Protein homology detection with sparse models
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[1] Trevor Hastie,et al. The Elements of Statistical Learning , 2001 .
[2] Bernhard Schölkopf,et al. Kernel Principal Component Analysis , 1997, ICANN.
[3] B. Scholkopf,et al. Fisher discriminant analysis with kernels , 1999, Neural Networks for Signal Processing IX: Proceedings of the 1999 IEEE Signal Processing Society Workshop (Cat. No.98TH8468).
[4] Tom. Mitchell. GENERATIVE AND DISCRIMINATIVE CLASSIFIERS: NAIVE BAYES AND LOGISTIC REGRESSION Machine Learning , 2005 .
[5] David Haussler,et al. A Discriminative Framework for Detecting Remote Protein Homologies , 2000, J. Comput. Biol..
[6] Israel M. Gelfand,et al. Common features in structures and sequences of sandwich-like proteins , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[7] Thomas G. Dietterich,et al. Solving Multiclass Learning Problems via Error-Correcting Output Codes , 1994, J. Artif. Intell. Res..
[8] J. Weston,et al. Support Vector Machines for Multi-class Pattern Recognition 1. K-class Pattern Recognition 2. Solving K-class Problems with Binary Svms , 1999 .
[9] S F Altschul,et al. Local alignment statistics. , 1996, Methods in enzymology.
[10] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[11] Eleazar Eskin,et al. The Spectrum Kernel: A String Kernel for SVM Protein Classification , 2001, Pacific Symposium on Biocomputing.
[12] Sean R. Eddy,et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .
[13] Ryan M. Rifkin,et al. In Defense of One-Vs-All Classification , 2004, J. Mach. Learn. Res..
[14] Nicu Sebe,et al. Semisupervised learning of classifiers: theory, algorithms, and their application to human-computer interaction , 2004, IEEE Transactions on Pattern Analysis and Machine Intelligence.
[15] A. D. McLachlan,et al. Profile analysis: detection of distantly related proteins. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[16] Lawrence R. Rabiner,et al. A tutorial on hidden Markov models and selected applications in speech recognition , 1989, Proc. IEEE.
[17] Jerald F. Lawless,et al. Statistical Models and Methods for Lifetime Data. , 1983 .
[18] D. Lipman,et al. Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[19] Jason Weston,et al. Mismatch String Kernels for SVM Protein Classification , 2002, NIPS.
[20] Xiaojin Zhu,et al. --1 CONTENTS , 2006 .
[21] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[22] Vladimir Pavlovic,et al. Protein homology detection with biologically inspired features and interpretable statistical models , 2008, Int. J. Data Min. Bioinform..
[23] Robert D. Finn,et al. The Pfam protein families database , 2004, Nucleic Acids Res..
[24] David Madigan,et al. Large-Scale Bayesian Logistic Regression for Text Categorization , 2007, Technometrics.
[25] Jason Weston,et al. Support vector machines for multi-class pattern recognition , 1999, ESANN.
[26] Vladimir Vapnik,et al. Statistical learning theory , 1998 .
[27] Antonio Torralba,et al. Sharing features: efficient boosting procedures for multiclass object detection , 2004, CVPR 2004.
[28] Tommi S. Jaakkola,et al. Partially labeled classification with Markov random walks , 2001, NIPS.
[29] J. Lawless. Statistical Models and Methods for Lifetime Data , 2002 .
[30] M. A. McClure,et al. Hidden Markov models of biological primary sequence information. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[31] Michael I. Jordan,et al. On Discriminative vs. Generative Classifiers: A comparison of logistic regression and naive Bayes , 2001, NIPS.
[32] V. Pavlovic,et al. Spatially-constrained sample kernel for sequence classification , 2008 .
[33] Patrice Koehl,et al. The ASTRAL compendium for protein structure and sequence analysis , 2000, Nucleic Acids Res..
[34] Mário A. T. Figueiredo. Adaptive Sparseness for Supervised Learning , 2003, IEEE Trans. Pattern Anal. Mach. Intell..
[35] Tim J. P. Hubbard,et al. SCOP: a Structural Classification of Proteins database , 1999, Nucleic Acids Res..
[36] David Haussler,et al. Using the Fisher Kernel Method to Detect Remote Protein Homologies , 1999, ISMB.
[37] Janet M. Thornton,et al. PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids , 2004, Nucleic Acids Res..
[38] David Haussler,et al. Using Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families , 1993, ISMB.
[39] S. Karlin,et al. Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.
[40] I. Gelfand,et al. Determining the roles of different chain fragments in recognition of immunoglobulin fold. , 2002, Protein engineering.
[41] Cathy H. Wu,et al. The Universal Protein Resource (UniProt) , 2006, Nucleic Acids Research.
[42] I M Gelfand,et al. The sequence determinants of cadherin molecules , 2001, Protein science : a publication of the Protein Society.
[43] Amos Bairoch,et al. The PROSITE database , 2005, Nucleic Acids Res..
[44] Michael Gribskov,et al. Use of Receiver Operating Characteristic (ROC) Analysis to Evaluate Sequence Matching , 1996, Comput. Chem..
[45] Kiyoshi Asai,et al. Marginalized kernels for biological sequences , 2002, ISMB.
[46] Ke Wang,et al. Profile-based string kernels for remote homology detection and motif extraction , 2004, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004..
[47] S. Henikoff,et al. Position-based sequence weights. , 1994, Journal of molecular biology.
[48] Maria Jesus Martin,et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..
[49] T. Hubbard,et al. Fold recognition and ab initio structure predictions using hidden markov models and β‐strand pair potentials , 1995, Proteins.
[50] Sebastian Thrun,et al. Text Classification from Labeled and Unlabeled Documents using EM , 2000, Machine Learning.
[51] Ji Zhu,et al. Kernel Logistic Regression and the Import Vector Machine , 2001, NIPS.
[52] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[53] Christina S. Leslie,et al. Fast String Kernels using Inexact Matching for Protein Sequences , 2004, J. Mach. Learn. Res..
[54] Anil K. Jain,et al. Bayesian learning of sparse classifiers , 2001, Proceedings of the 2001 IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR 2001.
[55] Henry Tirri,et al. On Discriminative Bayesian Network Classifiers and Logistic Regression , 2005, Machine Learning.
[56] Adam Godzik,et al. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..
[57] Li Liao,et al. Combining pairwise sequence similarity and support vector machines for remote protein homology detection , 2002, RECOMB '02.
[58] C. Chothia,et al. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. , 2001, Journal of molecular biology.
[59] Nello Cristianini,et al. An Introduction to Support Vector Machines and Other Kernel-based Learning Methods , 2000 .
[60] D. Rubin,et al. Maximum likelihood from incomplete data via the EM - algorithm plus discussions on the paper , 1977 .
[61] Lawrence R. Rabiner,et al. A tutorial on Hidden Markov Models , 1986 .
[62] David Haussler,et al. Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology , 1996, Comput. Appl. Biosci..
[63] Antonio Torralba,et al. Sharing Visual Features for Multiclass and Multiview Object Detection , 2007, IEEE Transactions on Pattern Analysis and Machine Intelligence.
[64] Sean R. Eddy,et al. Profile hidden Markov models , 1998, Bioinform..
[65] Robert E. Schapire,et al. The Boosting Approach to Machine Learning An Overview , 2003 .
[66] Peter Meinicke,et al. Remote homology detection based on oligomer distances , 2006, Bioinform..
[67] Jason Weston,et al. Semi-supervised Protein Classification Using Cluster Kernels , 2003, NIPS.