Inference algorithms and learning theory for Bayesian sparse factor analysis
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| Authors | Magnus Rattray, Oliver Stegle, Kevin Sharp, John Winn |
| Journal/Conference Name | Journal of Physics: Conference Series |
| Paper Category | Physics and Astronomy (miscellaneous) |
| Paper Abstract | Bayesian sparse factor analysis has many applications; for example, it has been applied to the problem of inferring a sparse regulatory network from gene expression data. We describe a number of inference algorithms for Bayesian sparse factor analysis using a slab and spike mixture prior. These include well-established Markov chain Monte Carlo (MCMC) and variational Bayes (VB) algorithms as well as a novel hybrid of VB and Expectation Propagation (EP). For the case of a single latent factor we derive a theory for learning performance using the replica method. We compare the MCMC and VB/EP algorithm results with simulated data to the theoretical prediction. The results for MCMC agree closely with the theory as expected. Results for VB/EP are slightly sub-optimal but show that the new algorithm is effective for sparse inference. In large-scale problems MCMC is infeasible due to computational limitations and the VB/EP algorithm then provides a very useful computationally efficient alternative. |
| Date of publication | 2009 |
| Code Programming Language | C++ |
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