Who Learns Better Bayesian Network Structures: Accuracy and Speed of Structure Learning Algorithms

Three classes of algorithms to learn the structure of Bayesian networks from data are common in the literature: constraint-based algorithms, which use conditional independence tests to learn the dependence structure of the data; score-based algorithms, which use goodness-of-fit scores as objective functions to maximise; and hybrid algorithms that combine both approaches. Constraint-based and score-based algorithms have been shown to learn the same structures when conditional independence and goodness of fit are both assessed using entropy and the topological ordering of the network is known (Cowell, 2001). In this paper, we investigate how these three classes of algorithms perform outside the assumptions above in terms of speed and accuracy of network reconstruction for both discrete and Gaussian Bayesian networks. We approach this question by recognising that structure learning is defined by the combination of a statistical criterion and an algorithm that determines how the criterion is applied to the data. Removing the confounding effect of different choices for the statistical criterion, we find using both simulated and real-world complex data that constraint-based algorithms are often less accurate than score-based algorithms, but are seldom faster (even at large sample sizes); and that hybrid algorithms are neither faster nor more accurate than constraint-based algorithms. This suggests that commonly held beliefs on structure learning in the literature are strongly influenced by the choice of particular statistical criteria rather than just by the properties of the algorithms themselves.Comment: 27 pages, 8 figure

An Efficient Methodology for Learning Bayesian Networks

Statistics from the National Cancer Institute indicate that 1 in 8 women will develop Breast cancer in their lifetime. Researchers have developed numerous statistical models to predict breast cancer risk however physicians are hesitant to use these models because of disparities in the predictions they produce. In an effort to reduce these disparities, we use Bayesian networks to capture the joint distribution of risk factors, and simulate artificial patient populations (clinical avatars) for interrogating the existing risk prediction models. The challenge in this effort has been to produce a Bayesian network whose dependencies agree with literature and are good estimates of the joint distribution of risk factors. In this work, we propose a methodology for learning Bayesian networks that uses prior knowledge to guide a collection of search algorithms in identifying an optimum structure. Using data from the breast cancer surveillance consortium we have shown that our methodology produces a Bayesian network with consistent dependencies and a better estimate of the distribution of risk factors compared with existing method

Learning the structure of Bayesian Networks: A quantitative assessment of the effect of different algorithmic schemes

One of the most challenging tasks when adopting Bayesian Networks (BNs) is the one of learning their structure from data. This task is complicated by the huge search space of possible solutions, and by the fact that the problem is NP-hard. Hence, full enumeration of all the possible solutions is not always feasible and approximations are often required. However, to the best of our knowledge, a quantitative analysis of the performance and characteristics of the different heuristics to solve this problem has never been done before. For this reason, in this work, we provide a detailed comparison of many different state-of-the-arts methods for structural learning on simulated data considering both BNs with discrete and continuous variables, and with different rates of noise in the data. In particular, we investigate the performance of different widespread scores and algorithmic approaches proposed for the inference and the statistical pitfalls within them