This paper focuses on the computational complexity of computing empirical plug-in estimates for causal effect queries. Given a causal graph and observational data, any identifiable causal query can be estimated from an expression over the observed variables, called the estimand. The estimand can then be evaluated by plugging in probabilities computed empirically from data. In contrast to conventional wisdom which assumes that high dimensional probabilistic functions will lead to exponential evaluation time, we show that estimand evaluation can be done efficiently, potentially in time linear in the data size, depending on the estimand’s hypergraph. In particular, we show that both the $\it{treewidth}$ and $\it{hypertree width}$ of the estimand’s structure bound the evaluation complexity, analogous to their role in bounding the complexity of inference in probabilistic graphical models. In settings with high dimensional functions, the hypertree width often provides a more effective bound, since the empirical distributions are sparse.

Spatial evolutionary games are used to model large systems of interacting agents. In earlier work, a method was developed using Bayesian Networks to approximate the population dynamics in these games. One of the advantages of the Bayesian Network modeling approach is that it is possible to smoothly adjust the size of the network to get more accurate approximations. However, scaling the method up can be intractable if the number of strategies in the evolutionary game increases. In this paper, we propose a new method for computing more accurate approximations by using surrogate Bayesian Networks. Instead of computing inference on larger networks directly, we perform inference on a much smaller surrogate network extended with parameters that exploit the symmetry inherent to the domain. We learn the parameters on the surrogate network using KL-divergence as the loss function. We illustrate the value of this method empirically through a comparison on several evolutionary games.

The standard approach to answering an identifiable causal-effect query (e.g., P(Y|do(X)) given a causal diagram and observational data is to first generate an estimand, or probabilistic expression over the observable variables, which is then evaluated using the observational data. In this paper, we propose an alternative paradigm for answering causal-effect queries over discrete observable variables. We propose to instead learn the causal Bayesian network and its confounding latent variables directly from the observational data. Then, efficient probabilistic graphical model (PGM) algorithms can be applied to the learned model to answer queries. Perhaps surprisingly, we show that this model completion learning approach can be more effective than estimand approaches, particularly for larger models in which the estimand expressions become computationally difficult. We illustrate our method’s potential using a benchmark collection of Bayesian networks and synthetically generated causal models.

Monte Carlo methods are powerful tools for solving problems involving complex probability distributions. Despite their versatility, these methods often suffer from inefficiencies, especially when dealing with rare events. As such, importance sampling emerged as a prominent technique for alleviating these challenges. Recently, a new scheme called Abstraction Sampling was developed that incorporated stratification to importance sampling over graphical models. However, existing work only explored a limited set of abstraction functions that guide stratification. This study introduces three new classes of abstraction functions combined with seven distinct partitioning schemes, resulting in twenty-one new abstraction functions, each motivated by theory and intuition from both search and sampling domains. An extensive empirical analysis on over 400 problems compares these new schemes highlighting several well-performing candidates.

Scientific computing has experienced a surge empowered by advancements in technologies such as neural networks. However, certain important tasks are less amenable to these technologies, benefiting from innovations to traditional inference schemes. One such task is protein re-design. Recently a new re-design algorithm, {AOBB-K\textsuperscript{*}}, was introduced and was competitive with state-of-the-art {BBK\textsuperscript{*}} on small protein re-design problems. However, {AOBB-K\textsuperscript{*}} did not scale well. In this work, we focus on scaling up {AOBB-K\textsuperscript{*}} and introduce three new versions: {AOBB-K\textsuperscript{*}}-b (boosted), {AOBB-K\textsuperscript{*}}-{DH} (with dynamic heuristics), and {AOBB-K\textsuperscript{*}}-{UFO} (with underflow optimization) that significantly enhance scalability.

Bayesian Networks are useful for analyzing the properties of systems with large populations of interacting agents (e.g., in social modeling applications and distributed service applications). These networks typically have large functions (CPTs), making exact inference intractable. However, often these models have additive symmetry. In this paper we show how summation-based CPTs, especially in the presence of symmetry, can be computed efficiently through the usage of the Fast Fourier Transform (FFT). In particular, we propose an efficient method using the FFT for reducing the size of Conditional Probability Tables (CPTs) in Bayesian Networks with summation-based causal independence (CI). We then show how to apply this reduction directly towards the acceleration of Bucket Elimination, and we subsequently provide experimental results demonstrating the computational speedup provided by our method.

A major limiting factor in graphical model inference is the complexity of computing the partition function. Exact message-passing algorithms such as Bucket Elimination (BE) require exponential memory to compute the partition function; therefore, approximations are necessary. In this paper, we build upon a recently introduced methodology called Deep Bucket Elimination (DBE) that uses classical Neural Networks to approximate messages generated by BE for large buckets. The main feature of our new scheme, renamed NeuroBE, is that it customizes the architecture of the neural networks, their learning process and in particular, adapts the loss function to the internal form or distribution of messages. Our experiments demonstrate significant improvements in accuracy and time compared with the earlier DBE scheme.

The importance of designing proteins, such as high affinity antibodies, has become ever more apparent. Computational Protein Design can cast such design problems as optimization tasks with the objective of maximizing K*, an approximation of binding affinity. Here we lay out a graphical model framework for K* optimization that enables use of compact AND/OR search algorithms. We designed an AND/OR branch-and-bound algorithm, AOBB-K*, for optimizing K* that is guided by a new K* heuristic and can incorporate specialized performance improvements with theoretical guarantees. As AOBB-K* is inspired by algorithms from the well studied task of Marginal MAP, this work provides a foundation for harnessing advancements in state-of-the-art mixed inference schemes and adapting them to protein design.

Influence diagrams (IDs) are graphical models for representing and reasoning with sequential decision-making problems under uncertainty. Limited memory influence diagrams (LIMIDs) model a decision-maker (DM) who forgets the history in the course of making a sequence of decisions. The standard inference task in IDs and LIMIDs is to compute the maximum expected utility (MEU), which is one of the most challenging tasks in graphical models. We present a model decomposition framework in both IDs and LIMIDs, which we call submodel decomposition that generates a tree of single-stage decision problems through a tree clustering scheme. We also develop a valuation algebra over the submodels that leads to a hierarchical message passing algorithm that propagates conditional expected utility functions over a submodel-tree as external messages. We show that the overall complexity is bounded by the maximum tree-width over the submodels, common in graphical model algorithms. Finally, we present a new method for computing upper bounds over a submodel-tree by first exponentiating the utility functions yielding a standard probabilistic graphical model as an upper bound and then applying standard variational upper bounds for the marginal MAP inference, yielding tighter upper bounds compared with state-of-the-art bounding schemes for the MEU task.

Influence diagrams provide a modeling and inference framework for sequential decision problems, representing the probabilistic knowledge by a Bayesian network and the preferences of an agent by utility functions over the random variables and decision variables. Computing the maximum expected utility (MEU) and the optimizing policy is exponential in the constrained induced width and therefore is notoriously difficult for larger models. In this paper, we develop a new bounding scheme for MEU that applies partitioning based approximations on top of the decomposition scheme called a multi-operator cluster DAG for influence diagrams that is more sensitive to the underlying structure of the model than the classical join-tree decomposition of influence diagrams. Our bounding scheme utilizes a cost-shifting mechanism to tighten the bound further. We demonstrate the effectiveness of the proposed scheme on various hard benchmarks.

Bucket Elimination (BE) is a universal inference scheme that can solve most tasks over probabilistic and deterministic graphical models exactly. However, it often requires exponentially high levels of memory (in the induced-width) preventing its execution. In the spirit of exploiting Deep Learning for inference tasks, in this paper, we will use neural networks to approximate BE. The resulting Deep Bucket Elimination (DBE) algorithm is developed for computing the partition function. We provide a proof-of-concept empirically using instances from several different benchmarks, showing that DBE can be a more accurate approximation than current state-of-the-art approaches for approximating BE (e.g. the mini-bucket schemes), especially when problems are sufficiently hard.

Abstraction Sampling (AS) is a recently introduced enhancement of Importance Sampling that exploits stratification by using a notion of abstractions: groupings of similar nodes into abstract states. It was previously shown that AS performs particularly well when sampling over an AND/OR search space; however, existing schemes were limited to ``proper'' abstractions in order to ensure unbiasedness, severely hindering scalability. In this paper, we introduce AOAS, a new Abstraction Sampling scheme on AND/OR search spaces that allow more flexible use of abstractions by circumventing the properness requirement. We analyze the properties of this new algorithm and, in an extensive empirical evaluation on five benchmarks, over 480 problems, and comparing against other state of the art algorithms, illustrate AOAS's properties and show that it provides a far more powerful and competitive Abstraction Sampling framework.

An influence diagram is a graphical representation of sequential decision-making under uncertainty, defining a structured decision problem by conditional probability functions and additive utility functions over discrete state and action variables. The task of finding the maximum expected utility of influence diagrams is closely related to the cost-optimal probabilistic planning, stochastic programmings, or model-based reinforcement learning. In this position paper, we address the heuristic search for solving influence diagram, where we generate admissible heuristic functions from graph decomposition schemes. Then, we demonstrate how such heuristics can guide an AND/OR branch and bound search. Finally, we briefly discuss the future directions for improving the quality of heuristic functions and search strategies.

Computing the partition function of a graphical model is a fundamental task in probabilistic inference. Variational bounds and Monte Carlo methods, two important approximate paradigms for this task, each has its respective strengths for solving different types of problems, but it is often nontrivial to decide which one to apply to a particular problem instance without significant prior knowledge and a high level of expertise. In this paper, we propose a general framework that interleaves optimization of variational bounds (via message passing) with Monte Carlo sampling. Our adaptive interleaving policy can automatically balance the computational effort between these two schemes in an instance-dependent way, which provides our framework with the strengths of both schemes, leads to tighter anytime bounds and an unbiased estimate of the partition function, and allows flexible tradeoffs between memory, time, and solution quality. We verify our approach empirically on real-world problems taken from recent UAI inference competitions.

We introduce #opt, a new inference task for graphical models which calls for counting the number of optimal solutions of the model. We describe a novel variable elimination based approach for solving this task, as well as a depth-first branch and bound algorithm that traverses the AND/OR search space of the model. The key feature of the proposed algorithms is that their complexity is exponential in the induced width of the model only. It does not depend on the actual number of optimal solutions. Our empirical evaluation on various benchmarks demonstrates the effectiveness of the proposed algorithms compared with existing depth-first and best-first search based approaches that enumerate explicitly the optimal solutions.

Marginal MAP is a key task in Bayesian inference and decision-making. It is known to be very difficult in general, particularly because the evaluation of each MAP assignment requires solving an internal summation problem. In this paper, we propose a best-first search algorithm that provides anytime upper bounds for marginal MAP in graphical models. It folds the computation of external maximization and internal summation into an AND/OR tree search framework, and solves them simultaneously using a unified best-first search algorithm. The algorithm avoids some unnecessary computation of summation sub-problems associated with MAP assignments, and thus yields significant time savings. Furthermore, our algorithm is able to operate within limited memory. Empirical evaluation on three challenging benchmarks demonstrates that our unified best-first search algorithm using pre-compiled variational heuristics often provides tighter anytime upper bounds compared to those state-of-the-art baselines.

The Marginal MAP inference task is known to be extremely hard particularly because the evaluation of each complete MAP assignment involves an exact likelihood computation (a combinatorial sum). For this reason, most recent state-of-the-art solvers that focus on computing anytime upper and lower bounds on the optimal value are limited to solving instances with tractable conditioned summation subproblems. In this paper, we develop new search-based bounding schemes for Marginal MAP that produce anytime upper and lower bounds without performing exact likelihood computations. The empirical evaluation demonstrates the effectiveness of our new methods against the current best-performing search-based bounds.

Mixed inference such as the marginal MAP query (some variables marginalized by summation and others by maximization) is key to many prediction and decision models. It is known to be extremely hard; the problem is NPPP-complete while the decision problem for MAP is only NP-complete and the summation problem is #P-complete. Consequently, approximation anytime schemes are essential. In this paper, we show that the framework of heuristic AND/OR search, which exploits conditional independence in the graphical model, coupled with variational-based mini-bucket heuristics can be extended to this task and yield powerful state-of-the-art schemes. Specifically, we explore the complementary properties of best-first search for reducing the number of conditional sums and providing time-improving upper bounds, with depth-first search for rapidly generating and improving solutions and lower bounds. We show empirically that a class of solvers that interleaves depth-first with best-first schemes emerges as the most competitive anytime scheme.

We introduce new anytime search algorithms that combine best-first with depth-first search into hybrid schemes for Marginal MAP inference in graphical models. The main goal is to facilitate the generation of upper bounds (via the best-first part) alongside the lower bounds of solutions (via the depth-first part) in an anytime fashion. We compare against two of the best current state-of-the-art schemes and show that our best+depth search scheme produces higher quality solutions faster while also producing a bound on their accuracy, which can be used to measure solution quality during search. An extensive empirical evaluation demonstrates the effectiveness of our new methods which enjoy the strength of best-first (optimality of search) and of depth-first (memory robustness), leading to solutions for difficult instances where previous solvers were unable to find even a single solution.

Bounding the partition function is a key inference task in many graphical models. In this paper, we develop an anytime anyspace search algorithm taking advantage of AND/OR tree structure and optimized variational heuristics to tighten deterministic bounds on the partition function. We study how our priority-driven best-first search scheme can improve on state-of-the-art variational bounds in an anytime way within limited memory resources, as well as the effect of the AND/OR framework to exploit conditional independence structure within the search process within the context of summation. We compare our resulting bounds to a number of existing methods, and show that our approach offers a number of advantages on real-world problem instances taken from recent UAI competitions.

Computing the partition function is a key inference task in many graphical models. In this paper, we propose a dynamic importance sampling scheme that provides anytime finite-sample bounds for the partition function. Our algorithm balances the advantages of the three major inference strategies, heuristic search, variational bounds, and Monte Carlo methods, blending sampling with search to refine a variationally defined proposal. Our algorithm combines and generalizes recent work on anytime search and probabilistic bounds of the partition function. By using an intelligently chosen weighted average over the samples, we construct an unbiased estimator of the partition function with strong finite-sample confidence intervals that inherit both the rapid early improvement rate of sampling and the long-term benefits of an improved proposal from search. This gives significantly improved anytime behavior, and more flexible trade-offs between memory, time, and solution quality. We demonstrate the effectiveness of our approach empirically on real-world problem instances taken from recent UAI competitions.

We introduce the concept of local bucket error for the mini-bucket heuristics and show how it can be used to improve the power of AND/OR search for combinatorial optimization tasks in graphical models (e.g. MAP/MPE or weighted CSPs). The local bucket error illuminates how the heuristic errors are distributed in the search space, guided by the mini-bucket heuristic. We present and analyze methods for compiling the local bucket-errors (exactly and approximately) and show that they can be used to yield an effective tool for balancing look-ahead overhead during search. This can be especially instrumental when memory is restricted, accommodating the generation of only weak compiled heuristics. We illustrate the impact of the proposed schemes in an extensive empirical evaluation for both finding exact solutions and anytime suboptimal solutions.

We present a parallel AND/OR Branch-and-Bound scheme that uses the power of a computational grid to push the boundaries of feasibility for combinatorial optimization. Two variants of the scheme are described, one of which aims to use machine learning techniques for parallel load balancing. In-depth analysis identifies two inherent sources of parallel search space redundancies that, together with general parallel execution overhead, can impede parallelization and render the problem far from embarrassingly parallel. We conduct extensive empirical evaluation on hundreds of CPUs, the first of its kind, with overall positive results. In a significant number of cases parallel speedup is close to the theoretical maximum and we are able to solve many very complex problem instances orders of magnitude faster than before; yet analysis of certain results also serves to demonstrate the inherent limitations of the approach due to the aforementioned redundancies.

This paper explores the anytime performance of search-based algorithms for solving the Marginal MAP task over graphical models. The current state of the art for solving this challenging task is based on best-first search exploring the AND/OR graph with the guidance of heuristics based on mini-bucket and variational cost-shifting principles. Yet, those schemes are uncompromising in that they solve the problem exactly, or not at all, and often suffer from memory problems. In this work, we explore the well known principle of weighted search for converting best-first search solvers into anytime schemes. The weighted best-first search schemes report a solution early in the process by using inadmissible heuristics, and subsequently improve the solution. While it was demonstrated recently that weighted schemes can yield effective anytime behavior for pure MAP tasks, Marginal MAP is far more challenging (e.g., a conditional sum must be evaluated for every solution). Yet, in an extensive empirical analysis we show that weighted schemes are indeed highly effective for Marginal MAP yielding the most competitive schemes to date for this task.

Best-first search can be regarded as anytime scheme for producing lower bounds on the optimal solution, a characteristic that is mostly overlooked. We explore this topic in the context of AND/OR best-first search, guided by the MBE heuristic, when solving graphical models. In that context, the impact of the secondary heuristic for subproblem ordering may be significant, especially in the anytime context. Indeed, our paper illustrates this, showing that the new concept of bucket errors can advise in providing effective subproblem orderings in AND/OR search.

The paper focuses on finding the m best solutions to combinatorial optimization problems using best-first or depth-first branch and bound search. Specifically, we present a new algorithm m-A*, extending the well-known A* to the m-best task, and for the first time prove that all its desirable properties, including soundness, completeness and optimal efficiency, are maintained. Since best-first algorithms require extensive memory, we also extend the memory-efficient depth-first branch and bound to the m-best task. We adapt both algorithms to optimization tasks over graphical models (e.g., Weighted CSP and MPE in Bayesian networks), provide complexity analysis and an empirical evaluation. Our experiments confirm theory that the best-first approach is largely superior when memory is available, but depth-first branch and bound is more robust. We also show that our algorithms are competitive with related schemes recently developed for the m-best task.

In empirical studies we observed that caching can have very little impact in reducing the search effort in Branch and Bound search over context-minimal OR spaces. For example, in one of the problem domains used in our experiments we reduce only by 1% the number of nodes expanded when using caching in context-minimal OR spaces. By contrast, we reduce by 74% the number of nodes expanded when using caching in context-minimal AND/OR spaces on the same instances. In this work we document this unexpected empirical finding and provide explanations for the phenomenon.

The paper explores the potential of look-ahead methods within the context of AND/OR search in graphical models using the Mini-Bucket heuristic for combinatorial optimization tasks (e.g., weighted CSPS or MAP inference). We study how these methods can be used to compensate for the approximation error of the initially generated Mini-Bucket heuristics, within the context of anytime Branch-And-Bound search.

Weighted search was explored significantly in recent years for path-finding problems, but until now was barely considered for optimization tasks such as MPE/MAP and Weighted CSPs. An important virtue of weighted search schemes, especially in the context of anytime search, is that they are w-optimal, i.e. when terminated, they return a weight w, and a solution cost C, such that C ≤ w · C*, where C* is the optimal cost. In this paper we introduce Weighted Branch and Bound (WBB) for graphical models and provide a broad empirical evaluation of its performance compared with one of the best unweighted anytime search scheme, BRAOBB (won Pascal 2011 competition). We also compare against weighted best-first (WBF). Our results show that W BB can be superior to both unweighted BB and to weighted BF on a significant number of instances. We also illustrate the benefit of weighted search in providing suboptimality relative error bounds.

We explore the use of iterative cost-shifting as a dynamic heuristic generator for solving MPE in graphical models via Branch and Bound. When mini-bucket elimination is limited by its memory budget, it may not provide good heuristics. This can happen often when the graphical model has a very high induced width with large variable domain sizes. In addition, we explore a hybrid setup where both MBE and the iterative cost-shifting bound are used in a combined heuristic. We compare these approaches with the most advanced statically generated heuristics.

In this paper we present Stochastic Tree-based Local Search or STLS, a local search algorithm combining the notion of cycle-cutsets with the well-known Belief Propagation to approximatethe optimum of sums of unary and binary potentials. This is done by the previously unexplored concept oftraversal from one cutset to another and updating the induced forest, thus creating a local search algorithm, whose updatephase spans over all the forest variables. We study empirically two pure variants of STLS against the state-of-the art GLS+ scheme and against a hybrid.

MOTIVATION: The use of dense single nucleotide polymorphism (SNP) data in genetic linkage analysis of large pedigrees is impeded by significant technical, methodological and computational challenges. Here we describe Superlink-Online SNP, a new powerful online system that streamlines the linkage analysis of SNP data. It features a fully integrated flexible processing workflow comprising both well-known and novel data analysis tools, including SNP clustering, erroneous data filtering, exact and approximate LOD calculations and maximum-likelihood haplotyping. The system draws its power from thousands of CPUs, performing data analysis tasks orders of magnitude faster than a single computer. By providing an intuitive interface to sophisticated state-of-the-art analysis tools coupled with high computing capacity, Superlink-Online SNP helps geneticists unleash the potential of SNP data for detecting disease genes. RESULTS: Computations performed by Superlink-Online SNP are automatically parallelized using novel paradigms, and executed on unlimited number of private or public CPUs. One novel service is large-scale approximate Markov Chain-Monte Carlo (MCMC) analysis. The accuracy of the results is reliably estimated by running the same computation on multiple CPUs and evaluating the Gelman-Rubin Score to set aside unreliable results. Another service within the workflow is a novel parallelized exact algorithm for inferring maximum-likelihood haplotyping. The reported system enables genetic analyses that were previously infeasible. We demonstrate the system capabilities through a study of a large complex pedigree affected with metabolic syndrome. AVAILABILITY: Superlink-Online SNP is freely available for researchers at http://cbl-hap.cs.technion.ac.il/superlink-snp. The system source code can also be downloaded from the system website. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Vol. 29, No. 2, 2013, pp. 197–205 doi:10.1093/bioinformatics/bts658 The publishers regret that the author affiliations for this paper should appear as follows: Mark Silberstein1,2, Omer Weissbrod1,*, Lars Otten3, Anna Tzemach1, Andrei Anisenia1,4, Oren Shtark1, Dvir Tuberg1, Eddie Galfrin1, Irena Gannon1, Adel Shalata5,6,7, Zvi U. Borochowitz5,8, Rina Dechter3, Elizabeth Thompson9 and Dan Geiger1 1Department of Computer Science, Technion-Israel Institute of Technology, Haifa, Israel, 2Department of Computer Science, University of Texas at Austin, Austin, TX, USA, 3Donald Bren School of Information and Computer Sciences, UC Irvine, CA, USA, 4Department of Computer Science, University of Ottawa, Ottawa, Canada, 5The Simon Winter Institute for Human Genetics, Bnai-Zion Medical Center, Haifa, Israel, 6Research and Development Center, The Galilee Society, Shefa-Amr, Israel, 7Holy Family Hospital, Nazareth, Israel, 8The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel and 9Department of Statistics, University of Washington, Seattle, WA, USA

The paper focuses on finding the m best solutions to combinatorial optimization problems using Best-First or Branchand- Bound search. Specifically, we present m-A*, extending the well-known A* to the m-best task, and prove that all its desirable properties, including soundness, completeness and optimal efficiency, are maintained. Since Best-First algorithms have memory problems, we also extend the memoryefficient Depth-First Branch-and-Bound to the m-best task. We extend both algorithms to optimization tasks over graphical models (e.g., Weighted CSP and MPE in Bayesian networks), provide complexity analysis and an empirical evaluation. Our experiments with 5 variants of Best-First and Branch-and-Bound confirm that Best-First is largely superior when memory is available, but Branch-and-Bound is more robust, while both styles of search benefit greatly when the heuristic evaluation function has increased accuracy.

Many algorithms for performing inference in graphical models have complexity that is exponential in the treewidth — a parameter of the underlying graph structure. Computing the (minimal) treewidth is NPcomplete, so stochastic algorithms are sometimes used to find low width tree decompositions. A common approach for finding good decompositions is iteratively executing a greedy triangulation algorithm (e.g. minfill) with randomized tie-breaking. However, utilizing a stochastic algorithm as part of the inference task introduces a new problem — namely, deciding how long the stochastic algorithm should be allowed to execute before performing inference on the best tree decomposition found so far. We refer to this dilemma as the Stopping Problem and formalize it in terms of the total time needed to answer a probabilistic query. We propose a rule for discontinuing the search for improved decompositions and demonstrate the benefit (in terms of time saved) of applying this rule to Bayes and Markov network instances.

We study iterative randomized greedy algorithms for generating (elimination) orderings with small induced width and state space size — two parameters known to bound the complexity of inference in graphical models. We propose and implement the Iterative Greedy Variable Ordering (IGVO) algorithm, a new variant within this algorithm class. An empirical evaluation using different ranking functions and conditions of randomness, demonstrates that IGVO finds significantly better orderings than standard greedy ordering implementations when evaluated within an anytime framework. Additional order of magnitude improvements are demonstrated on a multi-core system, thus further expanding the set of solvable graphical models. The experiments also confirm the superiority of the MinFill heuristic within the iterative scheme.

One popular and efficient scheme for solving exactly combinatorial optimization problems over graphical models is depth-first Branch and Bound. However, when the algorithm exploits problem decomposition using AND/OR search spaces, its anytime behavior breaks down. This paper 1) analyzes and demonstrates this inherent conflict between effective exploitation of problem decomposition (through AND/OR search spaces) and the anytime behavior of depth-first search (DFS), 2) presents a first scheme to address this issue while maintaining desirable DFS memory properties, 3) analyzes and demonstrates its effectiveness. Our work is applicable to any problem that can be cast as search over an AND/OR search space.

Mini-Bucket Elimination (MBE) is a well-known approximation algorithm deriving lower and upper bounds on quantities of interest over graphical models. It relies on a procedure that partitions a set of functions, called bucket, into smaller subsets, called mini-buckets. The method has been used with a single partitioning heuristic throughout, so the impact of the partitioning algorithm on the quality of the generated bound has never been investigated. This paper addresses this issue by presenting a framework within which partitioning strategies can be described, analyzed and compared. We derive a new class of partitioning heuristics from first-principles geared for likelihood queries, demonstrate their impact on a number of benchmarks for probabilistic reasoning and show that the results are competitive (often superior) to state-of-the-art bounding schemes.

The paper presents a scheme for computing lower and upper bounds on the posterior marginals in Bayesian networks with discrete variables. Its power lies in its ability to use any available scheme that bounds the probability of evidence or posterior marginals and enhance its performance in an anytime manner. The scheme uses the cutset conditioning principle to tighten existing bounding schemes and to facilitate anytime behavior, utilizing a fixed number of cutset tuples. The accuracy of the bounds improves as the number of used cutset tuples increases and so does the computation time. We demonstrate empirically the value of our scheme for bounding posterior marginals and probability of evidence using a variant of the bound propagation algorithm as a plug-in scheme.

The paper investigates parameterized approximate message-passing schemes that are based on bounded inference and are inspired by Pearl's belief propagation algorithm (BP). We start with the bounded inference mini-clustering algorithm and then move to the iterative scheme called Iterative Join-Graph Propagation (IJGP), that combines both iteration and bounded inference. Algorithm IJGP belongs to the class of Generalized Belief Propagation algorithms, a framework that allowed connections with approximate algorithms from statistical physics and is shown empirically to surpass the performance of mini-clustering and belief propagation, as well as a number of other state-of-the-art algorithms on several classes of networks. We also provide insight into the accuracy of iterative BP and IJGP by relating these algorithms to well known classes of constraint propagation schemes.

The recently introduced notion of hypertree width has been shown to provide a broader characterization of tractable constraint and probabilistic networks than the tree width. This paper demonstrates empirically that in practice the bounding power of the tree width is still superior to the hypertree width for many benchmark instances of both probabilistic and deterministic networks.

Inspired by the recently introduced framework of AND/OR search spaces for graphical models, we propose to augment Multi-Valued Decision Diagrams (MDD) with AND nodes, in order to capture function decomposition structure and to extend these compiled data structures to general weighted graphical models (e.g., probabilistic models). We present the AND/OR Multi-Valued Decision Diagram (AOMDD) which compiles a graphical model into a canonical form that supports polynomial (e.g., solution counting, belief updating) or constant time (e.g. equivalence of graphical models) queries. We provide two algorithms for compiling the AOMDD of a graphical model. The first is search-based, and works by applying reduction rules to the trace of the memory intensive AND/OR search algorithm. The second is inference-based and uses a Bucket Elimination schedule to combine the AOMDDs of the input functions via the the APPLY operator. For both algorithms, the compilation time and the size of the AOMDD are, in the worst case, exponential in the treewidth of the graphical model, rather than pathwidth as is known for ordered binary decision diagrams (OBDDs). We introduce the concept of semantic treewidth, which helps explain why the size of a decision diagram is often much smaller than the worst case bound. We provide an experimental evaluation that demonstrates the potential of AOMDDs.

The paper presents a new sampling methodology for Bayesian networks that samples only a subset of variables and applies exact inference to the rest. Cutset sampling is a network structure-exploiting application of the Rao-Blackwellisation principle to sampling in Bayesian networks. It improves convergence by exploiting memory-based inference algorithms. It can also be viewed as an anytime approximation of the exact cutset-conditioning algorithm developed by Pearl. Cutset sampling can be implemented efficiently when the sampled variables constitute a loop-cutset of the Bayesian network and, more generally, when the induced width of the network's graph conditioned on the observed sampled variables is bounded by a constant w. We demonstrate empirically the benefit of this scheme on a range of benchmarks.

This article presents a class of approximation algorithms that extend the idea of bounded-complexity inference, inspired by successful constraint propagation algorithms, to probabilistic inference and combinatorial optimization. The idea is to bound the dimensionality of dependencies created by inference algorithms. This yields a parameterized scheme, called mini-buckets , that offers adjustable trade-off between accuracy and efficiency. The mini-bucket approach to optimization problems, such as finding the most probable explanation (MPE) in Bayesian networks, generates both an approximate solution and bounds on the solution quality. We present empirical results demonstrating successful performance of the proposed approximation scheme for the MPE task, both on randomly generated problems and on realistic domains such as medical diagnosis and probabilistic decoding.

Constraint networks are a simple representation and reasoning framework with diverse applications. In this paper, we identify two new complementary properties on the restrictiveness of the constraints in a network— constraint tightness and constraint looseness —and we show their usefulness for estimating the level of local consistency needed to ensure global consistency, and for estimating the level of local consistency present in a network. In particular, we present a sufficient condition, based on constraint tightness and the level of local consistency, that guarantees that a solution can be found in a backtrack-free manner. The condition can be useful in applications where a knowledge base will be queried over and over and the preprocessing costs can be amortized over many queries. We also present a sufficient condition for local consistency, based on constraint looseness, that is straightforward and inexpensive to determine. The condition can be used to estimate the level of local consistency of a network. This in turn can be used in deciding whether it would be useful to preprocess the network before a backtracking search, and in deciding which local consistency conditions, if any, still need to be enforced if we want to ensure that a solution can be found in a backtrack-free manner. Two definitions of local consistency are employed in characterizing the conditions: the traditional variable-based notion and a recently introduced definition of local consistency called relational consistency .

Constraint networks have been shown to be useful in formulating such diverse problems as scene labeling, natural language parsing, and temporal reasoning. Given a constraint network, we often wish to (i) find a solution that satisfies the constraints and (ii) find the corresponding minimal network where the constraints are as explicit as possible. Both tasks are known to be NP-complete in the general case. Task (1) is usually solved using a backtracking algorithm, and task (ii) is often solved only approximately by enforcing various levels of local consistency. In this paper, we identify a property of binary constraint called row convexity and show its usefulness in deciding when a form of local consistency called path consistency is sufficient to guarantee that a network is both minimal and globally consistent. Globally consistent networks have the property that a solution can be found without backtracking. We show that one can test for the row convexity property efficiently and we show, by examining applications of constraint networks discussed in the literature, that our results are useful in practice. Thus, we identify a class of binary constraint networks for which we can solve both tasks (i) and (ii) efficiently. Finally, we generalize the results for binary constraint networks to networks with nonbinary constraints.

Symmetric networks designed for energy minimization such as Boltzman machines and Hopfield nets are frequently investigated for use in optimization, constraint satisfaction and approximation of NP-hard problems. Nevertheless, finding a global solution (i.e., a global minimum for the energy function) is not guaranteed and even a local solution may take an exponential number of steps. We propose an improvement to the standard local activation function used for such networks. The improved algorithm guarantees that a global minimum is found in linear time for tree-like subnetworks. The algorithm, called activate, is uniform and does not assume that the network is tree-like. It can identify tree-like subnetworks even in cyclic topologies (arbitrary networks) and avoid local minima along these trees. For acyclic networks, the algorithm is guaranteed to converge to a global minimum from any initial state of the system (self-stabilization) and remains correct under various types of schedulers. On the negative side, we show that in the presence of cycles, no uniform algorithm exists that guarantees optimality even under a sequential asynchronous scheduler. An asynchronous scheduler can activate only one unit at a time while a synchronous scheduler can activate any number of units in a single time step. In addition, no uniform algorithm exists to optimize even acyclic networks when the scheduler is synchronous. Finally, we show how the algorithm can be improved using the cycle-cutset scheme. The general algorithm, called activate-with-cutset, improves over activate and has some performance guarantees that are related to the size of the network's cycle-cutset.

The greedy method is a well-known approach for problem solving directed mainly at the solution of optimization problems. Leading theoretical frameworks dealing with the optimality of greedy solutions (e.g., the matroid and greedoid theories) tacitly assume that the greedy algorithm is always guided by the cost function to be optimized, namely, it builds a solution by adding, in each step, an element that contributes the most to the value of the cost function. This paper studies a class of problems for which this type of a greedy algorithm does not optimize the given cost function, but for which there exists a secondary objective function, called a greedy rule, such that applying the greedy algorithm to the secondary objective function yields a solution which is optimal with respect to the original cost function. INFORMS Journal on Computing, ISSN 1091-9856, was published as ORSA Journal on Computing from 1989 to 1995 under ISSN 0899-1499.

We present an efficient algorithm for decomposing an n-ary relation into a tree of binary relations, and provide an efficient test for checking whether or not the tree formed represents the relation. If there exists a tree-decomposition, the algorithm is guaranteed to find one, otherwise, the tree generated will fail the test, then indicating that no tree decomposition exist. The unique features of the algorithm presented in this paper, is that it does not apriori assume any dependencies in the initial relation, rather it derives such dependencies from the bare relation instance.

The paper addresses ways in which one can use "broadcast communication" in distributed algorithms and the relevant issues of design and complexity. We present an algorithm for merging k sorted lists of n/k elements using k processors and prove its worst case complexity to be 2n, regardless of the number of processors, while neglecting the cost arising from possible conflicts on the broadcast channel. We also show that this algorithm is optimal under single-channel broadcast communication. In a variation of the algorithm, we show that by using an extra local memory of O(k) the number of broadcasts is reduced to n. When the algorithm is used for sorting n elements with k processors, where each processor sorts its own list first and then merging, it has a complexity of O(n/k log(n/k) + n), and is thus asymptotically optimal for large n. We also discuss the cost incurred by the channel access scheme and prove that resolving conflicts whenever k processors are involved introduces a cost factor of at least log k.

This paper reports several properties of heuristic best-first search strategies whose scoring functions ƒ depend on all the information available from each candidate path, not merely on the current cost g and the estimated completion cost h . It is shown that several known properties of A* retain their form (with the minmax of f playing the role of the optimal cost), which helps establish general tests of admissibility and general conditions for node expansion for these strategies. On the basis of this framework the computational optimality of A*, in the sense of never expanding a node that can be skipped by some other algorithm having access to the same heuristic information that A* uses, is examined. A hierarchy of four optimality types is defined and three classes of algorithms and four domains of problem instances are considered. Computational performances relative to these algorithms and domains are appraised. For each class-domain combination, we then identify the strongest type of optimality that exists and the algorithm for achieving it. The main results of this paper relate to the class of algorithms that, like A*, return optimal solutions (i.e., admissible) when all cost estimates are optimistic (i.e., h ≤ h *). On this class, A* is shown to be not optimal and it is also shown that no optimal algorithm exists, but if the performance tests are confirmed to cases in which the estimates are also consistent, then A* is indeed optimal. Additionally, A* is also shown to be optimal over a subset of the latter class containing all best-first algorithms that are guided by path-dependent evaluation functions.