Optimizing exact genetic linkage computations

Genetic linkage analysis is a challenging application which requires Bayesian networks consisting of thousands of vertices. Consequently, computing the likelihood of data, which is needed for learning linkage parameters, using exact inference procedures calls for an extremely efficient implementation that carefully optimizes the order of conditioning and summation operations. In this paper we present the use of stochastic greedy algorithms for optimizing this order. Our algorithm has been incorporated into the newest version of superlink, which is currently the fastest genetic linkage program for exact likelihood computations in general pedigrees. We demonstrate an order of magnitude improvement in run times of likelihood computations using our new optimization algorithm, and hence enlarge the class of problems that can be handled effectively by exact computations. Categories and Subject Descriptors J.3 [Computer Applications]: Life and Medical Sciences-Biology and genetics; G.2.2 [Di...

• Type: Conference
• Year: 2003
• Where: RECOMB
• Authors: Dan Geiger, Maáyan Fishelson
• Keywords: Bayesian Networks, Computational Biology, Exact Inference Procedures, Genetic Linkage Analysis, RECOMB 2003