PASCAL - Pattern Analysis, Statistical Modelling and Computational Learning

Searching for functional gene modules with interaction component models
Juuso Parkkinen and Samuel Kaski
In: NIPS 2007 workshop on Machine Learning in Computational Biology, 7-8 Dec 2007, Whistler, BC.


Genetic functional modules and protein complexes are being sought from combinations of gene expression and protein-protein interaction data with various clustering-type methods. As far as we know, up to now these methods have used the interaction data as constraints on the clustering of expression data, instead of modeling the noise in the interactions. We model the interaction links with a simple generative ``topic model,'' which is augmented to generate also the expression data. The results outperform a representative set of earlier models in the task of finding modules having enriched functional classes. Moreover, it turns out that the generative model for the links alone works very well in this task.

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EPrint Type:Conference or Workshop Item (Talk)
Project Keyword:Project Keyword UNSPECIFIED
Subjects:Theory & Algorithms
ID Code:3558
Deposited By:Samuel Kaski
Deposited On:11 February 2008