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.

Recent work on approximate linear programming (ALP) techniques for first-order Markov Decision Processes (FOMDPs) represents the value function linearly w.r.t. a set of first-order basis functions and uses linear programming techniques to determine suitable weights. This approach offers the advantage that it does not require simplification of the first-order value function, and allows one to solve FOMDPs independent of a specific domain instantiation. In this paper, we address several questions to enhance the applicability of this work: (1) Can we extend the first-order ALP framework to approximate policy iteration to address performance deficiencies of previous approaches? (2) Can we automatically generate basis functions and evaluate their impact on value function quality? (3) How can we decompose intractable problems with universally quantified rewards into tractable subproblems? We propose answers to these questions along with a number of novel optimizations and provide a comparative empirical evaluation on logistics problems from the ICAPS 2004 Probabilistic Planning Competition.

Most causal inference algorithms in the literature (e.g., Pearl (2000), Spirtes et al. (2000), Heckerman et al. (1999)) exploit an assumption usually referred to as the causal Faithfulness or Stability condition. In this paper, we highlight two components of the condition used in constraint-based algorithms, which we call "Adjacency-Faithfulness" and "Orientation-Faithfulness". We point out that assuming Adjacency-Faithfulness is true, it is in principle possible to test the validity of Orientation-Faithfulness. Based on this observation, we explore the consequence of making only the Adjacency-Faithfulness assumption. We show that the familiar PC algorithm has to be modified to be (asymptotically) correct under the weaker, Adjacency-Faithfulness assumption. Roughly the modified algorithm, called Conservative PC (CPC), checks whether Orientation-Faithfulness holds in the orientation phase, and if not, avoids drawing certain causal conclusions the PC algorithm would draw. However, if the stronger, standard causal Faithfulness condition actually obtains, the CPC algorithm is shown to output the same pattern as the PC algorithm does in the large sample limit. We also present a simulation study showing that the CPC algorithm runs almost as fast as the PC algorithm, and outputs significantly fewer false causal arrowheads than the PC algorithm does on realistic sample sizes. We end our paper by discussing how score-based algorithms such as GES perform when the Adjacency-Faithfulness but not the standard causal Faithfulness condition holds, and how to extend our work to the FCI algorithm, which allows for the possibility of latent variables.

In many cases it makes sense to model a relationship symmetrically, not implying any particular directionality. Consider the classical example of a recommendation system where the rating of an item by a user should symmetrically be dependent on the attributes of both the user and the item. The attributes of the (known) relationships are also relevant for predicting attributes of entities and for predicting attributes of new relations. In recommendation systems, the exploitation of relational attributes is often referred to as collaborative filtering. Again, in many applications one might prefer to model the collaborative effect in a symmetrical way. In this paper we present a relational model, which is completely symmetrical. The key innovation is that we introduce for each entity (or object) an infinite-dimensional latent variable as part of a Dirichlet process (DP) model. We discuss inference in the model, which is based on a DP Gibbs sampler, i.e., the Chinese restaurant process. We extend the Chinese restaurant process to be applicable to relational modeling. Our approach is evaluated in three applications. One is a recommendation system based on the MovieLens data set. The second application concerns the prediction of the function of yeast genes/proteins on the data set of KDD Cup 2001 using a multi-relational model. The third application involves a relational medical domain. The experimental results show that our model gives significantly improved estimates of attributes describing relationships or entities in complex relational models.

We consider a Bayesian method for learning the Bayesian network structure from complete data. Recently, Koivisto and Sood (2004) presented an algorithm that for any single edge computes its marginal posterior probability in O(n 2^n) time, where n is the number of attributes; the number of parents per attribute is bounded by a constant. In this paper we show that the posterior probabilities for all the n (n - 1) potential edges can be computed in O(n 2^n) total time. This result is achieved by a forward-backward technique and fast Moebius transform algorithms, which are of independent interest. The resulting speedup by a factor of about n^2 allows us to experimentally study the statistical power of learning moderate-size networks. We report results from a simulation study that covers data sets with 20 to 10,000 records over 5 to 25 discrete attributes

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.

We observe that certain large-clique graph triangulations can be useful to reduce both computational and space requirements when making queries on mixed stochastic/deterministic graphical models. We demonstrate that many of these large-clique triangulations are non-minimal and are thus unattainable via the variable elimination algorithm. We introduce ancestral pairs as the basis for novel triangulation heuristics and prove that no more than the addition of edges between ancestral pairs need be considered when searching for state space optimal triangulations in such graphs. Empirical results on random and real world graphs show that the resulting triangulations that yield significant speedups are almost always non-minimal. We also give an algorithm and correctness proof for determining if a triangulation can be obtained via elimination, and we show that the decision problem associated with finding optimal state space triangulations in this mixed stochastic/deterministic setting is NP-complete.