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