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检索条件"任意字段=6th International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2015"

共 237 条记录，以下是21-30 订阅

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Sequential parallel LASSO models for eQTL analysis 15

Sequential parallel LASSO models for eQTL analysis

引用

6th ACM conference on bioinformatics, Computational Biology, and Health Informatics, BCB 2015

作者： He, Anhong Hall, Benika Wen, Jia Liang, Yingbin Shi, Xinghua Syracuse University 900 South Crouse Ave. SyracuseNY13244 United States University of North Carolina at Charlotte 9201 University City Blvd. CharlotteNC28223 United States

ISBN: (纸本)9781450338530

the availability of large-scale genomic and transcriptomic data on populations makes it necessary to perform computationally intensive expression quantitative trait locus (eQTL) analysis. Modeling in a sparse learning framework, LASSO based tools are powerful for eQTL analysis. However, classical LASSO becomes limited for big genomic data. We thus propose two novel methods, namely sequential LASSO and parallel LASSO, to conduct eQTL analysis for datasets of ultra-high dimension. We theoretically prove the consistency of our methods under mild conditions and perform extensive simulations on synthetic data to validate our methods. We also apply our methods to a real human genomics database demonstrate the application of our method. Copyright is held by the author/owner(s). Copyright is held by the author/owner(s).

关键词： Genome

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algorithms for computing X-minimal models

引用

6th international conference on Logic Programming and Nonmonotonic Reasoning, LPNMR 2001

作者： Avin, Chen Ben-Eliyahu-Zohary, Rachel Communication Systems Engineering Department Ben-Gurion University of the Negev Beer-Sheva 84105 Israel

ISBN: (纸本)3540425934

the problem of computing X-minimal models, that is, models minimal with respect to a subset X of all the atoms in a theory, is very relevant for computing circumscriptions and diagnosis. Unfortunately, the problem is NP-hard. In this paper we present two novel algorithms for computing X-minimal models. the advantage of these new algorithms is that, unlike existing ones, they are capable of generating the models one by one. there is no need to compute a superset of all minimal models before finding the first X-minimal one. Our procedures may use local serach techniques, or, alternatively, complete methods. We have implemented and tested the algorithms and the preliminary experimental results are encouraging. © Springer-Verlag Berlin Heidelberg 2001.

关键词： Artificial intelligence

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6th international Symposium on Leveraging Applications of Formal methods, Verification and Validation, ISoLA 2014

6th International Symposium on Leveraging Applications of Fo...

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6th international Symposium on Leveraging Applications of Formal methods, Verification and Validation, ISoLA 2014

ISBN: (纸本)9783662452332

the proceedings contain 44 papers. the special focus in this conference is on Critical Systems, Rigorous Engineering of Autonomic Ensembles, Automata Learning, Formal methods and Analysis, Model-Based Code Generators and Automata Learning in Practice. the topics include: Statistical abstraction boosts design and test efficiency of evolving critical systems;incremental syntactic-semantic reliability analysis of evolving structured workflows;domain-specific languages for enterprise systems;formalizing self-adaptive clouds with knowlang;towards performance-aware engineering of autonomic component ensembles;rigorous system design flow for autonomous systems;algorithms for inferring register automata;active learning of nondeterministic systems from an ioco perspective;fomal methods and analyses in software product line engineering;domain specific languages for managing feature models;deployment variability in delta-oriented models;coverage criteria for behavioural testing of software product lines;DSL implementation for model-based development of pumps;domain-specific code generator modeling;LNCS transactions on foundations for mastering change;formal methods for collective adaptive ensembles;current issues on model-based software quality assurance for mastering change and compositional model-based system design as a foundation for mastering change.

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Visual comparison of 3D medical image segmentation algorithms based on statistical shape models 6th

Visual comparison of 3D medical image segmentation algorithm...

引用

6th international conference on Digital Human Modeling, DHM 2015 Held as Part of 17th international conference on Human-Computer Interaction, HCI international 2015

作者： Geurts, Alexander Sakas, Georgios Kuijper, Arjan Becker, Meike von Landesberger, Tatiana TU Darmstadt Darmstadt Germany

ISBN: (纸本)9783319210698

3D medical image segmentation is needed for diagnosis and treatment. As manual segmentation is very costly, automatic segmentation algorithms are needed. For finding best algorithms, several algorithms need to be evaluated on a set of organ instances. this is currently difficult due to dataset size and complexity. In this paper, we present a novel method for comparison and evaluation of several algorithms that automatically segment 3D medical images. It combines algorithmic data analysis with interactive data visualization. A clustering algorithm identifies regions of common quality across the segmented data set for each algorithm. the comparison identifies best algorithms per region. Interactive views show the algorithm quality. We applied our approach to a real-world cochlea dataset, which was segmented with several algorithms. Our approach allowed segmentation experts to compare algorithms on regional level and to identify best algorithms per region. © Springer international Publishing Switzerland 2015.

关键词： Clustering algorithms

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Compare local pocket and global protein structure models by small structure patterns 15

Compare local pocket and global protein structure models by ...

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6th ACM conference on bioinformatics, Computational Biology, and Health Informatics, BCB 2015

作者： Cui, Xuefeng Kuwahara, Hiroyuki Li, Shuai Cheng Gao, Xin Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal Saudi Arabia Department of Computer Science City University of Hong Kong Kowloon Hong Kong

ISBN: (纸本)9781450338530

Researchers proposed several criteria to assess the quality of predicted protein structures because it is one of the essential tasks in the Critical Assessment of Techniques for Protein Structure Prediction (CASP) competitions. Popular criteria include root mean squared deviation (RMSD), MaxSub score, TM-score, GDT-TS and GDT-HA scores. All these criteria require calculation of rigid transformations to superimpose the the predicted protein structure to the native protein structure. Yet, how to obtain the rigid transformations is unknown or with high time complexity, and, hence, heuristic algorithms were proposed. In this work, we carefully design various small structure patterns, including the ones specifically tuned for local pockets. Such structure patterns are biologically meaningful, and address the issue of relying on a sufficient number of backbone residue fragments for existing methods. We sample the rigid transformations from these small structure patterns;and the optimal superpositions yield by these small structures are refined and reported. As a result, among 11;669 pairs of predicted and native local protein pocket models from the CASP10 dataset, the GDT-TS scores calculated by our method are significantly higher than those calculated by LGA. Moreover, our program is computationally much more efficient. Source codes and executables are publicly available at http://***/prosta/. Copyright is held by the author/owner(s).

关键词： Proteins

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MICAI 2007: Advances in Artificial Intelligence - 6th Mexican international conference on Artificial Intelligence, Proceedings

MICAI 2007: Advances in Artificial Intelligence - 6th Mexica...

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6th Mexican international conference on Artificial Intelligence, MICAI 2007

ISBN: (纸本)9783540766308

the proceedings contain 116 papers. the topics discussed include: rough set approach under dynamic granulation in incomplete information systems;generalized fuzzy operations for digital hardware implementation;a novel model of artificial immune system for solving constrained optimization problems with dynamic tolerance factor;a genetic representation for dynamic system qualitative models on genetic programming: a gene expression programming approach;handling constraints in particle swarm optimization using a small population size;collective methods on flock traffic navigation based on negotiation;a new global optimization algorithm inspired by parliamentary political competitions;discovering promising regions to help global numerical optimization algorithms;and clustering search approach for the traveling tournament problem.

关键词： Artificial intelligence

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6th international conference on Information Technology in Bio-and Medical Informatics, ITBAM 2015

6th International Conference on Information Technology in Bi...

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6th international conference on Information Technology in Bio- and Medical Informatics, ITBAM 2015

ISBN: (纸本)9783319227405

the proceedings contain 10 papers. the special focus in this conference is on Medical Terminology, Clinical Processes and Machine Learning in Biomedicine. the topics include: Exploiting PubMed to answer biomedical questions in natural language;using twitter data and sentiment analysis to study diseases dynamics;an open data approach for clinical appropriateness;a logistic regression approach for identifying hot spots in protein interfaces;the discovery of prognosis factors using association rule mining in acute myocardial infarction with ST-segment elevation;data mining techniques in health informatics;artificial neural networks in diagnosis of liver diseases;how to increase the effectiveness of the hepatitis diagnostics by means of appropriate machine learning methods;ant-inspired algorithms for decision tree induction;microsleep classifier using EOG channel recording.

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On-line Searching in IUPAC Nucleotide Sequences 10

On-line Searching in IUPAC Nucleotide Sequences

引用

12th international Joint conference on Biomedical Engineering Systems and Technologies / 10th international conference on bioinformatics models, methods and algorithms (bioinformatics)

作者： Prochazka, Petr Holub, Jan Czech Tech Univ Fac Informat Technol Dept Theoret Comp Sci Thakurova 2700-9 Prague 6 Czech Republic

ISBN: (纸本)9789897583537

We propose a novel pattern matching algorithm for consensus nucleotide sequences over IUPAC alphabet, called BADPM (Byte-Aligned Degenerate Pattern Matching). the consensus nucleotide sequences represent a consensus obtained by sequencing a population of the same species and they are considered as so-called degenerate strings. BADPM works at the level of single bytes and it achieves sublinear search time on average. the algorithm is based on tabulating all possible factors of the searched pattern. It needs O (m + m alpha(2) logm)space data structure and O (m alpha(2)) time for preprocessing where m is a length of the pattern and a represents a maximum number of variants implied from a 4-gram over IUPAC alphabet. the worst-case locate time is bounded by O (nm(2)alpha(4)) for BADPM where n is the length of the input text. However, the experiments performed on real genomic data proved the sublinear search time. BADPM can easily cooperate with the block q-gram inverted index and so achieve still better locate time. We implemented two other pattern matching algorithms for IUPAC nucleotide sequences as a baseline: Boyer-Moore-Horspool (BMH) and Parallel Naive Search (PNS). Especially PNS proves its efficiency insensitive to the length of the searched pattern m. BADPM proved its strong superiority for searching middle and long patterns.

关键词： Consensus Nucleotide Sequences Genomic Sequences Degenerate Pattern Matching q-gram Inverted Index

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Integrated Analysis from Abstract Stochastic Process Algebra models

引用

6th international conference on Computational methods in Systems Biology

作者： Hillston, Jane Ciocchetta, Federica Duguid, Adam Gilmore, Stephen Univ Edinburgh Lab Fdn Comp Sci Edinburgh EH8 9YL Midlothian Scotland

ISBN: (纸本)9783540885610

Bio-PEPA is a novel stochastic process algebra which has been recently developed for modelling biochemical pathways [5,6]. In Bio-PEPA a reagent-centric style of modelling is adopted, and a variety of analysis techniques can be applied to a single model expression. Such an approach facilitates easy validation of analysis results when the analyses address the same issues [3] and enhanced insight when the analyses are complementary [4]. Currently supported analysis techniques include stochastic simulation at the molecular level, ordinary di..erential equations, probabilistic model checking and numerical analysis of a continuous time Markov chain. © 2008 Springer Berlin Heidelberg.

关键词： Stochastic systems

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Efficient k-mer Indexing with Application to Mapping-free SNP Genotyping

Efficient k-mer Indexing with Application to Mapping-free SN...

引用

13th international conference on bioinformatics models, methods and algorithms (bioinformatics) held as part of 15th international Joint conference on Biomedical Engineering Systems and Technologies (BIOSTEC)

作者： Marcolin, Mattia Andreace, Francesco Comin, Matteo Univ Padua Dept Informat Engn Via Gradenigo 6-A I-35100 Padua Italy

ISBN: (纸本)9789897585524

Advances in sequencing technologies and computational methods have enabled rapid and accurate identification of genetic variants. Accurate genotype calls and allele frequency estimations are crucial for population genomics analyses. One of the most demanding step in the genotyping pipeline is mapping reads to the human reference genome. Recently mapping-free methods, like Lava and VarGeno, have been proposed for the genotyping problem. they are reported to perform 30 times faster than a standard alignment-based genotyping pipeline while achieving comparable accuracy. Moreover, these methods are able to include known genomic variants in the reference making read mapping, and genotyping variant-aware. However, in order to run they require a large k-mers database, of about 60GB, to be loaded in memory. In this paper we study the problem of genotyping using new efficient data structures based on k-mers set compression, and we present a fast mapping-free genotyping tool, named GenoLight. GenoLight reports accuracy results similar to the standard pipeline, but it is up to 8 times faster. Also, GenoLight uses between 5 to 10 times less memory than the other mapping-free tools, and it can be run on a laptop. Availability: https://***/CominLab/GenoLight.

关键词： Genotyping Mapping-free k-mers Set Representation

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