We propose a nonparametric Bayesian factor regression model that accounts for uncertainty in the number of factors, and the relationship between factors. To accomplish this, we propose a sparse variant of the Indian Buffet Process and couple this with a hierarchical model over factors, based on Kingman's coalescent. We apply this model to two problems (factor analysis and factor regression) in gene-expression data analysis.
A number of probabilistic approaches have been proposed in the past for the problem of gene-regulatory network reconstruction @cite_10 @cite_13 @cite_4 @cite_3 . Some take into account the information on the prior network topology @cite_10 , which is not always available. Most assume the number of factors is known. To get around this, one can perform model selection via Reversible Jump MCMC @cite_0 or evolutionary stochastic model search @cite_12 . Unfortunately, these methods are often difficult to design and may take quite long to converge. Moreover, they are difficult to integrate with other forms of prior knowledge (eg., factor hierarchies). A somewhat similar approach to ours is the infinite independent component analysis (iICA) model of @cite_8 which treats factor analysis as a special case of ICA. However, their model is limited to factor analysis and does not take into account feature selection, factor hierarchy and factor regression. As a generalization to the standard ICA model, @cite_11 proposed a model in which the components can be related via a tree-structured graphical model. It, however, assumes a fixed number of components.
@cite_4 @cite_8 @cite_10 @cite_3 @cite_0 @cite_13 @cite_12 @cite_11
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We consider the problem of discovering gene regulatory networks from time-series microarray data. Recently, graphical Granger modeling has gained considerable attention as a promising direction for addressing this problem. These methods apply graphical modeling methods on time-series data and invoke the notion of ‘Granger causality’ to make assertions on causality through inference on time-lagged effects. Existing algorithms, however, have neglected an important aspect of the problem—the group structure among the lagged temporal variables naturally imposed by the time series they belong to. Specifically, existing methods in computational biology share this shortcoming, as well as additional computational limitations, prohibiting their effective applications to the large datasets including a large number of genes and many data points. In the present article, we propose a novel methodology which we term ‘grouped graphical Granger modeling method’, which overcomes the limitations mentioned above by applying a regression method suited for high-dimensional and large data, and by leveraging the group structure among the lagged temporal variables according to the time series they belong to. We demonstrate the effectiveness of the proposed methodology on both simulated and actual gene expression data, specifically the human cancer cell (HeLa S3) cycle data. The simulation results show that the proposed methodology generally exhibits higher accuracy in recovering the underlying causal structure. Those on the gene expression data demonstrate that it leads to improved accuracy with respect to prediction of known links, and also uncovers additional causal relationships uncaptured by earlier works. Contact: aclozano@us.ibm.com The identification of probabilistic cellular automata (PCA) is studied using a new two stage neighborhood detection algorithm. It is shown that a binary probabilistic cellular automaton (BPCA) can be described by an integer-parameterized polynomial corrupted by noise. Searching for the correct neighborhood of a BPCA is then equivalent to selecting the correct terms which constitute the polynomial model of the BPCA, from a large initial term set. It is proved that the contribution values for the correct terms can be calculated independently of the contribution values for the noise terms. This allows the neighborhood detection technique developed for deterministic rules in to be applied with a larger cutoff value to discard the majority of spurious terms and to produce an initial presearch for the BPCA neighborhood. A multiobjective genetic algorithm (GA) search with integer constraints is then evolved to refine the reduced neighborhood and to identify the polynomial rule which is equivalent to the probabilistic rule with the largest probability. A probability table representing the BPCA can then be determined based on the identified neighborhood and the deterministic rule. The new algorithm is tested over a large set of one-dimensional (1D), two-dimensional (2D), and three-dimensional (3D) BPCA rules. Simulation results demonstrate the efficiency of the new method. Objective Build probabilistic topic model representations of hospital admissions processes and compare the ability of such models to predict clinical order patterns as compared to preconstructed order sets. @PARASPLIT Materials and Methods The authors evaluated the first 24 hours of structured electronic health record data for > 10 K inpatients. Drawing an analogy between structured items (e.g., clinical orders) to words in a text document, the authors performed latent Dirichlet allocation probabilistic topic modeling. These topic models use initial clinical information to predict clinical orders for a separate validation set of > 4 K patients. The authors evaluated these topic model-based predictions vs existing human-authored order sets by area under the receiver operating characteristic curve, precision, and recall for subsequent clinical orders. @PARASPLIT Results Existing order sets predict clinical orders used within 24 hours with area under the receiver operating characteristic curve 0.81, precision 16 , and recall 35 . This can be improved to 0.90, 24 , and 47 ( P < 10−20) by using probabilistic topic models to summarize clinical data into up to 32 topics. Many of these latent topics yield natural clinical interpretations (e.g., “critical care,” “pneumonia,” “neurologic evaluation”). @PARASPLIT Discussion Existing order sets tend to provide nonspecific, process-oriented aid, with usability limitations impairing more precise, patient-focused support. Algorithmic summarization has the potential to breach this usability barrier by automatically inferring patient context, but with potential tradeoffs in interpretability. @PARASPLIT Conclusion Probabilistic topic modeling provides an automated approach to detect thematic trends in patient care and generate decision support content. A potential use case finds related clinical orders for decision support. Motivation: Approaches for testing sets of variants, such as a set of rare or common variants within a gene or pathway, for association with complex traits are important. In particular, set tests allow for aggregation of weak signal within a set, can capture interplay among variants and reduce the burden of multiple hypothesis testing. Until now, these approaches did not address confounding by family relatedness and population structure, a problem that is becoming more important as larger datasets are used to increase power. Results: We introduce a new approach for set tests that handles confounders. Our model is based on the linear mixed model and uses two random effects—one to capture the set association signal and one to capture confounders. We also introduce a computational speedup for two random-effects models that makes this approach feasible even for extremely large cohorts. Using this model with both the likelihood ratio test and score test, we find that the former yields more power while controlling type I error. Application of our approach to richly structured Genetic Analysis Workshop 14 data demonstrates that our method successfully corrects for population structure and family relatedness, whereas application of our method to a 15 000 individual Crohn’s disease case–control cohort demonstrates that it additionally recovers genes not recoverable by univariate analysis. Availability: A Python-based library implementing our approach is available at http: mscompbio.codeplex.com. Contact:jennl@microsoft.com or lippert@microsoft.com or heckerma@microsoft.com Supplementary information:Supplementary data are available at Bioinformatics online. A novel regularizer of the PARAFAC decomposition factors capturing the tensor's rank is proposed in this paper, as the key enabler for completion of three-way data arrays with missing entries. Set in a Bayesian framework, the tensor completion method incorporates prior information to enhance its smoothing and prediction capabilities. This probabilistic approach can naturally accommodate general models for the data distribution, lending itself to various fitting criteria that yield optimum estimates in the maximum-a-posteriori sense. In particular, two algorithms are devised for Gaussian- and Poisson-distributed data, that minimize the rank-regularized least-squares error and Kullback-Leibler divergence, respectively. The proposed technique is able to recover the “ground-truth” tensor rank when tested on synthetic data, and to complete brain imaging and yeast gene expression datasets with 50 and 15 of missing entries respectively, resulting in recovery errors at -11 dB and -15 dB. Consider the random graph models G(n, #edges = M) and G(n, Prob(edge) = p) with M = M(n) = (1 + )n-1 3)n 2 and p = p(n) = (1 +An-1 3) n . For 1 > -1 define an i-component of a random graph as a component which has exactly I more edges than vertices. Call an i-component with I > 1 a complex component. For both models, we show that when A is constant, the expected number of complex components is bounded, almost surely (a.s.) each of these components (if any exist) has size of order n2 3, and the maximum value of I is bounded in probability. We prove that a.s. the largest suspended tree in each complex component has size of order n2 3, and deletion of all suspended trees results in a "smoothed" graph of size of order n 3, with the maximum vertex degree 3. The total number of branching vertices, i.e., of degree 3, is bounded in probability. Thus, each complex component is almost surely topologically equivalent to a 3-regular multigraph of a uniformly bounded size. Lengths of the shortest cycle and of the shortest path between two branching vertices of a smoothed graph are each of order n 3. We find a relatively simple integral formula for the limit distribution of the numbers of complex components, which implies, in particular, that all values of the "complexity spectrum" have positive limiting probabilities. We also answer questions raised by Erdos and Renyi back in 1960. It is proven that there exists p(A), the limiting planarity probability, with 0 < p(A) < 1, p(-oo) = 1, p(oo) = 0. In particular, G(n, M) (G(n, p), resp.) is almost surely nonplanar iff (M n 2)n-213 -* 00 ((np I)n-1 3) -+ oo, resp.). In many multivariate domains, we are interested in analyzing the dependency structure of the underlying distribution, e.g., whether two variables are in direct interaction. We can represent dependency structures using Bayesian network models. To analyze a given data set, Bayesian model selection attempts to find the most likely (MAP) model, and uses its structure to answer these questions. However, when the amount of available data is modest, there might be many models that have non-negligible posterior. Thus, we want compute the Bayesian posterior of a feature, i.e., the total posterior probability of all models that contain it. In this paper, we propose a new approach for this task. We first show how to efficiently compute a sum over the exponential number of networks that are consistent with a fixed order over network variables. This allows us to compute, for a given order, both the marginal probability of the data and the posterior of a feature. We then use this result as the basis for an algorithm that approximates the Bayesian posterior of a feature. Our approach uses a Markov Chain Monte Carlo (MCMC) method, but over orders rather than over network structures. The space of orders is smaller and more regular than the space of structures, and has much a smoother posterior “landscape”. We present empirical results on synthetic and real-life datasets that compare our approach to full model averaging (when possible), to MCMC over network structures, and to a non-Bayesian bootstrap approach. A recent and effective approach to probabilistic inference calls for reducing the problem to one of weighted model counting (WMC) on a propositional knowledge base. Specifically, the approach calls for encoding the probabilistic model, typically a Bayesian network, as a propositional knowledge base in conjunctive normal form (CNF) with weights associated to each model according to the network parameters. Given this CNF, computing the probability of some evidence becomes a matter of summing the weights of all CNF models consistent with the evidence. A number of variations on this approach have appeared in the literature recently, that vary across three orthogonal dimensions. The first dimension concerns the specific encoding used to convert a Bayesian network into a CNF. The second dimensions relates to whether weighted model counting is performed using a search algorithm on the CNF, or by compiling the CNF into a structure that renders WMC a polytime operation in the size of the compiled structure. The third dimension deals with the specific properties of network parameters (local structure) which are captured in the CNF encoding. In this paper, we discuss recent work in this area across the above three dimensions, and demonstrate empirically its practical importance in significantly expanding the reach of exact probabilistic inference. We restrict our discussion to exact inference and model counting, even though other proposals have been extended for approximate inference and approximate model counting. We introduce a dynamic mechanism for the solution of analytically-tractable substructure in probabilistic programs, using conjugate priors and affine transformations to reduce variance in Monte Carlo estimators. For inference with Sequential Monte Carlo, this automatically yields improvements such as locally-optimal proposals and Rao-Blackwellization. The mechanism maintains a directed graph alongside the running program that evolves dynamically as operations are triggered upon it. Nodes of the graph represent random variables, edges the analytically-tractable relationships between them. Random variables remain in the graph for as long as possible, to be sampled only when they are used by the program in a way that cannot be resolved analytically. In the meantime, they are conditioned on as many observations as possible. We demonstrate the mechanism with a few pedagogical examples, as well as a linear-nonlinear state-space model with simulated data, and an epidemiological model with real data of a dengue outbreak in Micronesia. In all cases one or more variables are automatically marginalized out to significantly reduce variance in estimates of the marginal likelihood, in the final case facilitating a random-weight or pseudo-marginal-type importance sampler for parameter estimation. We have implemented the approach in Anglican and a new probabilistic programming language called Birch. Random graph models with limited choice have been studied extensively with the goal of understanding the mechanism of the emergence of the giant component. One of the standard models are the Achlioptas random graph processes on a fixed set of (n ) vertices. Here at each step, one chooses two edges uniformly at random and then decides which one to add to the existing configuration according to some criterion. An important class of such rules are the bounded-size rules where for a fixed (K 1 ), all components of size greater than (K ) are treated equally. While a great deal of work has gone into analyzing the subcritical and supercritical regimes, the nature of the critical scaling window, the size and complexity (deviation from trees) of the components in the critical regime and nature of the merging dynamics has not been well understood. In this work we study such questions for general bounded-size rules. Our first main contribution is the construction of an extension of Aldous’s standard multiplicative coalescent process which describes the asymptotic evolution of the vector of sizes and surplus of all components. We show that this process, referred to as the standard augmented multiplicative coalescent (AMC) is ‘nearly’ Feller with a suitable topology on the state space. Our second main result proves the convergence of suitably scaled component size and surplus vector, for any bounded-size rule, to the standard AMC. This result is new even for the classical Erdős–Renyi setting. The key ingredients here are a precise analysis of the asymptotic behavior of various susceptibility functions near criticality and certain bounds from (The barely subcritical regime. Arxiv preprint, 2012) on the size of the largest component in the barely subcritical regime. Motivation: Quantitative estimation of the regulatory relationship between transcription factors and genes is a fundamental stepping stone when trying to develop models of cellular processes. Recent experimental high-throughput techniques, such as Chromatin Immunoprecipitation (ChIP) provide important information about the architecture of the regulatory networks in the cell. However, it is very difficult to measure the concentration levels of transcription factor proteins and determine their regulatory effect on gene transcription. It is therefore an important computational challenge to infer these quantities using gene expression data and network architecture data. Results: We develop a probabilistic state space model that allows genome-wide inference of both transcription factor protein concentrations and their effect on the transcription rates of each target gene from microarray data. We use variational inference techniques to learn the model parameters and perform posterior inference of protein concentrations and regulatory strengths. The probabilistic nature of the model also means that we can associate credibility intervals to our estimates, as well as providing a tool to detect which binding events lead to significant regulation. We demonstrate our model on artificial data and on two yeast datasets in which the network structure has previously been obtained using ChIP data. Predictions from our model are consistent with the underlying biology and offer novel quantitative insights into the regulatory structure of the yeast cell. Availability: MATLAB code is available from http: umber.sbs.man.ac.uk resources puma Contact: guido@dcs.shef.ac.uk Supplementary information: Supplementary Data are available at Bioinformatics online Graphical models (e.g., Bayesian and constraint networks, influence diagrams, and Markov decision processes) have become a central paradigm for knowledge representation and reasoning in both artificial intelligence and computer science in general. These models are used to perform many reasoning tasks, such as scheduling, planning and learning, diagnosis and prediction, design, hardware and software verification, and bioinformatics. These problems can be stated as the formal tasks of constraint satisfaction and satisfiability, combinatorial optimization, and probabilistic inference. It is well known that the tasks are computationally hard, but research during the past three decades has yielded a variety of principles and techniques that significantly advanced the state of the art. In this book we provide comprehensive coverage of the primary exact algorithms for reasoning with such models. The main feature exploited by the algorithms is the model's graph. We present inference-based, message-passing schemes (e.g., variable-elimination) and search-based, conditioning schemes (e.g., cycle-cutset conditioning and AND OR search). Each class possesses distinguished characteristics and in particular has different time vs. space behavior. We emphasize the dependence of both schemes on few graph parameters such as the treewidth, cycle-cutset, and (the pseudo-tree) height. We believe the principles outlined here would serve well in moving forward to approximation and anytime-based schemes. The target audience of this book is researchers and students in the artificial intelligence and machine learning area, and beyond. Table of Contents: Preface Introduction What are Graphical Models Inference: Bucket Elimination for Deterministic Networks Inference: Bucket Elimination for Probabilistic Networks Tree-Clustering Schemes AND OR Search Spaces and Algorithms for Graphical Models Combining Search and Inference: Trading Space for Time Conclusion Bibliography Author's Biography Tasks such as record linkage and multi-target tracking, which involve reconstructing the set of objects that underlie some observed data, are particularly challenging for probabilistic inference. Recent work has achieved efficient and accurate inference on such problems using Markov chain Monte Carlo (MCMC) techniques with customized proposal distributions. Currently, implementing such a system requires coding MCMC state representations and acceptance probability calculations that are specific to a particular application. An alternative approach, which we pursue in this paper, is to use a general-purpose probabilistic modeling language (such as BLOG) and a generic Metropolis-Hastings MCMC algorithm that supports user-supplied proposal distributions. Our algorithm gains flexibility by using MCMC states that are only partial descriptions of possible worlds; we provide conditions under which MCMC over partial worlds yields correct answers to queries. We also show how to use a context-specific Bayes net to identify the factors in the acceptance probability that need to be computed for a given proposed move. Experimental results on a citation matching task show that our general-purpose MCMC engine compares favorably with an application-specific system. Most tasks require a person or an automated system to reason -- to reach conclusions based on available information. The framework of probabilistic graphical models, presented in this book, provides a general approach for this task. The approach is model-based, allowing interpretable models to be constructed and then manipulated by reasoning algorithms. These models can also be learned automatically from data, allowing the approach to be used in cases where manually constructing a model is difficult or even impossible. Because uncertainty is an inescapable aspect of most real-world applications, the book focuses on probabilistic models, which make the uncertainty explicit and provide models that are more faithful to reality. Probabilistic Graphical Models discusses a variety of models, spanning Bayesian networks, undirected Markov networks, discrete and continuous models, and extensions to deal with dynamical systems and relational data. For each class of models, the text describes the three fundamental cornerstones: representation, inference, and learning, presenting both basic concepts and advanced techniques. Finally, the book considers the use of the proposed framework for causal reasoning and decision making under uncertainty. The main text in each chapter provides the detailed technical development of the key ideas. Most chapters also include boxes with additional material: skill boxes, which describe techniques; case study boxes, which discuss empirical cases related to the approach described in the text, including applications in computer vision, robotics, natural language understanding, and computational biology; and concept boxes, which present significant concepts drawn from the material in the chapter. Instructors (and readers) can group chapters in various combinations, from core topics to more technically advanced material, to suit their particular needs. Probabilistic topic models are widely used in different contexts to uncover the hidden structure in large text corpora. One of the main (and perhaps strong) assumption of these models is that generative process follows a bag-of-words assumption, i.e. each token is independent from the previous one. We extend the popular Latent Dirichlet Allocation model by exploiting three different conditional Markovian assumptions: (i) the token generation depends on the current topic and on the previous token; (ii) the topic associated with each observation depends on topic associated with the previous one; (iii) the token generation depends on the current and previous topic. For each of these modeling assumptions we present a Gibbs Sampling procedure for parameter estimation. Experimental evaluation over real-word data shows the performance advantages, in terms of recall and precision, of the sequence-modeling approaches. This article considers approaches which rerank the output of an existing probabilistic parser. The base parser produces a set of candidate parses for each input sentence, with associated probabilities that define an initial ranking of these parses. A second model then attempts to improve upon this initial ranking, using additional features of the tree as evidence. The strength of our approach is that it allows a tree to be represented as an arbitrary set of features, without concerns about how these features interact or overlap and without the need to define a derivation or a generative model which takes these features into account. We introduce a new method for the reranking task, based on the boosting approach to ranking problems described in (1998). We apply the boosting method to parsing the Wall Street Journal treebank. The method combined the log-likelihood under a baseline model (that of Collins [1999]) with evidence from an additional 500,000 features over parse trees that were not included in the original model. The new model achieved 89.75 F-measure, a 13 relative decrease in F measure error over the baseline model's score of 88.2 . The article also introduces a new algorithm for the boosting approach which takes advantage of the sparsity of the feature space in the parsing data. Experiments show significant efficiency gains for the new algorithm over the obvious implementation of the boosting approach. We argue that the method is an appealing alternative—in terms of both simplicity and efficiency—to work on feature selection methods within log-linear (maximum-entropy) models. Although the experiments in this article are on natural language parsing (NLP), the approach should be applicable to many other NLP problems which are naturally framed as ranking tasks, for example, speech recognition, machine translation, or natural language generation. We introduce a novel training principle for probabilistic models that is an alternative to maximum likelihood. The proposed Generative Stochastic Networks (GSN) framework is based on learning the transition operator of a Markov chain whose stationary distribution estimates the data distribution. The transition distribution of the Markov chain is conditional on the previous state, generally involving a small move, so this conditional distribution has fewer dominant modes, being unimodal in the limit of small moves. Thus, it is easier to learn because it is easier to approximate its partition function, more like learning to perform supervised function approximation, with gradients that can be obtained by backprop. We provide theorems that generalize recent work on the probabilistic interpretation of denoising autoencoders and obtain along the way an interesting justification for dependency networks and generalized pseudolikelihood, along with a definition of an appropriate joint distribution and sampling mechanism even when the conditionals are not consistent. GSNs can be used with missing inputs and can be used to sample subsets of variables given the rest. We validate these theoretical results with experiments on two image datasets using an architecture that mimics the Deep Boltzmann Machine Gibbs sampler but allows training to proceed with simple backprop, without the need for layerwise pretraining. The proliferation of models for networks raises challenging problems of model selection: the data are sparse and globally dependent, and models are typically high-dimensional and have large numbers of latent variables. Together, these issues mean that the usual model-selection criteria do not work properly for networks. We illustrate these challenges, and show one way to resolve them, by considering the key network-analysis problem of dividing a graph into communities or blocks of nodes with homogeneous patterns of links to the rest of the network. The standard tool for undertaking this is the stochastic block model, under which the probability of a link between two nodes is a function solely of the blocks to which they belong. This imposes a homogeneous degree distribution within each block; this can be unrealistic, so degree-corrected block models add a parameter for each node, modulating its overall degree. The choice between ordinary and degree-corrected block models matters because they make very different inferences about communities. We present the first principled and tractable approach to model selection between standard and degree-corrected block models, based on new large-graph asymptotics for the distribution of log-likelihood ratios under the stochastic block model, finding substantial departures from classical results for sparse graphs. We also develop linear-time approximations for log-likelihoods under both the stochastic block model and the degree-corrected model, using belief propagation. Applications to simulated and real networks show excellent agreement with our approximations. Our results thus both solve the practical problem of deciding on degree correction and point to a general approach to model selection in network analysis. We present a new Markov Chain Monte Carlo (MCMC) sampling algorithm for probabilistic programs. Our approach and tool, called R2, has the unique feature of employing program analysis in order to improve the efficiency of MCMC sampling. Given an input program P, R2 propagates observations in P backwards to obtain a semantically equivalent program P′ in which every probabilistic assignment is immediately followed by an observe statement. Inference is performed by a suitably modified version of the Metropolis-Hastings algorithm that exploits the structure of the program P′. This has the overall effect of preventing rejections due to program executions that fail to satisfy observations in P. We formalize the semantics of probabilistic programs and rigorously prove the correctness of R2. We also empirically demonstrate the effectiveness of R2--in particular, we show that R2 is able to produce results of similar quality as the CHURCH and STAN probabilistic programming tools with much shorter execution time. Topic models, such as Latent Dirichlet Allocation (LDA), posit that documents are drawn from admixtures of distributions over words, known as topics. The inference problem of recovering topics from admixtures, is NP-hard. Assuming separability, a strong assumption, [4] gave the first provable algorithm for inference. For LDA model, [6] gave a provable algorithm using tensor-methods. But [4,6] do not learn topic vectors with bounded @math error (a natural measure for probability vectors). Our aim is to develop a model which makes intuitive and empirically supported assumptions and to design an algorithm with natural, simple components such as SVD, which provably solves the inference problem for the model with bounded @math error. A topic in LDA and other models is essentially characterized by a group of co-occurring words. Motivated by this, we introduce topic specific Catchwords, group of words which occur with strictly greater frequency in a topic than any other topic individually and are required to have high frequency together rather than individually. A major contribution of the paper is to show that under this more realistic assumption, which is empirically verified on real corpora, a singular value decomposition (SVD) based algorithm with a crucial pre-processing step of thresholding, can provably recover the topics from a collection of documents drawn from Dominant admixtures. Dominant admixtures are convex combination of distributions in which one distribution has a significantly higher contribution than others. Apart from the simplicity of the algorithm, the sample complexity has near optimal dependence on @math , the lowest probability that a topic is dominant, and is better than [4]. Empirical evidence shows that on several real world corpora, both Catchwords and Dominant admixture assumptions hold and the proposed algorithm substantially outperforms the state of the art [5].