Investigation into biomedical literature classification using support vector machines

• Published in: 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05) pp. 366 - 374
• Main Authors: Polavarapu, N., Navathe, S.B., Ramnarayanan, R., ul Haque, A., Sahay, S., Liu, Y.
• Format: Conference Proceeding Journal Article
• Language: English
• Published: United States IEEE 2005
• Subjects: Abstracting and Indexing as Topic - methods; Algorithms; Artificial Intelligence; Automatic control; Bioinformatics; Database Management Systems; Diseases; Genomics; Humans; Information resources; Information Storage and Retrieval - methods; Kernel; Natural Language Processing; Pattern Recognition, Automated - methods; Periodicals as Topic; PubMed; Support vector machine classification; Support vector machines; Vocabulary, Controlled
• DOI: 10.1109/CSB.2005.36
• ISBN: 0769523447; 9780769523446
• ISSN: 1551-7497

Specific topic search in the PubMed Database, one of the most important information resources for scientific community, presents a big challenge to the users. The researcher typically formulates boolean queries followed by scanning the retrieved records for relevance, which is very time consuming and error prone. We applied Support Vector Machines (SVM) for automatic retrieval of PubMed articles related to Human genome epidemiological research at CDC (Center for disease Control and Prevention). In this paper, we discuss various investigations into biomedical literature classification and analyze the effect of various issues related to the choice of keywords, training sets, kernel functions and parameters for the SVM technique. We report on the various factors above to show that SVM is a viable technique for automatic classification of biomedical literature into topics of interest such as epidemiology, cancer, birth defects etc. In all our experiments, we achieved high values of PPV, sensitivity and specificity.