The paper analyzes theoretically and empirically the performance of likelihood weighting (LW) on a subset of nodes in Bayesian networks. The proposed scheme requires fewer samples to converge due to reduction in sampling variance. The method exploits the structure of the network to bound the complexity of exact inference used to compute sampling distributions, similar to Gibbs cutset sampling. Yet, the extension of the previosly proposed cutset sampling principles to likelihood weighting is non-trivial due to differences in the sampling processes of Gibbs sampler and LW. We demonstrate empirically that likelihood weighting on a cutset (LWLC) is effective time-wise and has a lower rejection rate than LW when applied to networks with many deterministic probabilities. Finally, we show that the performance of likelihood weighting on a cutset can be improved further by caching computed sampling distributions and, consequently, learning 'zeros' of the target distribution.

In Bayesian networks, a Most Probable Explanation (MPE) is a complete variable instantiation with a highest probability given the current evidence. In this paper, we discuss the problem of finding robustness conditions of the MPE under single parameter changes. Specifically, we ask the question: How much change in a single network parameter can we afford to apply while keeping the MPE unchanged? We will describe a procedure, which is the first of its kind, that computes this answer for each parameter in the Bayesian network variable in time O(n exp(w)), where n is the number of network variables and w is its treewidth.

The effect of inaccuracies in the parameters of a dynamic Bayesian network can be investigated by subjecting the network to a sensitivity analysis. Having detailed the resulting sensitivity functions in our previous work, we now study the effect of parameter inaccuracies on a recommended decision in view of a threshold decision-making model. We detail the effect of varying a single and multiple parameters from a conditional probability table and present a computational procedure for establishing bounds between which assessments for these parameters can be varied without inducing a change in the recommended decision. We illustrate the various concepts involved by means of a real-life dynamic network in the field of infectious disease.

We describe an expert system, Maies, under development for analysing forensic identification problems involving DNA mixture traces using quantitative peak area information. Peak area information is represented by conditional Gaussian distributions, and inference based on exact junction tree propagation ascertains whether individuals, whose profiles have been measured, have contributed to the mixture. The system can also be used to predict DNA profiles of unknown contributors by separating the mixture into its individual components. The use of the system is illustrated with an application to a real world example. The system implements a novel MAP (maximum a posteriori) search algorithm that is briefly described.

Predicting the outcomes of future events is a challenging problem for which a variety of solution methods have been explored and attempted. We present an empirical comparison of a variety of online and offline adaptive algorithms for aggregating experts' predictions of the outcomes of five years of US National Football League games (1319 games) using expert probability elicitations obtained from an Internet contest called ProbabilitySports. We find that it is difficult to improve over simple averaging of the predictions in terms of prediction accuracy, but that there is room for improvement in quadratic loss. Somewhat surprisingly, a Bayesian estimation algorithm which estimates the variance of each expert's prediction exhibits the most consistent superior performance over simple averaging among our collection of algorithms.

Learning from electronic medical records (EMR) is challenging due to their relational nature and the uncertain dependence between a patient's past and future health status. Statistical relational learning is a natural fit for analyzing EMRs but is less adept at handling their inherent latent structure, such as connections between related medications or diseases. One way to capture the latent structure is via a relational clustering of objects. We propose a novel approach that, instead of pre-clustering the objects, performs a demand-driven clustering during learning. We evaluate our algorithm on three real-world tasks where the goal is to use EMRs to predict whether a patient will have an adverse reaction to a medication. We find that our approach is more accurate than performing no clustering, pre-clustering, and using expert-constructed medical heterarchies.

We consider the incorporation of causal knowledge about the presence or absence of (possibly indirect) causal relations into a causal model. Such causal relations correspond to directed paths in a causal model. This type of knowledge naturally arises from experimental data, among others. Specifically, we consider the formalisms of Causal Bayesian Networks and Maximal Ancestral Graphs and their Markov equivalence classes: Partially Directed Acyclic Graphs and Partially Oriented Ancestral Graphs. We introduce sound and complete procedures which are able to incorporate causal prior knowledge in such models. In simulated experiments, we show that often considering even a few causal facts leads to a significant number of new inferences. In a case study, we also show how to use real experimental data to infer causal knowledge and incorporate it into a real biological causal network. The code is available at mensxmachina.org.

The covariance graph (aka bi-directed graph) of a probability distribution $p$ is the undirected graph $G$ where two nodes are adjacent iff their corresponding random variables are marginally dependent in $p$. In this paper, we present a graphical criterion for reading dependencies from $G$, under the assumption that $p$ satisfies the graphoid properties as well as weak transitivity and composition. We prove that the graphical criterion is sound and complete in certain sense. We argue that our assumptions are not too restrictive. For instance, all the regular Gaussian probability distributions satisfy them.

In recent years a number of methods have been developed for automatically learning the (sparse) connectivity structure of Markov Random Fields. These methods are mostly based on L1-regularized optimization which has a number of disadvantages such as the inability to assess model uncertainty and expensive cross-validation to find the optimal regularization parameter. Moreover, the model's predictive performance may degrade dramatically with a suboptimal value of the regularization parameter (which is sometimes desirable to induce sparseness). We propose a fully Bayesian approach based on a "spike and slab" prior (similar to L0 regularization) that does not suffer from these shortcomings. We develop an approximate MCMC method combining Langevin dynamics and reversible jump MCMC to conduct inference in this model. Experiments show that the proposed model learns a good combination of the structure and parameter values without the need for separate hyper-parameter tuning. Moreover, the model's predictive performance is much more robust than L1-based methods with hyper-parameter settings that induce highly sparse model structures.

An automated technique has recently been proposed to transfer learning in the hierarchical Bayesian optimization algorithm (hBOA) based on distance-based statistics. The technique enables practitioners to improve hBOA efficiency by collecting statistics from probabilistic models obtained in previous hBOA runs and using the obtained statistics to bias future hBOA runs on similar problems. The purpose of this paper is threefold: (1) test the technique on several classes of NP-complete problems, including MAXSAT, spin glasses and minimum vertex cover; (2) demonstrate that the technique is effective even when previous runs were done on problems of different size; (3) provide empirical evidence that combining transfer learning with other efficiency enhancement techniques can often yield nearly multiplicative speedups.