the proceedings contain 38 papers. the topics discussed include: evolutionary parameters in sequence families: cold adaptation of enzymes;MProfiler: a profile-based method for DNA motif discovery;on utilizing optimal ...
ISBN:
(纸本)3642040306
the proceedings contain 38 papers. the topics discussed include: evolutionary parameters in sequence families: cold adaptation of enzymes;MProfiler: a profile-based method for DNA motif discovery;on utilizing optimal and information theoretic syntactic modeling for peptide classification;multiclass microarray gene expression analysis based on mutual dependency models;an efficient convex nonnegative network component analysis for gene regulatory network reconstruction;using higher-order dynamic Bayesian networks to model periodic data from the circadian clock of Arabidopsis thaliana;syntactic patternrecognition using finite inductive strings;evidence-based clustering of reads and taxonomic analysis of metagenomic data;and avoiding spurious feedback loops in the reconstruction of gene regulatory networks with dynamic Bayesian networks.
High throughput mass spectrometry technique has been extensively studied for the diagnosis of cancers. the detection of the pancreatic cancer at a very early stage is important to heal patients, but is very difficult ...
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ISBN:
(纸本)9783642341236
High throughput mass spectrometry technique has been extensively studied for the diagnosis of cancers. the detection of the pancreatic cancer at a very early stage is important to heal patients, but is very difficult due to biological and computational challenges. this paper proposes a simple classification approach which can be applied to the premalignant pancreatic cancer detection using mass spectrometry technique. Computational experiments show that our method outperforms the benchmark methods in accuracy and sensitivity without resorting to any biomarker selection, and the comparison with previous works shows that our method can obtain competitive performance.
DNA microarrays are used in order to recognize the presence or absence of different biological components (targets) in a sample. therefore, the design of the microarrays which includes selecting short Oligonucleotide ...
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Microarray gene expression technique can provide snap shots of gene expression levels of samples. this technique is promising to be used in clinical diagnosis and genomic pathology. However, the curse of dimensionalit...
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ISBN:
(纸本)9783642341236
Microarray gene expression technique can provide snap shots of gene expression levels of samples. this technique is promising to be used in clinical diagnosis and genomic pathology. However, the curse of dimensionality and other problems have been challenging researchers for a decade. Selecting a few discriminative genes is an important choice. But gene subset selection is a NP hard problem. this paper proposes an effective gene selection framework. this framework integrates gene filtering, sample selection, and multiobjective evolutionary algorithm (MOEA). We use MOEA to optimize four objective functions taking into account of class relevance, feature redundancy, classification performance, and the number of selected genes. Experimental comparison shows that the proposed approach is better than a well-known recursive feature elimination method in terms of classification performance and time complexity.
Most of the current practice of pattern matching tools is oriented towards finding efficient ways to compare sequences. this is useful but insufficient: as the knowledge and understanding of some functional or structu...
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ISBN:
(纸本)9783319091921;9783319091914
Most of the current practice of pattern matching tools is oriented towards finding efficient ways to compare sequences. this is useful but insufficient: as the knowledge and understanding of some functional or structural aspects of living systems improve, analysts in molecular biology progressively shift from mere classification tasks to modeling tasks. People need to be able to express global sequence architectures and check various hypotheses on the way their sequences are structured. It appears necessary to offer generic tools for this task, allowing to build more expressive models of biological sequence families, on the basis of their content and structure. this article introduces Logol, a new application designed to achieve pattern matching in possibly large sequences with customized biological patterns. Logol consists in both a language for describing patterns, and the associated parser for effective pattern search in sequences (RNA, DNA or protein) with such patterns. the Logol language, based on an high level grammatical formalism, allows to express flexible patterns (with mispairings and indels) composed of both sequential elements (such as motifs) and structural elements (such as repeats or pseudoknots). Its expressive power is presented through an application using the main components of the language : the identification of -1 programmed ribosomal frameshifting (PRF) events in messenger RNA sequences. Logol allows the design of sophisticated patterns, and their search in large nucleic or amino acid sequences. It is available on the GenOuest bioinformatics platform at http://***. the core application is a command-line application, available for different operating systems. the Logol suite also includes interfaces, e. g. an interface for graphically drawing the pattern.
Non-negative matrix factorization and sparse representation models have been successfully applied in high-throughput biological data analysis. In this paper, we propose our versatile sparse matrix factorization (VSMF)...
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the proceedings contain 65 papers. the topics discussed include: inference and learning for active sensing, experimental design and control;large scale online learning of image similarity through ranking;inpainting id...
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ISBN:
(纸本)3642021719
the proceedings contain 65 papers. the topics discussed include: inference and learning for active sensing, experimental design and control;large scale online learning of image similarity through ranking;inpainting ideas for image compression;smoothed disparity maps for continuous American sign language recognition;human action recognition using optical flow accumulated local histograms;trajectory modeling using mixtures of vector fields;high speed human detection using a multiresolution cascade of histograms of oriented gradients;face-to-face social activity detection using data collected with a wearable device;estimating vehicle velocity using Image profiles on rectified images;kernel based multi-object tracking using gabor functions embedded in a region covariance matrix;and autonomous configuration of parameters in robotic digital cameras.
Markov Random Fields (MRF) have been shown to be good predictors of functional annotation, using protein-protein interaction data. Many other sources of data can also be used in this prediction task, but they are typi...
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A syntactic patternrecognition technique is described based upon a mathematical principle associated with finite sequences of symbols. the technique allows for fast recognition of patterns within strings, including t...
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ISBN:
(纸本)9783642040306
A syntactic patternrecognition technique is described based upon a mathematical principle associated with finite sequences of symbols. the technique allows for fast recognition of patterns within strings, including the ability to recognize expected symbols that are close to the desired symbols, and mutations as well as both local and global substring matching. this allowance of deviation permits sequences to be subject to error and still be recognized. Some examples are provided illustrating the technique.
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