Protein Fold Recognition with Combined SVM-RDA Classifier

Predicting the three-dimensional (3D) structure of a protein is a key problem in molecular biology It is also an interesting issue for statistical methods recognition There are many approaches to this problem considering discriminative and generative classifiers In this paper a classifier combining the well-known Support Vector Machine (SVM) classifier with Regularized Discriminant Analysis (RDA) classifier is presented It is used on a real world data set The obtained results improve previously published methods.

[1]  Thomas G. Dietterich,et al.  Solving Multiclass Learning Problems via Error-Correcting Output Codes , 1994, J. Artif. Intell. Res..

[2]  Boonserm Kijsirikul,et al.  Multiclass support vector machines using adaptive directed acyclic graph , 2002, Proceedings of the 2002 International Joint Conference on Neural Networks. IJCNN'02 (Cat. No.02CH37290).

[3]  I. Muchnik,et al.  Prediction of protein folding class using global description of amino acid sequence. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Xiaotong Shen,et al.  MULTI-CATEGORY SUPPORT VECTOR MACHINES, FEATURE SELECTION AND SOLUTION PATH , 2006 .

[5]  Tim J. P. Hubbard,et al.  SCOP: a structural classification of proteins database , 1998, Nucleic Acids Res..

[6]  U. Hobohm,et al.  Selection of representative protein data sets , 1992, Protein science : a publication of the Protein Society.

[7]  Jennifer G. Dy,et al.  A hierarchical method for multi-class support vector machines , 2004, ICML.

[8]  Loris Nanni,et al.  Ensemble of classifiers for protein fold recognition , 2006, Neurocomputing.

[9]  Nello Cristianini,et al.  Large Margin DAGs for Multiclass Classification , 1999, NIPS.

[10]  Chin-Teng Lin,et al.  Recognition of Structure Classification of Protein Folding by NN and SVM Hierarchical Learning Architecture , 2003, ICANN.

[11]  J. Friedman Regularized Discriminant Analysis , 1989 .

[12]  Keinosuke Fukunaga,et al.  Introduction to Statistical Pattern Recognition , 1972 .

[13]  Chris H. Q. Ding,et al.  Multi-class protein fold recognition using support vector machines and neural networks , 2001, Bioinform..

[14]  Inna Dubchak,et al.  Protein Folding Class Predictor for SCOP: Approach Based on Global Descriptors , 1997, ISMB.

[15]  Robert Tibshirani,et al.  Classification by Pairwise Coupling , 1997, NIPS.

[16]  C. Chothia One thousand families for the molecular biologist , 1992, Nature.

[17]  Loris Nanni A novel ensemble of classifiers for protein fold recognition , 2006, Neurocomputing.

[18]  Nikhil R. Pal,et al.  Some New Features for Protein Fold Prediction , 2003, ICANN.

[19]  Cheng-Lin Liu,et al.  Classification and Learning for Character Recognition: Comparison of Methods and Remaining Problems , 2005 .

[20]  Vladimir N. Vapnik,et al.  The Nature of Statistical Learning Theory , 2000, Statistics for Engineering and Information Science.

[21]  Kuo-Chen Chou,et al.  Ensemble classifier for protein fold pattern recognition , 2006, Bioinform..

[22]  Pierre Baldi,et al.  Assessing the accuracy of prediction algorithms for classification: an overview , 2000, Bioinform..

[23]  Guido Bologna,et al.  A comparison study on protein fold recognition , 2002, Proceedings of the 9th International Conference on Neural Information Processing, 2002. ICONIP '02..

[24]  Chih-Jen Lin,et al.  LIBSVM: A library for support vector machines , 2011, TIST.

[25]  Franco Scarselli,et al.  Are Multilayer Perceptrons Adequate for Pattern Recognition and Verification? , 1998, IEEE Trans. Pattern Anal. Mach. Intell..

[26]  Keinosuke Fukunaga,et al.  Introduction to statistical pattern recognition (2nd ed.) , 1990 .

[27]  Erkki Oja,et al.  Artificial Neural Networks and Neural Information Processing — ICANN/ICONIP 2003 , 2003, Lecture Notes in Computer Science.

[28]  Infotech Oulu,et al.  Protein Fold Recognition with K-Local Hyperplane Distance Nearest Neighbor Algorithm , 2004 .

[29]  U. Hobohm,et al.  Enlarged representative set of protein structures , 1994, Protein science : a publication of the Protein Society.

[30]  B. Fei,et al.  Binary tree of SVM: a new fast multiclass training and classification algorithm , 2006, IEEE Transactions on Neural Networks.

[31]  Lionel Prevost,et al.  Hybrid generative/discriminative classifier for unconstrained character recognition , 2005, Pattern Recognit. Lett..