arXiv subjects

Russell Greiner

Publications and source records attributed to Russell Greiner.

49 records · Page 3Linked to original sources

arXiv2015

Revisiting Algebra and Complexity of Inference in Graphical Models

This paper studies the form and complexity of inference in graphical models using the abstraction offered by algebraic structures. In particular, we broadly formalize inference problems in graphical models by viewing them as a sequence of operations based on commutative semigroups. We then study the computational complexity of inference by organizing various problems into an "inference hierarchy". When the underlying structure of an inference problem is a commutative semiring -- i.e. a combination of two commutative semigroups with the distributive law -- a message passing procedure called belief propagation can leverage this distributive law to perform polynomial-time inference for certain problems. After establishing the NP-hardness of inference in any commutative semiring, we investigate the relation between algebraic properties in this setting and further show that polynomial-time inference using distributive law does not (trivially) extend to inference problems that are expressed using more than two commutative semigroups. We then extend the algebraic treatment of message passing procedures to survey propagation, providing a novel perspective using a combination of two commutative semirings. This formulation generalizes the application of survey propagation to new settings.

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arXiv2015

Perturbed Message Passing for Constraint Satisfaction Problems

We introduce an efficient message passing scheme for solving Constraint Satisfaction Problems (CSPs), which uses stochastic perturbation of Belief Propagation (BP) and Survey Propagation (SP) messages to bypass decimation and directly produce a single satisfying assignment. Our first CSP solver, called Perturbed Blief Propagation, smoothly interpolates two well-known inference procedures; it starts as BP and ends as a Gibbs sampler, which produces a single sample from the set of solutions. Moreover we apply a similar perturbation scheme to SP to produce another CSP solver, Perturbed Survey Propagation. Experimental results on random and real-world CSPs show that Perturbed BP is often more successful and at the same time tens to hundreds of times more efficient than standard BP guided decimation. Perturbed BP also compares favorably with state-of-the-art SP-guided decimation, which has a computational complexity that generally scales exponentially worse than our method (wrt the cardinality of variable domains and constraints). Furthermore, our experiments with random satisfiability and coloring problems demonstrate that Perturbed SP can outperform SP-guided decimation, making it the best incomplete random CSP-solver in difficult regimes.

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arXiv2014

Accurate, fully-automated NMR spectral profiling for metabolomics

Many diseases cause significant changes to the concentrations of small molecules (aka metabolites) that appear in a person's biofluids, which means such diseases can often be readily detected from a person's "metabolic profile". This information can be extracted from a biofluid's NMR spectrum. Today, this is often done manually by trained human experts, which means this process is relatively slow, expensive and error-prone. This paper presents a tool, Bayesil, that can quickly, accurately and autonomously produce a complex biofluid's (e.g., serum or CSF) metabolic profile from a 1D1H NMR spectrum. This requires first performing several spectral processing steps then matching the resulting spectrum against a reference compound library, which contains the "signatures" of each relevant metabolite. Many of these steps are novel algorithms and our matching step views spectral matching as an inference problem within a probabilistic graphical model that rapidly approximates the most probable metabolic profile. Our extensive studies on a diverse set of complex mixtures, show that Bayesil can autonomously find the concentration of all NMR-detectable metabolites accurately (~90% correct identification and ~10% quantification error), in <5minutes on a single CPU. These results demonstrate that Bayesil is the first fully-automatic publicly-accessible system that provides quantitative NMR spectral profiling effectively -- with an accuracy that meets or exceeds the performance of trained experts. We anticipate this tool will usher in high-throughput metabolomics and enable a wealth of new applications of NMR in clinical settings. Available at http://www.bayesil.ca.

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arXiv2014

Augmentative Message Passing for Traveling Salesman Problem and Graph Partitioning

The cutting plane method is an augmentative constrained optimization procedure that is often used with continuous-domain optimization techniques such as linear and convex programs. We investigate the viability of a similar idea within message passing -- which produces integral solutions -- in the context of two combinatorial problems: 1) For Traveling Salesman Problem (TSP), we propose a factor-graph based on Held-Karp formulation, with an exponential number of constraint factors, each of which has an exponential but sparse tabular form. 2) For graph-partitioning (a.k.a., community mining) using modularity optimization, we introduce a binary variable model with a large number of constraints that enforce formation of cliques. In both cases we are able to derive surprisingly simple message updates that lead to competitive solutions on benchmark instances. In particular for TSP we are able to find near-optimal solutions in the time that empirically grows with N^3, demonstrating that augmentation is practical and efficient.

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arXiv2014

Training Restricted Boltzmann Machine by Perturbation

A new approach to maximum likelihood learning of discrete graphical models and RBM in particular is introduced. Our method, Perturb and Descend (PD) is inspired by two ideas (I) perturb and MAP method for sampling (II) learning by Contrastive Divergence minimization. In contrast to perturb and MAP, PD leverages training data to learn the models that do not allow efficient MAP estimation. During the learning, to produce a sample from the current model, we start from a training data and descend in the energy landscape of the "perturbed model", for a fixed number of steps, or until a local optima is reached. For RBM, this involves linear calculations and thresholding which can be very fast. Furthermore we show that the amount of perturbation is closely related to the temperature parameter and it can regularize the model by producing robust features resulting in sparse hidden layer activation.

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arXiv2013

Learning Bayesian Nets that Perform Well

A Bayesian net (BN) is more than a succinct way to encode a probabilistic distribution; it also corresponds to a function used to answer queries. A BN can therefore be evaluated by the accuracy of the answers it returns. Many algorithms for learning BNs, however, attempt to optimize another criterion (usually likelihood, possibly augmented with a regularizing term), which is independent of the distribution of queries that are posed. This paper takes the "performance criteria" seriously, and considers the challenge of computing the BN whose performance - read "accuracy over the distribution of queries" - is optimal. We show that many aspects of this learning task are more difficult than the corresponding subtasks in the standard model.

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arXiv2013

Comparing Bayesian Network Classifiers

In this paper, we empirically evaluate algorithms for learning four types of Bayesian network (BN) classifiers - Naive-Bayes, tree augmented Naive-Bayes, BN augmented Naive-Bayes and general BNs, where the latter two are learned using two variants of a conditional-independence (CI) based BN-learning algorithm. Experimental results show the obtained classifiers, learned using the CI based algorithms, are competitive with (or superior to) the best known classifiers, based on both Bayesian networks and other formalisms; and that the computational time for learning and using these classifiers is relatively small. Moreover, these results also suggest a way to learn yet more effective classifiers; we demonstrate empirically that this new algorithm does work as expected. Collectively, these results argue that BN classifiers deserve more attention in machine learning and data mining communities.

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arXiv2013

Bayesian Error-Bars for Belief Net Inference

A Bayesian Belief Network (BN) is a model of a joint distribution over a setof n variables, with a DAG structure to represent the immediate dependenciesbetween the variables, and a set of parameters (aka CPTables) to represent thelocal conditional probabilities of a node, given each assignment to itsparents. In many situations, these parameters are themselves random variables - this may reflect the uncertainty of the domain expert, or may come from atraining sample used to estimate the parameter values. The distribution overthese "CPtable variables" induces a distribution over the response the BNwill return to any "What is Pr(H | E)?" query. This paper investigates thevariance of this response, showing first that it is asymptotically normal,then providing its mean and asymptotical variance. We then present aneffective general algorithm for computing this variance, which has the samecomplexity as simply computing the (mean value of) the response itself - ie,O(n 2^w), where n is the number of variables and w is the effective treewidth. Finally, we provide empirical evidence that this algorithm, whichincorporates assumptions and approximations, works effectively in practice,given only small samples.

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arXiv2012

Budgeted Learning of Naive-Bayes Classifiers

Frequently, acquiring training data has an associated cost. We consider the situation where the learner may purchase data during training, subject TO a budget. IN particular, we examine the CASE WHERE each feature label has an associated cost, AND the total cost OF ALL feature labels acquired during training must NOT exceed the budget.This paper compares methods FOR choosing which feature label TO purchase next, given the budget AND the CURRENT belief state OF naive Bayes model parameters.Whereas active learning has traditionally focused ON myopic(greedy) strategies FOR query selection, this paper presents a tractable method FOR incorporating knowledge OF the budget INTO the decision making process, which improves performance.

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arXiv2012

Active Model Selection

Classical learning assumes the learner is given a labeled data sample, from which it learns a model. The field of Active Learning deals with the situation where the learner begins not with a training sample, but instead with resources that it can use to obtain information to help identify the optimal model. To better understand this task, this paper presents and analyses the simplified "(budgeted) active model selection" version, which captures the pure exploration aspect of many active learning problems in a clean and simple problem formulation. Here the learner can use a fixed budget of "model probes" (where each probe evaluates the specified model on a random indistinguishable instance) to identify which of a given set of possible models has the highest expected accuracy. Our goal is a policy that sequentially determines which model to probe next, based on the information observed so far. We present a formal description of this task, and show that it is NPhard in general. We then investigate a number of algorithms for this task, including several existing ones (eg, "Round-Robin", "Interval Estimation", "Gittins") as well as some novel ones (e.g., "Biased-Robin"), describing first their approximation properties and then their empirical performance on various problem instances. We observe empirically that the simple biased-robin algorithm significantly outperforms the other algorithms in the case of identical costs and priors.

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arXiv2012

A Generalized Loop Correction Method for Approximate Inference in Graphical Models

Belief Propagation (BP) is one of the most popular methods for inference in probabilistic graphical models. BP is guaranteed to return the correct answer for tree structures, but can be incorrect or non-convergent for loopy graphical models. Recently, several new approximate inference algorithms based on cavity distribution have been proposed. These methods can account for the effect of loops by incorporating the dependency between BP messages. Alternatively, region-based approximations (that lead to methods such as Generalized Belief Propagation) improve upon BP by considering interactions within small clusters of variables, thus taking small loops within these clusters into account. This paper introduces an approach, Generalized Loop Correction (GLC), that benefits from both of these types of loop correction. We show how GLC relates to these two families of inference methods, then provide empirical evidence that GLC works effectively in general, and can be significantly more accurate than both correction schemes.

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arXiv2012

Speeding Up Planning in Markov Decision Processes via Automatically Constructed Abstractions

In this paper, we consider planning in stochastic shortest path (SSP) problems, a subclass of Markov Decision Problems (MDP). We focus on medium-size problems whose state space can be fully enumerated. This problem has numerous important applications, such as navigation and planning under uncertainty. We propose a new approach for constructing a multi-level hierarchy of progressively simpler abstractions of the original problem. Once computed, the hierarchy can be used to speed up planning by first finding a policy for the most abstract level and then recursively refining it into a solution to the original problem. This approach is fully automated and delivers a speed-up of two orders of magnitude over a state-of-the-art MDP solver on sample problems while returning near-optimal solutions. We also prove theoretical bounds on the loss of solution optimality resulting from the use of abstractions.

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arXiv2012

Improved Mean and Variance Approximations for Belief Net Responses via Network Doubling

A Bayesian belief network models a joint distribution with an directed acyclic graph representing dependencies among variables and network parameters characterizing conditional distributions. The parameters are viewed as random variables to quantify uncertainty about their values. Belief nets are used to compute responses to queries; i.e., conditional probabilities of interest. A query is a function of the parameters, hence a random variable. Van Allen et al. (2001, 2008) showed how to quantify uncertainty about a query via a delta method approximation of its variance. We develop more accurate approximations for both query mean and variance. The key idea is to extend the query mean approximation to a "doubled network" involving two independent replicates. Our method assumes complete data and can be applied to discrete, continuous, and hybrid networks (provided discrete variables have only discrete parents). We analyze several improvements, and provide empirical studies to demonstrate their effectiveness.

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