Efficient feature selection and multiclass classification with integrated instance and model based learning.

Evolutionary Bioinformatics Online
Zhenqiu LiuMing Tan

Abstract

Multiclass classification and feature (variable) selections are commonly encountered in many biological and medical applications. However, extending binary classification approaches to multiclass problems is not trivial. Instance-based methods such as the K nearest neighbor (KNN) can naturally extend to multiclass problems and usually perform well with unbalanced data, but suffer from the curse of dimensionality. Their performance is degraded when applied to high dimensional data. On the other hand, model-based methods such as logistic regression require the decomposition of the multiclass problem into several binary problems with one-vs.-one or one-vs.-rest schemes. Even though they can be applied to high dimensional data with L(1) or L(p) penalized methods, such approaches can only select independent features and the features selected with different binary problems are usually different. They also produce unbalanced classification problems with one vs. the rest scheme even if the original multiclass problem is balanced.By combining instance-based and model-based learning, we propose an efficient learning method with integrated KNN and constrained logistic regression (KNNLog) for simultaneous multiclass classification and feat...Continue Reading

References

Dec 25, 2002·Bioinformatics·Kyeong Eun LeeBani K Mallick
Apr 4, 2007·Statistical Applications in Genetics and Molecular Biology·Zhenqiu LiuMing Tan
Mar 1, 2008·Proceedings of the National Academy of Sciences of the United States of America·Ramiro GarzonBrunangelo Falini
Jul 14, 2009·The Journal of Pathology·Raffaele BaffaAnne Rosenberg
Nov 7, 2009·Science·Elizabeth K CostelloRob Knight
Feb 13, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Zhenqiu LiuMing T Tan
Jun 24, 2010·IEEE Transactions on Neural Networks·Zenglin XuRong Jin
Dec 2, 2010·Proceedings of the National Academy of Sciences of the United States of America·Marina BousquetHarvey F Lodish

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Citations

May 12, 2017·The International Journal of Biostatistics·Dandan Jiang, Jianguo Sun
Nov 27, 2018·Nucleic Acids Research·Rose OughtredMike Tyers

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Datasets Mentioned

BETA
E-TABM-969
E-TABM-972
E-TABM-973

Software Mentioned

KNNLog
Mothur package
MATLAB
linprog
lpsolve

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