Learning an enriched representation from unlabeled data for protein-protein interaction extraction

BMC Bioinformatics

Volumn 11, Issue SUPPL. 2, 2010, Pages

  Li, Yanpeng ^a,b   Hu, Xiaohua ^b   Lin, Hongfei ^a   Yang, Zhihao ^a  

^a DALIAN UNIVERSITY OF TECHNOLOGY   (China)

^b Drexel University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMEDICAL LITERATURE; BIOMEDICAL TEXT MININGS; EXPERIMENTAL ANALYSIS; PROTEIN-PROTEIN INTERACTION EXTRACTIONS; PROTEIN-PROTEIN INTERACTIONS; SEMI-SUPERVISED LEARNING; SUPERVISED MACHINE LEARNING; SYNTACTIC INFORMATION;

DATA MINING; NATURAL LANGUAGE PROCESSING SYSTEMS; SUPERVISED LEARNING;

PROTEINS;

ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; BIOLOGY; CHI SQUARE DISTRIBUTION; DATA MINING; METHODOLOGY; PROTEIN ANALYSIS;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; CHI-SQUARE DISTRIBUTION; COMPUTATIONAL BIOLOGY; DATA MINING; PROTEIN INTERACTION MAPPING;

EID: 77952927415     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S2-S7     Document Type: Article

References (23)

1. Cohen AM, Hersh WR. A survey of current work in biomedical text mining. Briefings in Bioinformatics 2005, 6:57-71. 10.1093/bib/6.1.57, 15826357.
2. Bunescu R, Ge R, Kate R, Marcotte E, Mooney R, Ramani A, Wong Y. Comparative Experiments on Learning Information Extractors for Proteins and their Interactions. Artificial Intelligence in Medicine 2005, 33(2):139-155. 10.1016/j.artmed.2004.07.016, 15811782.
3. Pyysalo S, Ginter F, Heimonen J, Björne J, Boberg J, Järvinen J, Salakoski T. BioInfer: A Corpus for Information Extraction in the Biomedical Domain. BMC Bioinformatics 2007, 8(50). 1808065, 17291334.
4. Corney DP, Buxton BF, Langdon WB, Jones DT. BioRAT: extracting biological information from fulllength papers. Bioinformatics 2004, 20:3206-3213. 10.1093/bioinformatics/bth386, 15231534.
5. Fundel K, Kuffner R, Zimmer R. RelEx-Relation extraction using dependency parse trees. Bioinformatics 2007, 23(3):365-371. 10.1093/bioinformatics/btl616, 17142812.
6. Hu X, Wu D. Data mining and predictive modeling of biomolecular network from biomedical literature databases. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 2007, 4(2):251-263.
7. Giuliano C, Lavelli A, Romano L. Exploiting Shallow Linguistic Information for Relation Extraction From Biomedical Literature. Proceedings of the 11th Conference of the European Chapter of the Association for Computational Linguistics 2006,
8. Bunescu R, Mooney R. A shortest path dependency kernel for relation extraction. Proceedings of Human Language Technology Conference and Conference on Empirical Methods in Natural Language Processing Association for Computational Linguistics 2005, 724-731.
9. Sætre R, Sagae K, Tsujii J. Syntactic features for protein-protein interaction extraction. Second International Symposium on Languages in Biology and Medicine 2007, short papers.
10. Airola A, Pyysalo S, Björne J, Pahikkala T, Ginter F, Salakoski T. All-paths Graph Kernel for Protein-protein Interaction Extraction with Evaluation of Cross-corpus Learning. BMC Bioinformatics 2008, 9(Suppl 11):S2. 10.1186/1471-2105-9-S11-S2, 2586751, 19025688.
11. Miyao Y, Sætre R, Sagae K, Matsuzaki T, Tsujii J. Evaluating Contributions of Natural Language Parsers to Protein-Protein Interaction Extraction. Bioinformatics 2009, 25(3):394-400. 10.1093/bioinformatics/btn631, 2639072, 19073593.
12. Miwa M, Sætre R, Miyao Y, Ohta T, Tsujii J. Combining Multiple Layers of Syntactic Information for Protein-Protein Interaction Extraction. Proceedings of the Third International Symposium on Semantic Mining in Biomedicine 2008, 101-108.
13. Bunescu R, Mooney R. Subsequence Kernels for Relation Extraction. Advances in Neural Information Processing Systems 18 MIT Press 2006, 171-178.
14. Mitsumori T, Murata M, Fukuda Y, Doi K, Doi H. Extracting Protein-Protein Interaction Information from Biomedical Text with SVM. IEICE - Transactions on Information and Systems 2006, E89D(8):2464-2466.
15. Van Landeghem S, Saeys Y, Peer Y VD, De Baets B. Extracting Protein-Protein Interactions from Text using Rich Feature Vectors and Feature Selection. Proceedings of the Third International Symposium on Semantic Mining in Biomedicine 2008, 77-84.
16. Miwa M, Sætre R, Miyao Y, Tsujii J. A Rich Feature Vector for Protein-Protein Interaction Extraction from Multiple Corpora. Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing 2009, 1(1):121-130.
17. Taylor J, Cristianini N. Vijay. Kernel methods for pattern analysis 2004, Cambridge Univ. Press.
18. Li Y, Lin H, Yang Z. Incorporating Rich Background Knowledge for Gene Named Entity Classification and Recognition. BMC Bioinformatics 2009, 10:223. 10.1186/1471-2105-10-223, 2725142, 19615051.
19. Li Y, Lin H, Yang Z. Applying Feature Coupling Generalization for Protein-Protein Interaction Extraction. 2009 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2009) 396-400.
20. Krallinger M, Leitner F, Rodriguez-Penagos C, Valencia A. Overview of the Protein-Protein Interaction Annotation Extraction Task of BioCreative II. Genome Biology 2008, 9(Suppl 2):S4-1. 10.1186/gb-2008-9-s2-s4, 2559988, 18834495.
21. Pyysalo S, Airola A, Heimonen J, Björne J, Ginter F, Salakoski T. Comparative Analysis of Five Protein-protein Interaction Corpora. BMC Bioinformatics 2008, 9(Suppl 3):S6. 10.1186/1471-2105-9-S3-S6, 2349296, 18426551.
22. Hersh W, Cohen A, Roberts P, Rekapalli HK. TREC 2006 genomics track overview. Proceedings of 15th Text REtrieval Conference (TREC) 2006,
23. Wilbur J, Smith L, Tanabe L. BioCreative 2. gene mention task. Proceedings of the Second BioCreative Challenge Evaluation Workshop 2007, 7-16.