Finding optimal models for small gene networks

Ott S, Imoto S, Miyano S

Human Genome Center, Institute of Medical Science, The University of Tokyo 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

Pac Symp Biocomput. 2004;:557-67.


Finding gene networks from microarray data has been one focus of research in recent years. Given search spaces of super-exponential size, researchers have been applying heuristic approaches like greedy algorithms or simulated annealing to infer such networks. However, the accuracy of heuristics is uncertain, which--in combination with the high measurement noise of microarrays--makes it very difficult to draw conclusions from networks estimated by heuristics. We present a method that finds optimal Bayesian networks of considerable size and show first results of the application to yeast data. Having removed the uncertainty due to the heuristic methods, it becomes possible to evaluate the power of different statistical models to find biologically accurate networks.

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