-75014 Paris (France)

    2014-06-20

    The cosmological simulations indicates that dark matter halos have specific self-similar properties. However, the halo similarity is affected by the baryonic feedback. By using momentum-driven winds as a model to represent the baryon feedback, an equilibrium condition is derived which directly implies the emergence of a new type of similarity. The new self-similar solution has constant acceleration at a reference radius for both dark matter and baryons. This model receives strong support from the observations of galaxies. The new self-similar properties imply that the total acceleration at larger distances is scale-free, the transition between the dark matter and baryons dominated regime occurs at a constant acceleration, and the maximum amplitude of the velocity curve at larger distances is proportional to M {sup 1/4}. These results demonstrate that this self-similar model is consistent with the basics of modified Newtonian dynamics (MOND) phenomenology. In agreement with the observations, the coincidence between the self-similar model and MOND breaks at the scale of clusters of galaxies. Some numerical experiments show that the behavior of the density near the origin is closely approximated by a Einasto profile.

  7. Finding Protein and Nucleotide Similarities with FASTA.

    Pearson, William R

    2016-01-01

    The FASTA programs provide a comprehensive set of rapid similarity searching tools (fasta36, fastx36, tfastx36, fasty36, tfasty36), similar to those provided by the BLAST package, as well as programs for slower, optimal, local, and global similarity searches (ssearch36, ggsearch36), and for searching with short peptides and oligonucleotides (fasts36, fastm36). The FASTA programs use an empirical strategy for estimating statistical significance that accommodates a range of similarity scoring matrices and gap penalties, improving alignment boundary accuracy and search sensitivity. The FASTA programs can produce "BLAST-like" alignment and tabular output, for ease of integration into existing analysis pipelines, and can search small, representative databases, and then report results for a larger set of sequences, using links from the smaller dataset. The FASTA programs work with a wide variety of database formats, including mySQL and postgreSQL databases. The programs also provide a strategy for integrating domain and active site annotations into alignments and highlighting the mutational state of functionally critical residues. These protocols describe how to use the FASTA programs to characterize protein and DNA sequences, using protein:protein, protein:DNA, and DNA:DNA comparisons. © 2016 by John Wiley & Sons, Inc. PMID:27010337

  8. Clustering by Pattern Similarity

    Hai-xun Wang; Jian Pei

    2008-01-01

    The task of clustering is to identify classes of similar objects among a set of objects. The definition of similarity varies from one clustering model to another. However, in most of these models the concept of similarity is often based on such metrics as Manhattan distance, Euclidean distance or other Lp distances. In other words, similar objects must have close values in at least a set of dimensions. In this paper, we explore a more general type of similarity. Under the pCluster model we proposed, two objects are similar if they exhibit a coherent pattern on a subset of dimensions. The new similarity concept models a wide range of applications. For instance, in DNA microarray analysis, the expression levels of two genes may rise and fall synchronously in response to a set of environmental stimuli. Although the magnitude of their expression levels may not be close, the patterns they exhibit can be very much alike. Discovery of such clusters of genes is essential in revealing significant connections in gene regulatory networks. E-commerce applications, such as collaborative filtering, can also benefit from the new model, because it is able to capture not only the closeness of values of certain leading indicators but also the closeness of (purchasing, browsing, etc.) patterns exhibited by the customers. In addition to the novel similarity model, this paper also introduces an effective and efficient algorithm to detect such clusters, and we perform tests on several real and synthetic data sets to show its performance.

  9. Laser accelerator

    Vigil, Ricardo

    2014-01-01

    Approved for public release; distribution is unlimited In 1979,W. B. Colson and S. K. Ride proposed a new kind of electron accelerator using a uniform magnetic field in combination with a circularly-polarized laser field. A key concept is to couple the oscillating electric field to the electron’s motion so that acceleration is sustained. This dissertation investigates the performance of the proposed laser accelerator using modern high powered lasers and mag-netic fields that are significan...

  10. The semantic similarity ensemble

    Andrea Ballatore

    2013-12-01

    Full Text Available Computational measures of semantic similarity between geographic terms provide valuable support across geographic information retrieval, data mining, and information integration. To date, a wide variety of approaches to geo-semantic similarity have been devised. A judgment of similarity is not intrinsically right or wrong, but obtains a certain degree of cognitive plausibility, depending on how closely it mimics human behavior. Thus selecting the most appropriate measure for a specific task is a significant challenge. To address this issue, we make an analogy between computational similarity measures and soliciting domain expert opinions, which incorporate a subjective set of beliefs, perceptions, hypotheses, and epistemic biases. Following this analogy, we define the semantic similarity ensemble (SSE as a composition of different similarity measures, acting as a panel of experts having to reach a decision on the semantic similarity of a set of geographic terms. The approach is evaluated in comparison to human judgments, and results indicate that an SSE performs better than the average of its parts. Although the best member tends to outperform the ensemble, all ensembles outperform the average performance of each ensemble's member. Hence, in contexts where the best measure is unknown, the ensemble provides a more cognitively plausible approach.

  11. Gender similarities and differences.

    Hyde, Janet Shibley

    2014-01-01

    Whether men and women are fundamentally different or similar has been debated for more than a century. This review summarizes major theories designed to explain gender differences: evolutionary theories, cognitive social learning theory, sociocultural theory, and expectancy-value theory. The gender similarities hypothesis raises the possibility of theorizing gender similarities. Statistical methods for the analysis of gender differences and similarities are reviewed, including effect sizes, meta-analysis, taxometric analysis, and equivalence testing. Then, relying mainly on evidence from meta-analyses, gender differences are reviewed in cognitive performance (e.g., math performance), personality and social behaviors (e.g., temperament, emotions, aggression, and leadership), and psychological well-being. The evidence on gender differences in variance is summarized. The final sections explore applications of intersectionality and directions for future research. PMID:23808917

  12. Cluster Tree Based Hybrid Document Similarity Measure

    M. Varshana Devi

    2015-10-01

    Full Text Available similarity measure is established to measure the hybrid similarity. In cluster tree, the hybrid similarity measure can be calculated for the random data even it may not be the co-occurred and generate different views. Different views of tree can be combined and choose the one which is significant in cost. A method is proposed to combine the multiple views. Multiple views are represented by different distance measures into a single cluster. Comparing the cluster tree based hybrid similarity with the traditional statistical methods it gives the better feasibility for intelligent based search. It helps in improving the dimensionality reduction and semantic analysis.

  13. LIBO accelerates

    2002-01-01

    The prototype module of LIBO, a linear accelerator project designed for cancer therapy, has passed its first proton-beam acceleration test. In parallel a new version - LIBO-30 - is being developed, which promises to open up even more interesting avenues.

  14. Induction accelerators

    Takayama, Ken

    2011-01-01

    A broad class of accelerators rests on the induction principle whereby the accelerating electrical fields are generated by time-varying magnetic fluxes. Particularly suitable for the transport of bright and high-intensity beams of electrons, protons or heavy ions in any geometry (linear or circular) the research and development of induction accelerators is a thriving subfield of accelerator physics. This text is the first comprehensive account of both the fundamentals and the state of the art about the modern conceptual design and implementation of such devices. Accordingly, the first part of the book is devoted to the essential features of and key technologies used for induction accelerators at a level suitable for postgraduate students and newcomers to the field. Subsequent chapters deal with more specialized and advanced topics.

  15. Acceleration and improvement of dental implants’ osseointegration. Current perspective

    Gregory VENETIS; Dimitris TATSIS; Florentia STYLIANOU; Charalampos SYMEONIDIS

    2014-01-01

    The possibility to accelerate osseointegration and/or to improve bone quality around an implant is the subject of the present literature review. The following key words were searched on Pubmed: ac-celerate, improvement, osseointegration. The publication date span was set from 2009 to 2013. Combinations of the search terms retrieved the following results: a) ac-celerate and osseointegration: 78 papers; b) improve-ment and sseointegration: 206 papers. A supplementary search on the surgical t...

  16. Constructive Similarity of Soils

    Koudelka, Petr

    Singapore : Design, CRC a iTEK CMS Web solutions, 2012 - (Phoon, K.; Beer, M.; Quek, S.; Pang, S.), s. 206-211 ISBN 978-981-07-2218-0. [APS on Structural Reliability and Its Application – Sustainable Civil Infrastructures /5./. Singapore (SG), 23.05.2012-25.05.2012] Grant ostatní: GA ČR(CZ) GAP105/11/1160 Institutional support: RVO:68378297 Keywords : model similarity * database of soil properties * soil similarity characteristic * statistical analysis * ultimate limit states Subject RIV: JM - Building Engineering

  17. Music Retrieval based on Melodic Similarity

    Typke, R.

    2007-01-01

    This thesis introduces a method for measuring melodic similarity for notated music such as MIDI files. This music search algorithm views music as sets of notes that are represented as weighted points in the two-dimensional space of time and pitch. Two point sets can be compared by calculating how mu

  18. Similarity of molecular shape.

    Meyer, A Y; Richards, W G

    1991-10-01

    The similarity of one molecule to another has usually been defined in terms of electron densities or electrostatic potentials or fields. Here it is expressed as a function of the molecular shape. Formulations of similarity (S) reduce to very simple forms, thus rendering the computerised calculation straightforward and fast. 'Elements of similarity' are identified, in the same spirit as 'elements of chirality', except that the former are understood to be variable rather than present-or-absent. Methods are presented which bypass the time-consuming mathematical optimisation of the relative orientation of the molecules. Numerical results are presented and examined, with emphasis on the similarity of isomers. At the extreme, enantiomeric pairs are considered, where it is the dissimilarity (D = 1 - S) that is of consequence. We argue that chiral molecules can be graded by dissimilarity, and show that D is the shape-analog of the 'chirality coefficient', with the simple form of the former opening up numerical access to the latter. PMID:1770379

  19. The Qualitative Similarity Hypothesis

    Paul, Peter V.; Lee, Chongmin

    2010-01-01

    Evidence is presented for the qualitative similarity hypothesis (QSH) with respect to children and adolescents who are d/Deaf or hard of hearing. The primary focus is on the development of English language and literacy skills, and some information is provided on the acquisition of English as a second language. The QSH is briefly discussed within…

  20. Limiting Similarity Revisited

    Szabo, P; Meszena, G.

    2005-01-01

    We reinvestigate the validity of the limiting similarity principle via numerical simulations of the Lotka-Volterra model. A Gaussian competition kernel is employed to describe decreasing competition with increasing difference in a one-dimensional phenotype variable. The simulations are initiated by a large number of species, evenly distributed along the phenotype axis. Exceptionally, the Gaussian carrying capacity supports coexistence of all species, initially present. In case of any other, d...

  1. Accelerating execution of the integrated TIGER series Monte Carlo radiation transport codes

    Execution of the integrated TIGER series (ITS) of coupled electron/photon Monte Carlo radiation transport codes has been accelerated by modifying the FORTRAN source code for more efficient computation. Each member code of ITS was benchmarked and profiled with a specific test case that directed the acceleration effort toward the most computationally intensive subroutines. Techniques for accelerating these subroutines included replacing linear search algorithms with binary versions, replacing the pseudo-random number generator, reducing program memory allocation, and proofing the input files for geometrical redundancies. All techniques produced identical or statistically similar results to the original code. Final benchmark timing of the accelerated code resulted in speed-up factors of 2.00 for TIGER (the one-dimensional slab geometry code), 1.74 for CYLTRAN (the two-dimensional cylindrical geometry code), and 1.90 for ACCEPT (the arbitrary three-dimensional geometry code)

  2. The Application of Similar Image Retrieval in Electronic Commerce

    YuPing Hu

    2014-01-01

    Full Text Available Traditional online shopping platform (OSP, which searches product information by keywords, faces three problems: indirect search mode, large search space, and inaccuracy in search results. For solving these problems, we discuss and research the application of similar image retrieval in electronic commerce. Aiming at improving the network customers’ experience and providing merchants with the accuracy of advertising, we design a reasonable and extensive electronic commerce application system, which includes three subsystems: image search display subsystem, image search subsystem, and product information collecting subsystem. This system can provide seamless connection between information platform and OSP, on which consumers can automatically and directly search similar images according to the pictures from information platform. At the same time, it can be used to provide accuracy of internet marketing for enterprises. The experiment shows the efficiency of constructing the system.

  3. The application of similar image retrieval in electronic commerce.

    Hu, YuPing; Yin, Hua; Han, Dezhi; Yu, Fei

    2014-01-01

    Traditional online shopping platform (OSP), which searches product information by keywords, faces three problems: indirect search mode, large search space, and inaccuracy in search results. For solving these problems, we discuss and research the application of similar image retrieval in electronic commerce. Aiming at improving the network customers' experience and providing merchants with the accuracy of advertising, we design a reasonable and extensive electronic commerce application system, which includes three subsystems: image search display subsystem, image search subsystem, and product information collecting subsystem. This system can provide seamless connection between information platform and OSP, on which consumers can automatically and directly search similar images according to the pictures from information platform. At the same time, it can be used to provide accuracy of internet marketing for enterprises. The experiment shows the efficiency of constructing the system. PMID:24883411

  4. A new approach for finding semantic similar scientific articles

    Masumeh Islami Nasab; Reza Javidan

    2015-01-01

    Calculating article similarities enables users to find similar articles and documents in a collection of articles. Two similar documents are extremely helpful for text applications such as document-to-document similarity search, plagiarism checker, text mining for repetition, and text filtering. This paper proposes a new method for calculating the semantic similarities of articles. WordNet is used to find word semantic associations. The proposed technique first compares the similarity of each...

  5. Exceptional Ground Accelerations and Velocities Caused by Earthquakes

    Anderson, John

    2008-01-17

    This project aims to understand the characteristics of the free-field strong-motion records that have yielded the 100 largest peak accelerations and the 100 largest peak velocities recorded to date. The peak is defined as the maximum magnitude of the acceleration or velocity vector during the strong shaking. This compilation includes 35 records with peak acceleration greater than gravity, and 41 records with peak velocities greater than 100 cm/s. The results represent an estimated 150,000 instrument-years of strong-motion recordings. The mean horizontal acceleration or velocity, as used for the NGA ground motion models, is typically 0.76 times the magnitude of this vector peak. Accelerations in the top 100 come from earthquakes as small as magnitude 5, while velocities in the top 100 all come from earthquakes with magnitude 6 or larger. Records are dominated by crustal earthquakes with thrust, oblique-thrust, or strike-slip mechanisms. Normal faulting mechanisms in crustal earthquakes constitute under 5% of the records in the databases searched, and an even smaller percentage of the exceptional records. All NEHRP site categories have contributed exceptional records, in proportions similar to the extent that they are represented in the larger database.

  6. Tandem accelerators

    After the installation of Ti-acceleration tubes and substantial modifications and additions to the EN tandem accelerator the performance of the machine has stabilized. The voltage behaviour of the tubes obviously improves as conditioning times necessary to run up to 6 MV decrease. A gridded lens has been added at the entrance of the first acceleration tube, and a second foil stripper is now installed in the short dead section between the high-energy tubes. The MP tandem also has been running stably during most of the year. However, beam instabilities originating from the last tube section and wear problems at the low-energy set of pelletron-chains caused some loss of beam time. During the fall, one set of pelletron charging chains has to be replaced after 49,000 hours of operation. In the course of the year, the MP and the EN tandem accelerators finished their 100,000th and 150,000th hours of operations, respectively. Preparations for the installation of the 3 MV negative heavy ion injector for the MP are progressing steadily. External beam transport, terminal ion optics, and data acquisition and control systems are to a major extent completed; the integration of the terminal power supplies has started. After the final assembly of the accelerator column structure, first voltage runs can be performed. (orig.)

  7. The qualitative similarity hypothesis.

    Paul, Peter V; Lee, Chongmin

    2010-01-01

    Evidence is presented for the qualitative similarity hypothesis (QSH) with respect to children and adolescents who are d/Deaf or hard of hearing. The primary focus is on the development of English language and literacy skills, and some information is provided on the acquisition of English as a second language. The QSH is briefly discussed within the purview of two groups of cognitive models: those that emphasize the cognitive development of individuals and those that pertain to disciplinary or knowledge structures. It is argued that the QSH has scientific merit with implications for classroom instruction. Future research should examine the validity of the QSH in other disciplines such as mathematics and science and should include perspectives from social as well as cognitive models. PMID:20415280

  8. Self Similar Optical Fiber

    Lai, Zheng-Xuan

    This research proposes Self Similar optical fiber (SSF) as a new type of optical fiber. It has a special core that consists of self similar structure. Such a structure is obtained by following the formula for generating iterated function systems (IFS) in Fractal Theory. The resulted SSF can be viewed as a true fractal object in optical fibers. In addition, the method of fabricating SSF makes it possible to generate desired structures exponentially in numbers, whereas it also allows lower scale units in the structure to be reduced in size exponentially. The invention of SSF is expected to greatly ease the production of optical fiber when a large number of small hollow structures are needed in the core of the optical fiber. This dissertation will analyze the core structure of SSF based on fractal theory. Possible properties from the structural characteristics and the corresponding applications are explained. Four SSF samples were obtained through actual fabrication in a laboratory environment. Different from traditional conductive heating fabrication system, I used an in-house designed furnace that incorporated a radiation heating method, and was equipped with automated temperature control system. The obtained samples were examined through spectrum tests. Results from the tests showed that SSF does have the optical property of delivering light in a certain wavelength range. However, SSF as a new type of optical fiber requires a systematic research to find out the theory that explains its structure and the associated optical properties. The fabrication and quality of SSF also needs to be improved for product deployment. As a start of this extensive research, this dissertation work opens the door to a very promising new area in optical fiber research.

  9. Concept Search: Semantics Enabled Information Retrieval

    Giunchiglia, Fausto; Kharkevich, Uladzimir; Zaihrayeu, Ilya

    2010-01-01

    In this paper we present a novel approach, called Concept Search, which extends syntactic search, i.e., search based on the computation of string similarity between words, with semantic search, i.e., search based on the computation of semantic relations between concepts. The key idea of Concept Search is to operate on complex concepts and to maximally exploit the semantic information available, reducing to syntactic search only when necessary, i.e., when no semantic information is available. ...

  10. Accelerator design

    The feasibility of constructing a TeV region electron-positron linear collider in Japan is discussed. The design target of the collider is given as follows: Energy, 1 TeV + 1 TeV; luminosity, 1032-1033/cm2/s; total length, 25km; electric power, 250MW; energy dispersion, 1%-10%; the start of the first experiment, early 1990s. For realizing the above target, the following research and developmental works are necessary. (a) Development of an acceleration tube with short filling time and high shunt resistance. (b) Short pulse microwave source with high peak power. (c) High current, single bunch linac. (d) Beam dynamics. As for the acceleration tube, some possibility is considered: For example, the use of DAW (Disk and Washer) which is being developed for TRISTAN as a traveling-wave tube; and the Jungle Gym-type acceleration tube. As a promising candidate for the microwave source, the Lasertron has been studied. The total cost of the collider construction is estimated to be about 310 billion yen, of which 120 billion yen is for the tunnel and buildings, and 190 billion yen for the accelerator facilities. The operation cost is estimated to be about 3 billion yen per month. (Aoki, K.)