There are several existing algorithms that under appropriate assumptions can reliably identify a subset of the underlying causal relationships from observational data. This paper introduces the first computationally feasible score-based algorithm that can reliably identify causal relationships in the large sample limit for discrete models, while allowing for the possibility that there are unobserved common causes. In doing so, the algorithm does not ever need to assign scores to causal structures with unobserved common causes. The algorithm is based on the identification of so called Y substructures within Bayesian network structures that can be learned from observational data. An example of a Y substructure is A -> C, B -> C, C -> D. After providing background on causal discovery, the paper proves the conditions under which the algorithm is reliable in the large sample limit.

Bayesian Networks (BNs) are useful tools giving a natural and compact representation of joint probability distributions. In many applications one needs to learn a Bayesian Network (BN) from data. In this context, it is important to understand the number of samples needed in order to guarantee a successful learning. Previous work have studied BNs sample complexity, yet it mainly focused on the requirement that the learned distribution will be close to the original distribution which generated the data. In this work, we study a different aspect of the learning, namely the number of samples needed in order to learn the correct structure of the network. We give both asymptotic results, valid in the large sample limit, and experimental results, demonstrating the learning behavior for feasible sample sizes. We show that structure learning is a more difficult task, compared to approximating the correct distribution, in the sense that it requires a much larger number of samples, regardless of the computational power available for the learner.

The main goal of this paper is to describe a method for exact inference in general hybrid Bayesian networks (BNs) (with a mixture of discrete and continuous chance variables). Our method consists of approximating general hybrid Bayesian networks by a mixture of Gaussians (MoG) BNs. There exists a fast algorithm by Lauritzen-Jensen (LJ) for making exact inferences in MoG Bayesian networks, and there exists a commercial implementation of this algorithm. However, this algorithm can only be used for MoG BNs. Some limitations of such networks are as follows. All continuous chance variables must have conditional linear Gaussian distributions, and discrete chance nodes cannot have continuous parents. The methods described in this paper will enable us to use the LJ algorithm for a bigger class of hybrid Bayesian networks. This includes networks with continuous chance nodes with non-Gaussian distributions, networks with no restrictions on the topology of discrete and continuous variables, networks with conditionally deterministic variables that are a nonlinear function of their continuous parents, and networks with continuous chance variables whose variances are functions of their parents.

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.

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.

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.

We address challenges of active learning under scarce informational resources in non-stationary environments. In real-world settings, data labeled and integrated into a predictive model may become invalid over time. However, the data can become informative again with switches in context and such changes may indicate unmodeled cyclic or other temporal dynamics. We explore principles for discarding, caching, and recalling labeled data points in active learning based on computations of value of information. We review key concepts and study the value of the methods via investigations of predictive performance and costs of acquiring data for simulated and real-world data sets.