Fast string kernels using inexact matching for protein sequences

MaRDI QIDQ3093231zbMATH OpenFDO

Authors C. Leslie, Rui Kuang

Publication date 12 October 2011

Full work available at URL http://www.jmlr.org/papers/v5/leslie04a.html

zbMATH Keywords

kernel methodscomputational biologystring kernels

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Learning and adaptive systems in artificial intelligence (68T05) Biochemistry, molecular biology (92C40)

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Cited in

(17)

• Versatile string kernels
• Extended pairwise local alignment of wild card DNA/RNA sequences using dynamic programming
• Optimal string clustering based on a Laplace-like mixture and EM algorithm on a set of strings
• Potential Functions for Signals and Symbolic Sequences
• Graph-Based Representations in Pattern Recognition
• Fast kernels for inexact string matching.
• A Class of New Kernels Based on High-Scored Pairs of k-Peptides for SVMs and Its Application for Prediction of Protein Subcellular Localization
• Machine Learning: ECML 2004
• Fast structural alignment of biomolecules using a hash table, n-grams and string descriptors
• Distance metric learning for graph structured data
• Maximum margin classifier working in a set of strings
• On using physico-chemical properties of amino acids in string kernels for protein classification via support vector machines
• Framework for kernel regularization with application to protein clustering
• Kernels for sequentially ordered data
• Efficient computation of gapped substring kernels on large alphabets
• The graph matching problem
• All fingers are not the same: handling variable-length sequences in a discriminative setting using conformal multi-instance kernels

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