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.

This paper proposes new formulas for the probabilities of causation difined by Pearl (2000). Tian and Pearl (2000a, 2000b) showed how to bound the quantities of the probabilities of causation from experimental and observational data, under the minimal assumptions about the data-generating process. We derive narrower bounds than Tian-Pearl bounds by making use of the covariate information measured in experimental and observational studies. In addition, we provide identifiable case under no-prevention assumption and discuss the covariate selection problem from the viewpoint of estimation accuracy. These results are helpful in providing more evidence for public policy assessment and dicision making problems.

Previous work in hierarchical reinforcement learning has faced a dilemma: either ignore the values of different possible exit states from a subroutine, thereby risking suboptimal behavior, or represent those values explicitly thereby incurring a possibly large representation cost because exit values refer to nonlocal aspects of the world (i.e., all subsequent rewards). This paper shows that, in many cases, one can avoid both of these problems. The solution is based on recursively decomposing the exit value function in terms of Q-functions at higher levels of the hierarchy. This leads to an intuitively appealing runtime architecture in which a parent subroutine passes to its child a value function on the exit states and the child reasons about how its choices affect the exit value. We also identify structural conditions on the value function and transition distributions that allow much more concise representations of exit state distributions, leading to further state abstraction. In essence, the only variables whose exit values need be considered are those that the parent cares about and the child affects. We demonstrate the utility of our algorithms on a series of increasingly complex environments.

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.

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.

In Passive POMDPs actions do not affect the world state, but still incur costs. When the agent is bounded by information-processing constraints, it can only keep an approximation of the belief. We present a variational principle for the problem of maintaining the information which is most useful for minimizing the cost, and introduce an efficient and simple algorithm for finding an optimum.

A central task in many applications is reasoning about processes that change in a continuous time. The mathematical framework of Continuous Time Markov Processes provides the basic foundations for modeling such systems. Recently, Nodelman et al introduced continuous time Bayesian networks (CTBNs), which allow a compact representation of continuous-time processes over a factored state space. In this paper, we introduce continuous time Markov networks (CTMNs), an alternative representation language that represents a different type of continuous-time dynamics. In many real life processes, such as biological and chemical systems, the dynamics of the process can be naturally described as an interplay between two forces - the tendency of each entity to change its state, and the overall fitness or energy function of the entire system. In our model, the first force is described by a continuous-time proposal process that suggests possible local changes to the state of the system at different rates. The second force is represented by a Markov network that encodes the fitness, or desirability, of different states; a proposed local change is then accepted with a probability that is a function of the change in the fitness distribution. We show that the fitness distribution is also the stationary distribution of the Markov process, so that this representation provides a characterization of a temporal process whose stationary distribution has a compact graphical representation. This allows us to naturally capture a different type of structure in complex dynamical processes, such as evolving biological sequences. We describe the semantics of the representation, its basic properties, and how it compares to CTBNs. We also provide algorithms for learning such models from data, and discuss its applicability to biological sequence evolution.

Inference for probabilistic graphical models is still very much a practical challenge in large domains. The commonly used and effective belief propagation (BP) algorithm and its generalizations often do not converge when applied to hard, real-life inference tasks. While it is widely recognized that the scheduling of messages in these algorithms may have significant consequences, this issue remains largely unexplored. In this work, we address the question of how to schedule messages for asynchronous propagation so that a fixed point is reached faster and more often. We first show that any reasonable asynchronous BP converges to a unique fixed point under conditions similar to those that guarantee convergence of synchronous BP. In addition, we show that the convergence rate of a simple round-robin schedule is at least as good as that of synchronous propagation. We then propose residual belief propagation (RBP), a novel, easy-to-implement, asynchronous propagation algorithm that schedules messages in an informed way, that pushes down a bound on the distance from the fixed point. Finally, we demonstrate the superiority of RBP over state-of-the-art methods for a variety of challenging synthetic and real-life problems: RBP converges significantly more often than other methods; and it significantly reduces running time until convergence, even when other methods converge.

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 study the problem of learning the best Bayesian network structure with respect to a decomposable score such as BDe, BIC or AIC. This problem is known to be NP-hard, which means that solving it becomes quickly infeasible as the number of variables increases. Nevertheless, in this paper we show that it is possible to learn the best Bayesian network structure with over 30 variables, which covers many practically interesting cases. Our algorithm is less complicated and more efficient than the techniques presented earlier. It can be easily parallelized, and offers a possibility for efficient exploration of the best networks consistent with different variable orderings. In the experimental part of the paper we compare the performance of the algorithm to the previous state-of-the-art algorithm. Free source-code and an online-demo can be found at http://b-course.hiit.fi/bene.