Recursive Conditioning (RC) was introduced recently as the first any-space algorithm for inference in Bayesian networks which can trade time for space by varying the size of its cache at the increment needed to store a floating point number. Under full caching, RC has an asymptotic time and space complexity which is comparable to mainstream algorithms based on variable elimination and clustering (exponential in the network treewidth and linear in its size). We show two main results about RC in this paper. First, we show that its actual space requirements under full caching are much more modest than those needed by mainstream methods and study the implications of this finding. Second, we show that RC can effectively deal with determinism in Bayesian networks by employing standard logical techniques, such as unit resolution, allowing a significant reduction in its time requirements in certain cases. We illustrate our results using a number of benchmark networks, including the very challenging ones that arise in genetic linkage analysis.

Backtracking search is a powerful algorithmic paradigm that can be used to solve many problems. It is in a certain sense the dual of variable elimination; but on many problems, e.g., SAT, it is vastly superior to variable elimination in practice. Motivated by this we investigate the application of backtracking search to the problem of Bayesian inference (Bayes). We show that natural generalizations of known techniques allow backtracking search to achieve performance guarantees similar to standard algorithms for Bayes, and that there exist problems on which backtracking can in fact do much better. We also demonstrate that these ideas can be applied to implement a Bayesian inference engine whose performance is competitive with standard algorithms. Since backtracking search can very naturally take advantage of context specific structure, the potential exists for performance superior to standard algorithms on many problems.

The paper studies empirically the time-space trade-off between sampling and inference in a sl cutset sampling algorithm. The algorithm samples over a subset of nodes in a Bayesian network and applies exact inference over the rest. Consequently, while the size of the sampling space decreases, requiring less samples for convergence, the time for generating each single sample increases. The w-cutset sampling selects a sampling set such that the induced-width of the network when the sampling set is observed is bounded by w, thus requiring inference whose complexity is exponential in w. In this paper, we investigate performance of w-cutset sampling over a range of w values and measure the accuracy of w-cutset sampling as a function of w. Our experiments demonstrate that the cutset sampling idea is quite powerful showing that an optimal balance between inference and sampling benefits substantially from restricting the cutset size, even at the cost of more complex inference.

This paper introduces new methodology to triangulate dynamic Bayesian networks (DBNs) and dynamic graphical models (DGMs). While most methods to triangulate such networks use some form of constrained elimination scheme based on properties of the underlying directed graph, we find it useful to view triangulation and elimination using properties only of the resulting undirected graph, obtained after the moralization step. We first briefly introduce the Graphical model toolkit (GMTK) and its notion of dynamic graphical models, one that slightly extends the standard notion of a DBN. We next introduce the 'boundary algorithm', a method to find the best boundary between partitions in a dynamic model. We find that using this algorithm, the notions of forward- and backward-interface become moot - namely, the size and fill-in of the best forward- and backward- interface are identical. Moreover, we observe that finding a good partition boundary allows for constrained elimination orders (and therefore graph triangulations) that are not possible using standard slice-by-slice constrained eliminations. More interestingly, with certain boundaries it is possible to obtain constrained elimination schemes that lie outside the space of possible triangulations using only unconstrained elimination. Lastly, we report triangulation results on invented graphs, standard DBNs from the literature, novel DBNs used in speech recognition research systems, and also random graphs. Using a number of different triangulation quality measures (max clique size, state-space, etc.), we find that with our boundary algorithm the triangulation quality can dramatically improve.

Nonmonotonic influences have associated an ambiguous sign. These ambiguous signs typically give rise to uninformative results upon inference. We argue that a nonmonotonic influence can be associated with a more informative sign that indicates its effect in the current state of the network. To capture this effect, we introduce the concept of situational sign. Furthermore, if the network converts to a state in which all variables that provoke the nonmonotonicity have been observed, a nonmonotonic influence reduces to a monotonic one. We study the persistence and propagation of situational signs upon inference and give a method for establishing the sign of a reduced influence.

Inferences in directed acyclic graphs associated with probability sets and probability intervals are NP-hard, even for polytrees. In this paper we focus on such inferences, and propose: 1) a substantial improvement on Tessems A / R algorithm FOR polytrees WITH probability intervals; 2) a new algorithm FOR direction - based local search(IN sets OF probability) that improves ON existing methods; 3) a collection OF branch - AND - bound algorithms that combine the previous techniques.The first two techniques lead TO approximate solutions, WHILE branch - AND - bound procedures can produce either exact OR approximate solutions.We report ON dramatic improvements ON existing techniques FOR inference WITH probability sets AND intervals, IN SOME cases reducing the computational effort BY many orders OF magnitude.

The motivation for this paper is to apply Bayesian structure learning using Model Averaging in large-scale networks. Currently, Bayesian model averaging algorithm is applicable to networks with only tens of variables, restrained by its super-exponential complexity. We present a novel framework, called LSBN(Large-Scale Bayesian Network), making it possible to handle networks with infinite size by following the principle of divide-and-conquer. The method of LSBN comprises three steps. In general, LSBN first performs the partition by using a second-order partition strategy, which achieves more robust results. LSBN conducts sampling and structure learning within each overlapping community after the community is isolated from other variables by Markov Blanket. Finally LSBN employs an efficient algorithm, to merge structures of overlapping communities into a whole. In comparison with other four state-of-art large-scale network structure learning algorithms such as ARACNE, PC, Greedy Search and MMHC, LSBN shows comparable results in five common benchmark datasets, evaluated by precision, recall and f-score. What's more, LSBN makes it possible to learn large-scale Bayesian structure by Model Averaging which used to be intractable. In summary, LSBN provides an scalable and parallel framework for the reconstruction of network structures. Besides, the complete information of overlapping communities serves as the byproduct, which could be used to mine meaningful clusters in biological networks, such as protein-protein-interaction network or gene regulatory network, as well as in social network.

Hybrid continuous-discrete models naturally represent many real-world applications in robotics, finance, and environmental engineering. Inference with large-scale models is challenging because relational structures deteriorate rapidly during inference with observations. The main contribution of this paper is an efficient relational variational inference algorithm that factors largescale probability models into simpler variational models, composed of mixtures of iid (Bernoulli) random variables. The algorithm takes probability relational models of largescale hybrid systems and converts them to a close-to-optimal variational models. Then, it efficiently calculates marginal probabilities on the variational models by using a latent (or lifted) variable elimination or a lifted stochastic sampling. This inference is unique because it maintains the relational structure upon individual observations and during inference steps.

Markov networks (MNs) are a powerful way to compactly represent a joint probability distribution, but most MN structure learning methods are very slow, due to the high cost of evaluating candidates structures. Dependency networks (DNs) represent a probability distribution as a set of conditional probability distributions. DNs are very fast to learn, but the conditional distributions may be inconsistent with each other and few inference algorithms support DNs. In this paper, we present a closed-form method for converting a DN into an MN, allowing us to enjoy both the efficiency of DN learning and the convenience of the MN representation. When the DN is consistent, this conversion is exact. For inconsistent DNs, we present averaging methods that significantly improve the approximation. In experiments on 12 standard datasets, our methods are orders of magnitude faster than and often more accurate than combining conditional distributions using weight learning.

Latent variable models are an elegant framework for capturing rich probabilistic dependencies in many applications. However, current approaches typically parametrize these models using conditional probability tables, and learning relies predominantly on local search heuristics such as Expectation Maximization. Using tensor algebra, we propose an alternative parameterization of latent variable models (where the model structures are junction trees) that still allows for computation of marginals among observed variables. While this novel representation leads to a moderate increase in the number of parameters for junction trees of low treewidth, it lets us design a local-minimum-free algorithm for learning this parameterization. The main computation of the algorithm involves only tensor operations and SVDs which can be orders of magnitude faster than EM algorithms for large datasets. To our knowledge, this is the first provably consistent parameter learning technique for a large class of low-treewidth latent graphical models beyond trees. We demonstrate the advantages of our method on synthetic and real datasets.