54,542 research outputs found
Uncovering Gene Regulatory Networks from Time-Series Microarray Data with Variational Bayesian Structural Expectation Maximization
We investigate in this paper reverse engineering of gene regulatory networks from time-series microarray data. We apply dynamic Bayesian networks (DBNs) for modeling cell cycle regulations. In developing a network inference algorithm, we focus on soft solutions that can provide a posteriori probability (APP) of network topology. In particular, we propose a variational Bayesian structural expectation maximization algorithm that can learn the posterior distribution of the network model parameters and topology jointly. We also show how the obtained APPs of the network topology can be used in a Bayesian data integration strategy to integrate two different microarray data sets. The proposed VBSEM algorithm has been tested on yeast cell cycle data sets. To evaluate the confidence of the inferred networks, we apply a moving block bootstrap method. The inferred network is validated by comparing it to the KEGG pathway map
Cutset Sampling for Bayesian Networks
The paper presents a new sampling methodology for Bayesian networks that
samples only a subset of variables and applies exact inference to the rest.
Cutset sampling is a network structure-exploiting application of the
Rao-Blackwellisation principle to sampling in Bayesian networks. It improves
convergence by exploiting memory-based inference algorithms. It can also be
viewed as an anytime approximation of the exact cutset-conditioning algorithm
developed by Pearl. Cutset sampling can be implemented efficiently when the
sampled variables constitute a loop-cutset of the Bayesian network and, more
generally, when the induced width of the networks graph conditioned on the
observed sampled variables is bounded by a constant w. We demonstrate
empirically the benefit of this scheme on a range of benchmarks
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