Probabilistic methods for predicting protein functions in protein-protein interaction networks

Christoph Best; Ralf Zimmer; Joannis Apostolakis

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Probabilistic methods for predicting protein functions in protein-protein interaction networks

Christoph Best·Ralf Zimmer·Joannis Apostolakis

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Abstract

We discuss probabilistic methods for predicting protein functions from protein-protein interaction networks. Previous work based on Markov Randon Fields is extended and compared to a general machine-learning theoretic approach. Using actual protein interaction networks for yeast from the MIPS database and GO-SLIM function assignments, we compare the predictions of the different probabilistic methods and of a standard support vector machine. It turns out that, with the currently available networks, the simple methods based on counting frequencies perform as well as the more sophisticated approaches.

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Christoph Best, Ralf Zimmer, Joannis Apostolakis. 2005-03-12. Probabilistic methods for predicting protein functions in protein-protein interaction networks. https://arxiv.org/abs/q-bio/0503018

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