Protein remote homology detection based on latent topic vector model

ICNIT 2010 - 2010 International Conference on Networking and Information Technology

Volumn , Issue , 2010, Pages 456-460

  Yeh, Jian Hua ^a   Chen, Chun Hsing ^a  

^a ALETHEIA UNIVERSITY   (Taiwan)

Author keywords

Latent Dirichlet Allocation; Latent topic; Protein sequence; Remote homology; Support Vector Machine

Indexed keywords

BASIC BUILDING BLOCK; CENTRAL PROBLEMS; COMPUTATIONAL BIOLOGY; DISCRIMINATIVE METHODS; FEATURE EXTRACTION TECHNIQUES; FEATURE VECTORS; KERNEL FUNCTION; LATENT DIRICHLET ALLOCATION; LATENT TOPIC; NATURAL LANGUAGE PROCESSING; PROTEIN CLASSIFICATION; PROTEIN DATABASE; PROTEIN SEQUENCE; PROTEIN SEQUENCES; REMOTE HOMOLOGY; STRUCTURAL CLASSIFICATION; SVM MODEL; SVM-BASED METHODS; TOPIC EXTRACTION; TOPIC VECTOR; WORD DOCUMENTS;

BIOINFORMATICS; COMPUTATIONAL LINGUISTICS; FEATURE EXTRACTION; IMAGE RETRIEVAL; INFORMATION TECHNOLOGY; NATURAL LANGUAGE PROCESSING SYSTEMS; SUPPORT VECTOR MACHINES; VECTORS;

PROTEINS;

EID: 77955603281     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICNIT.2010.5508474     Document Type: Conference Paper

References (13)

1. Karplus K, Barrett C, Hughey R, "Hidden Markov Models for Detecting Remote Protein Homologies, " Bioinformatics 14(10):846-856, 1998. (Pubitemid 29041540)
2. Vapnik VN. Statistical Learning Theory. New York, 1998.
3. Dong, Q. W. et aI., "A pattern-based SVM for protein remote homology detection, " in The Fourth International Conference on Machine Learning and Cybernetics. GuangZhou, China, pp. 3363-3368, 2005.
4. Ben-Hur,A. and Brutiag,D., "Remote homology detection: a motif based approach, " Bioinformatics. 19(Suppl 1), i26-i33, 2003. (Pubitemid 41185596)
5. Leslie,C., Eskin,E. and Noble, W.S., "The spectrum kernel: a string kernel for SVM protein classification, " in Proceedings of the Pacific Symposium on Biocomputing, Hawaii, USA, pp. 564-575, 2002.
6. Rigoutsos,I. and Floratos,A., "Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm, " Bioinformatics, 14, 55-67, 1998.
7. Bailey,T.L. and Elkan,C., "Fitting a mixture model by expectation maximization to discover motifs in biopolymers, " in proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. Menlo Park, California.pp. 28-36, 1994.
8. Salton, Gerard and Buckley, C., "Term-weighting approaches in automatic text retrieval, " Information Processing & Management 24 (5) 513-523, 1988.
9. D. M. Blei, A. Y. Ng and M. I. Jordan, "Latent Dirichlet allocation, " Journal of Machine Learning Research, vol. 3, no. 5, pp.993-1022, 2003.
10. Jian-hua Yeh, Meng-Iun Wu, "Recommendation Based on Latent Topics and Social Network Analysis ", to appear in Proceedings of the 2nd International Conference on Computer and Engineering Applications(lCCEA 2010), Bali, Indonesia, March 2010.
11. Jian-hua Yeh, Po-hung Sung, "Latent Topic and Social Network Based Web Image Retrieval ", in Proceedings of 2009 International Conference on Digital Content (ICDC2009), Chung-Ii, Taiwan, September 2009.
12. Jaakkola,T. et aI., "A discriminative framework for detecting remote protein homologies, " J. Compul. BioI., 7, 95-114, 2000.
13. Bin Liu, Xiaolong Wang, Lei Lin, Qiwen Dong and Xuan Wang, "A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis, " BMC Bioinformatics 9:510, 2008.