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Optimal Aggregation of Binary Classifiers for Multiclass Cancer Diagnosis Using Gene Expression Profiles
April-June 2009 (vol. 6 no. 2)
pp. 333-343
ASCII Text
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Naoto Yukinawa, Shigeyuki Oba, Kikuya Kato, Shin Ishii, "Optimal Aggregation of Binary Classifiers for Multiclass Cancer Diagnosis Using Gene Expression Profiles," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 2, pp. 333-343, April-June, 2009.
 
 
BibTex
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@article{ 10.1109/TCBB.2007.70239,
author = {Naoto Yukinawa and Shigeyuki Oba and Kikuya Kato and Shin Ishii},
title = {Optimal Aggregation of Binary Classifiers for Multiclass Cancer Diagnosis Using Gene Expression Profiles},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {6},
number = {2},
issn = {1545-5963},
year = {2009},
pages = {333-343},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2007.70239},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - Optimal Aggregation of Binary Classifiers for Multiclass Cancer Diagnosis Using Gene Expression Profiles
IS - 2
SN - 1545-5963
SP333
EP343
EPD - 333-343
A1 - Naoto Yukinawa,
A1 - Shigeyuki Oba,
A1 - Kikuya Kato,
A1 - Shin Ishii,
PY - 2009
KW - Multiclass classification
KW - error correcting output coding
KW - gene expression profiling
KW - cancer diagnosis.
VL - 6
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
Multiclass classification is one of the fundamental tasks in bioinformatics and typically arises in cancer diagnosis studies by gene expression profiling. There have been many studies of aggregating binary classifiers to construct a multiclass classifier based on one-versus-the-rest (1R), one-versus-one (11), or other coding strategies, as well as some comparison studies between them. However, the studies found that the best coding depends on each situation. Therefore, a new problem, which we call the “optimal coding problem,” has arisen: how can we determine which coding is the optimal one in each situation? To approach this optimal coding problem, we propose a novel framework for constructing a multiclass classifier, in which each binary classifier to be aggregated has a weight value to be optimally tuned based on the observed data. Although there is no a priori answer to the optimal coding problem, our weight tuning method can be a consistent answer to the problem. We apply this method to various classification problems including a synthesized data set and some cancer diagnosis data sets from gene expression profiling. The results demonstrate that, in most situations, our method can improve classification accuracy over simple voting heuristics and is better than or comparable to state-of-the-art multiclass predictors.

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Index Terms:
Multiclass classification, error correcting output coding, gene expression profiling, cancer diagnosis.
Citation:
Naoto Yukinawa, Shigeyuki Oba, Kikuya Kato, Shin Ishii, "Optimal Aggregation of Binary Classifiers for Multiclass Cancer Diagnosis Using Gene Expression Profiles," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 2, pp. 333-343, April-June 2009, doi:10.1109/TCBB.2007.70239
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