Bayesian Unsupervised Learning with Multiple Data Types

Agius Phaedra, Ying Yiming and Campbell Colin
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Agius Phaedra: MSKCC
Ying Yiming: University of Bristol
Campbell Colin: University of Bristol

Statistical Applications in Genetics and Molecular Biology, 2009, vol. 8, issue 1, 29

Abstract: We propose Bayesian generative models for unsupervised learning with two types of data and an assumed dependency of one type of data on the other. We consider two algorithmic approaches, based on a correspondence model, where latent variables are shared across datasets. These models indicate the appropriate number of clusters in addition to indicating relevant features in both types of data. We evaluate the model on artificially created data. We then apply the method to a breast cancer dataset consisting of gene expression and microRNA array data derived from the same patients. We assume partial dependence of gene expression on microRNA expression in this study. The method ranks genes within subtypes which have statistically significant abnormal expression and ranks associated abnormally expressing microRNA. We report a genetic signature for the basal-like subtype of breast cancer found across a number of previous gene expression array studies. Using the two algorithmic approaches we find that this signature also arises from clustering on the microRNA expression data and appears derivative from this data.

Keywords: multiple datasets; correspondence model; Bayesian learning; unsupervised learning; clusters; breast cancer; cancer subtypes; genes; microRNA (search for similar items in EconPapers)
Date: 2009
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DOI: 10.2202/1544-6115.1441

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