Abstract
Scientific papers are a primary source of information for investigators to know the current status in a topic or compare their results with other colleagues. However, mining biomedical texts remains to be a great challenge by the huge volume of scientific databases stored in the public databases and their imbalanced nature, with only a very small number of relevant papers to each user query. Classifying in the presence of data imbalances presents a great challenge to machine learning. Techniques such as support-vector machines (SVMs) have excellent performance for balanced data, but may fail when applied to imbalanced datasets. In this paper, we study the effects of undersampling, resampling and subsampling balancing strategies on four different biomedical text classifiers (with lineal, sigmoid, exponential and polynomial SVM kernels, respectively). Best results were obtained by normalized lineal and sigmoid kernels using the subsampling balancing technique. These results have been compared with those obtained by other authors using the TREC Genomics 2005 public corpus.
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References
Anand, A., Pugalenthi, G., Fogel, G.B., Suganthan, P.N.: An approach for classification of highly imbalanced data using weighting and undersampling. Amino Acids 39, 1385–1391 (2010)
Ando, R.K., Dredze, M., Zhang, T.: Trec 2005 genomics track experiments at ibm watson. In: Proceedings of TREC 2005. NIST Special Publication(2005)
Aronson, A.R.: Fusion of knowledge-intensive and statistical approaches for retrieving and annotating textual genomics documents. In: Proc TREC 2005, pp. 36–45 (2005)
Barandela, R., Sánchez, J.S., GarcÃa, V., Rangel, E.: Strategies for learning in class imbalance problems. Pattern Recognition 36(3), 849–851 (2003)
Caporaso, J.G.: Concept recognition and the trec genomics tasks. the fourteenth text retrieval. In: Conference Proceedings (TREC 2005). National Institute for Standards and Technology, Gaithersburg (2005)
Chang, C.-C., Lin, C.-J.: LIBSVM: a library for support vector machines (2001), Software available at http://www.csie.ntu.edu.tw/~cjlin/libsvm
Chawla, N.V., Japkowicz, N., Kotcz, A.: Editorial: special issue on learning from imbalanced data sets. SIGKDD Explorations 6(1), 1–6 (2004)
Collier, N., Ruch, P., Nazarenko, A. (eds.): JNLPBA 2004: Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications. ACL, Morristown (2004)
Cunningham, H., Wilks, Y., Gaizauskas, R.J.: Gate - a general architecture for text engineering (1996)
Hersh, W., Cohen, A., Yang, J., Bhupatiraju, R.T., Roberts, P., Hearst, M.: Trec 2005 genomics track overview. In: TREC 2005 Notebook, pp. 14–25 (2005)
Kang, P., Cho, S.: EUS SVMs: Ensemble of Under-Sampled SVMs for Data Imbalance Problems. In: King, I., Wang, J., Chan, L.-W., Wang, D. (eds.) ICONIP 2006. LNCS, vol. 4232, pp. 837–846. Springer, Heidelberg (2006)
Settles, B.: ABNER: An open source tool for automatically tagging genes, proteins, and other entity names in text. Bioinformatics 21(14), 3191–3192 (2005)
Si, L., Kanungo, T.: Thresholding strategies for text classifiers: Trec 2005 biomedical triage task experiments. the fourteenth text retrieval. In: Conference Proceedings (TREC 2005). National Institute for Standards and Technology, Gaithersburg (2005), http://trec.nist.gov/pubs/trec14/papers/carnegie-mu-kanungo.geo.pdf
Tan, S.: Neighbor-weighted k-nearest neighbor for unbalanced text corpus. Expert Systems with Applications 28(4), 667–671 (2005)
Tang, Y., Zhang, Y., Chawla, N.V.: Svms modeling for highly imbalanced classification. IEEE Transactions on Systems, Man, and Cybernetics, Part B: Cybernetics 39(1), 281–288 (2009)
Voorhees, E.M., Buckland, L.P. (eds.): Proceedings of the Fourteenth Text REtrieval Conference, TREC 2005, Gaithersburg, Maryland, November 15-18. National Institute of Standards and Technology (NIST), Special Publication 500-266 (2005)
Weiss, G.M.: Mining with rarity: a unifying framework. SIGKDD Explor. Newsl. 6, 7–19 (2004)
Zhaif, C.: Uiuc/musc at trec 2005 genomics track. the fourteenth text retrieval. In: Conference Proceedings (TREC 2005). National Institute for Standards and Technology, Gaithersburg (2005), http://trec.nist.gov/pubs/trec14/papers/uillinoisuc.geo.pdf
Zhang, J., Mani, I.: knn approach to unbalanced data distributions: A case study involving information extraction. In: Proceedings of the ICML 2003 Workshop on Learning from Imbalanced Datasets (2003)
Zheng, Z.H.: Applying probabilistic thematic clustering for classification in the trec 2005 genomics track. the fourteenth text retrieval. In: Conference Proceedings (TREC 2005). National Institute for Standards and Technology, Gaithersburg (2005), http://trec.nist.gov/pubs/trec14/papers/queensu.geo.pdf
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Romero, R., Iglesias, E.L., Borrajo, L. (2011). Building Biomedical Text Classifiers under Sample Selection Bias. In: Abraham, A., Corchado, J.M., González, S.R., De Paz Santana, J.F. (eds) International Symposium on Distributed Computing and Artificial Intelligence. Advances in Intelligent and Soft Computing, vol 91. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-19934-9_2
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DOI: https://doi.org/10.1007/978-3-642-19934-9_2
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