An Experimental Comparison of Hybrid Algorithms for Bayesian Network Structure Learning

International audienceWe present a novel hybrid algorithm for Bayesian network structure learning, called Hybrid HPC (H2PC). It first reconstructs the skeleton of a Bayesian network and then performs a Bayesian-scoring greedy hill-climbing search to orient the edges. It is based on a subroutine called HPC, that combines ideas from incremental and divide-and-conquer constraint-based methods to learn the parents and children of a target variable. We conduct an experimental comparison of H2PC against Max-Min Hill-Climbing (MMHC), which is currently the most powerful state-of-the-art algorithm for Bayesian network structure learning, on several benchmarks with various data sizes. Our extensive experiments show that H2PC outperforms MMHC both in terms of goodness of fit to new data and in terms of the quality of the network structure itself, which is closer to the true dependence structure of the data. The source code (in R) of H2PC as well as all data sets used for the empirical tests are publicly available

Information-Preserving Techniques Improve Chemosensitivity Prediction of Tumours Based on Expression Profiles

Part 19: Computational Intelligence Applications in Bioinformatics (CIAB) WorkshopInternational audiencePrior work has shown that the sensitivity of a tumour to a specific drug can be predicted from a molecular signature of gene expressions. This is an important finding for improving drug efficacy and personalizing drug use. In this paper, we present an analysis strategy that, compared to prior work, maintains more information and leads to improved chemosensitivity prediction. Specifically we show (a) that prediction is improved when the GI50 value of a drug is estimated by all available measurements and fitting a sigmoid curve and (b) application of regression techniques often results in more accurate models compared to classification techniques. In addition, we show that (c) modern variable selection techniques, such as MMPC result in better predictive performance than simple univariate filtering. We demonstrate the strategy on 59 tumor cell lines after treatment with 118 fully characterized drugs obtained by the National Cancer Institute (NCI 60 screening) and biologically comment on the identified molecular signatures of the best predicted drugs