Cancer classification based on micro-array data is one of the classic applications of machine learning in computational biology. The aim is to identify biomarker genes, the expression of which are diagnostic of a particular form of cancer. In this project, we extended the sparse logistic regression algorithm of Shevade and Keerthi  to provide Bayesian regularisation, where the regularisation parameter controlling sparsity is integrated out analytically, using an uninformative Jeffrey's prior (c.f. ). This not only obviates the need for costly cross-validation based model selection procedures but also entirely eliminates the possibility of selection bias - a common pitfall in this application . The results obtained using this approach are competitive with those obtained via cross-validation based regularisation and the with the Relevance Vector Machine (RVM) [4,5] on the well known colon cancer  and leukaemia  benchmark datasets. This page contains supplementary information for .
A MATLAB implementation of the BLogReg algorithm is made available for research purposes under the GNU General Public License (GPL). For efficiency, it is implemented as a C-language MEX file. If you download both files then, provided you have configured mex correctly, blogreg should automatically (an transparently) compile itself the first time it is executed.
- Bayesian logistic regression routine (blogreg.c)
- Online help file (blogreg.m)
- Minimal demonstration using Leukaemia dataset (demo.m)
- MAT file containing the Leukaemia dataset (leukaemia.mat)
This work was supported by grants from the U.K. Biotechnology and Biological Sciences Research Council (BBSRC) under the Exploiting Genomics initiative (grant numbers and 83/EGM16126 and 83/EGM16128 "Computational approaches to identifying gene regulatory systems in Arabidopsis"). N.B. the BLogReg algorithm was originaly developed for use in detection of transcription factor binding sites, see e.g. , this work in currently in progress.
N.B. doi represents a link to on-line material via the Digital Object Identifier DOI system, where available, while www represents a link to on-line materials available via the publisher's web-site.
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