An extensive comparison of feature ranking aggregation techniques in bioinformatics

Proceedings of the 2012 IEEE 13th International Conference on Information Reuse and Integration, IRI 2012

Volumn , Issue , 2012, Pages 377-384

  Wald, Randall ^a   Khoshgoftaar, Taghi M ^a   Dittman, David ^a   Awada, Wael ^a   Napolitano, Amri ^a  

^a NONE

Author keywords

bioinformatics; feature ranking; rank aggregation

Indexed keywords

DATA SETS; FEATURE RANKING; FEATURE SUBSET; GENE LISTS; RANK AGGREGATION; UNIVARIATE;

GENES; INFORMATION USE;

BIOINFORMATICS;

EID: 84868319284     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IRI.2012.6303034     Document Type: Conference Paper

References (31)

1. J. A. Aslam and M. Montague, "Models for metasearch," in Proceedings of the 24th annual international ACM SIGIR conference on Research and development in information retrieval, ser. SIGIR '01. New York, NY, USA: ACM, 2001, pp. 276-284.
2. R. Battiti, "Using mutual information for selecting features in supervised neural net learning," IEEE Transactions On Neural Networks, pp. 537-550, 1994.
3. D. G. Beer, S. L. Kardia, C.-C. Huang, T. J. Giordano, A. M. Levin, D. E. Misek, L. Lin, G. Chen, T. G. Gharib, D. G. Thomas, M. L. Lizyness, R. Kuick, S. Hayasaka, J. M. Taylor, M. D. Iannettoni, M. B. Orringer, and S. Hanash, "Gene-expression profiles predict survival of patients with lung adenocarcinoma," Nature Medicine, vol. 8, pp. 816-824, 2002.
4. A. Ben-Dor, L. Bruhn, N. Friedman, I. Nachman, M. Schummer, and Z. Yakhini, "Tissue classification with gene expression profiles," Journal of Computational Biology, vol. 7, no. 3-4, pp. 559-583, 2000. [Online]. Available: http://www.liebertonline.com/doi/abs/10.1089/106652700750050943
5. A.-L. Boulesteix and M. Slawski, "Stability and aggregation of ranked gene lists," Briefings in Bioinformatics, vol. 10, no. 5, pp. 556-568, 2009. [Online]. Available: http://bib.oxfordjournals.org/content/10/5/ 556.abstract
6. X. Chen and M. Wasikowski, "Fast: a roc-based feature selection metric for small samples and imbalanced data classification problems," in Proceedings of the 14th ACM SIGKDD Int'l Conf. Knowldege Discovery and Data Mining (KDD '08). New York, NY: ACM, 2008, pp. 124-132.
7. W. J. Conover, Practical Nonparametric Studies. John Wiley and Sons, 2nd edition, 1971.
8. D. Dittman, T. Khoshgoftaar, R. Wald, and A. Napolitano, "Random forest: A reliable tool for patient response prediction," in Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Workshops. BIBM, 2011, pp. 289-296.
9. D. Dittman, T. Khoshgoftaar, R. Wald, and J. Van Hulse, "Comparative analysis of dna microarray data through the use of feature selection techniques," in Proceedings of the Ninth IEEE International Conference on Machine Learning and Applications (ICMLA). ICMLA, 2010, pp. 147-152.
10. D. Dittman, T. Khoshgoftaar, R. Wald, and H. Wang, "Stability analysis of feature ranking techniques on biological datasets," in Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM). BIBM, 2011, pp. 252-256.
11. C. Dwork, R. Kumar, M. Naor, and D. Sivakumar, "Rank aggregation methods for the web," in Proceedings of the 10th international conference on World Wide Web, ser. WWW '01. New York, NY, USA: ACM, 2001, pp. 613-622.
12. I. Guyon, J. Weston, S. Barnhill, and V. Vapnik, "Gene selection for cancer classification using support vector machines," Machine Learning, vol. 46, pp. 389-422, 2002, 10.1023/A:1012487302797.
13. M. A. Hall and G. Holmes, "Benchmarking attribute selection techniques for discrete class data mining," IEEE Transactions on Knowledge and Data Engineering, vol. 15, no. 6, pp. 392-398, November/December 2003.
14. A.-C. Haury, P. Gestraud, and J.-P. Vert, "The influence of feature selection methods on accuracy, stability and interpretability of molecular signatures," PLoS ONE, vol. 6, no. 12, p. e28210, 12 2011.
15. R. Kolde, S. Laur, P. Adler, and J. Vilo, "Robust rank aggregation for gene list integration and meta-analysis," Bioinformatics, vol. 28, no. 4, pp. 573-580, 2012. [Online]. Available: http://bioinformatics. oxfordjournals.org/content/28/4/573.abstract
16. I. Kononenko, "Estimating attributes: Analysis and extensions of relief," Lecture Notes in Computer Science, pp. 171-182, 1994.
17. L. I. Kuncheva, "A stability index for feature selection," in Proceedings of the 25th conference on Proceedings of the 25th IASTED International Multi-Conference: artificial intelligence and applications. Anaheim, CA, USA: ACTA Press, 2007, pp. 390-395.
18. J. L. Lustgarten, V. Gopalakrishnan, and S. Visweswaran, "Measuring stability of feature selection in biomedical datasets," in AMIA 2009 Symposium Proceedings, 2009, pp. 406-410.
19. G. Mulligan, C. Mitsiades, B. Bryant, F. Zhan, W. J. Chng, S. Roels, E. Koenig, A. Fergus, Y. Huang, P. Richardson, W. L. Trepicchio, A. Broyl, P. Sonneveld, J. Shaughnessy, John D., P. Leif Bergsagel, D. Schenkein, D.-L. Esseltine, A. Boral, and K. C. Anderson, "Gene expression profiling and correlation with outcome in clinical trials of the proteasome inhibitor bortezomib," Blood, pp. 3177-3188, 2007.
20. R. Neumayer, R. Mayer, and K. Nrvg, "Combination of feature selection methods for text categorisation," in Advances in Information Retrieval, ser. Lecture Notes in Computer Science, 2011, vol. 6611, pp. 763-766.
21. V. Pihur, S. Datta, and S. Datta, "Finding cancer genes through meta-analysis of microarray experiments: Rank aggregation via the cross entropy algorithm," in 7th International Conference for the Critical Assessment of Microarray Data Analysis, ser. CAMDA'07, Dec. 2007.
22. Y. Saeys, T. Abeel, and Y. Peer, "Robust feature selection using ensemble feature selection techniques," in ECML PKDD '08: Proceedings of the European conference on Machine Learning and Knowledge Discovery in Databases - Part II. Berlin, Heidelberg: Springer-Verlag, 2008, pp. 313-325.
23. Y. Saeys, I. Inza, and P. Larraaga, "A review of feature selection techniques in bioinformatics," Bioinformatics, vol. 23, no. 19, pp. 2507-2517, 2007. [Online]. Available: http://bioinformatics.oxfordjournals. org/content/23/19/2507.abstract
24. N. Seliya, T. M. Khoshgoftaar, and J. Van Hulse, "A study on the relationships of classifier performance metrics," in Proceedings of the 21st IEEE International Conference on Tools with Artifical Intelligence (ICTAI'09). Newark, NJ: IEEE Computer Society, November 2009, pp. 59-66.
25. A. Shanab, T. Khoshgoftaar, R. Wald, and J. Van Hulse, "Comparison of approaches to alleviate problems with high-dimensional and class-imbalanced data," in Information Reuse and Integration (IRI), 2011 IEEE International Conference on, aug. 2011, pp. 234-239.
26. J. Van Hulse, T. M. Khoshgoftaar, A. Napolitano, and R. Wald, "Feature selection with high-dimensional imbalanced data." in ICDM Workshops'09, 2009, pp. 507-514.
27. -, "A comparative evaluation of feature ranking methods for high dimensional bioinformatics data," in Proceedings of the IEEE International Conference on Information Reuse and Integration - IRI'11, August 3-5, 2011, pp. 315-320.
28. M. Wasikowski and X. wen Chen, "Combating the small sample class imbalance problem using feature selection," IEEE Transactions on Knowledge and Data Engineering, vol. 22, pp. 1388-1400, 2010.
29. D. A. Wigle, I. Jurisica, N. Radulovich, M. Pintilie, J. Rossant, N. Liu, C. Lu, J. Woodgett, I. Seiden, M. Johnston, S. Keshavjee, G. Darling, T. Winton, and B.-J. Breitkreutz, "Molecular profiling of non-small cell lung cancer and correlation with disease-free survival1," Cancer Research, pp. 3005-3008, 2002.
30. I. H. Witten and E. Frank, Data Mining: Practical Machine Learning Tools and Techniques. Morgan Kaufmann, 2nd edition, 2005.
31. P. Yang, J. Ho, Y. Yang, and B. Zhou, "Gene-gene interaction filtering with ensemble of filters," BMC Bioinformatics, vol. 12, no. Suppl 1, p. S10, 2011. [Online]. Available: http://www.biomedcentral.com/1471-2105/ 12/S1/S10