A hierarchical Bayesian network approach for linkage disequilibrium modeling and data-dimensionality reduction prior to genome-wide association studies

<p>Abstract</p> <p>Background</p> <p>Discovering the genetic basis of common genetic diseases in the human genome represents a public health issue. However, the dimensionality of the genetic data (up to 1 million genetic markers) and its complexity make the statistical analysis a challenging task.</p> <p>Results</p> <p>We present an accurate modeling of dependences between genetic markers, based on a forest of hierarchical latent class models which is a particular class of probabilistic graphical models. This model offers an adapted framework to deal with the fuzzy nature of linkage disequilibrium blocks. In addition, the data dimensionality can be reduced through the latent variables of the model which synthesize the information borne by genetic markers. In order to tackle the learning of both forest structure and probability distributions, a generic algorithm has been proposed. A first implementation of our algorithm has been shown to be tractable on benchmarks describing 10⁵variables for 2000 individuals.</p> <p>Conclusions</p> <p>The forest of hierarchical latent class models offers several advantages for genome-wide association studies: accurate modeling of linkage disequilibrium, flexible data dimensionality reduction and biological meaning borne by latent variables.</p

Learning Hierarchical Bayesian Networks for Large-Scale Data Analysis

Abstract. Bayesian network learning is a useful tool for exploratory data analysis. However, applying Bayesian networks to the analysis of large-scale data, consisting of thousands of attributes, is not straightforward because of the heavy computational burden in learning and visualization. In this paper, we propose a novel method for large-scale data analysis based on hierarchical compression of information and constrained structural learning, i.e., hierarchical Bayesian networks (HBNs). The HBN can compactly visualize global probabilistic structure through a small number of hidden variables, approximately representing a large number of observed variables. An efficient learning algorithm for HBNs, which incrementally maximizes the lower bound of the likelihood function, is also suggested. The effectiveness of our method is demonstrated by the experiments on synthetic large-scale Bayesian networks and a real-life microarray dataset.