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23
Mixed membership stochastic block models for relational data with application to proteinprotein interactions
 In Proceedings of the International Biometrics Society Annual Meeting
, 2006
"... We develop a model for examining data that consists of pairwise measurements, for example, presence or absence of links between pairs of objects. Examples include protein interactions and gene regulatory networks, collections of authorrecipient email, and social networks. Analyzing such data with p ..."
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Cited by 174 (30 self)
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We develop a model for examining data that consists of pairwise measurements, for example, presence or absence of links between pairs of objects. Examples include protein interactions and gene regulatory networks, collections of authorrecipient email, and social networks. Analyzing such data with probabilistic models requires special assumptions, since the usual independence or exchangeability assumptions no longer hold. We introduce a class of latent variable models for pairwise measurements: mixed membership stochastic blockmodels. Models in this class combine a global model of dense patches of connectivity (blockmodel) and a local model to instantiate nodespecific variability in the connections (mixed membership). We develop a general variational inference algorithm for fast approximate posterior inference. We demonstrate the advantages of mixed membership stochastic blockmodels with applications to social networks and protein interaction networks.
From frequency to meaning : Vector space models of semantics
 Journal of Artificial Intelligence Research
, 2010
"... Computers understand very little of the meaning of human language. This profoundly limits our ability to give instructions to computers, the ability of computers to explain their actions to us, and the ability of computers to analyse and process text. Vector space models (VSMs) of semantics are begi ..."
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Cited by 116 (2 self)
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Computers understand very little of the meaning of human language. This profoundly limits our ability to give instructions to computers, the ability of computers to explain their actions to us, and the ability of computers to analyse and process text. Vector space models (VSMs) of semantics are beginning to address these limits. This paper surveys the use of VSMs for semantic processing of text. We organize the literature on VSMs according to the structure of the matrix in a VSM. There are currently three broad classes of VSMs, based on term–document, word–context, and pair–pattern matrices, yielding three classes of applications. We survey a broad range of applications in these three categories and we take a detailed look at a specific open source project in each category. Our goal in this survey is to show the breadth of applications of VSMs for semantics, to provide a new perspective on VSMs for those who are already familiar with the area, and to provide pointers into the literature for those who are less familiar with the field. 1.
Probabilistic topic models
 IEEE Signal Processing Magazine
, 2010
"... Probabilistic topic models are a suite of algorithms whose aim is to discover the ..."
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Cited by 51 (3 self)
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Probabilistic topic models are a suite of algorithms whose aim is to discover the
On smoothing and inference for topic models
 In Proceedings of the 25th Conference on Uncertainty in Artificial Intelligence
, 2009
"... Latent Dirichlet analysis, or topic modeling, is a flexible latent variable framework for modeling highdimensional sparse count data. Various learning algorithms have been developed in recent years, including collapsed Gibbs sampling, variational inference, and maximum a posteriori estimation, and ..."
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Cited by 49 (7 self)
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Latent Dirichlet analysis, or topic modeling, is a flexible latent variable framework for modeling highdimensional sparse count data. Various learning algorithms have been developed in recent years, including collapsed Gibbs sampling, variational inference, and maximum a posteriori estimation, and this variety motivates the need for careful empirical comparisons. In this paper, we highlight the close connections between these approaches. We find that the main differences are attributable to the amount of smoothing applied to the counts. When the hyperparameters are optimized, the differences in performance among the algorithms diminish significantly. The ability of these algorithms to achieve solutions of comparable accuracy gives us the freedom to select computationally efficient approaches. Using the insights gained from this comparative study, we show how accurate topic models can be learned in several seconds on text corpora with thousands of documents. 1
A Unified View of Matrix Factorization Models
"... Abstract. We present a unified view of matrix factorization that frames the differences among popular methods, such as NMF, Weighted SVD, EPCA, MMMF, pLSI, pLSIpHITS, Bregman coclustering, and many others, in terms of a small number of modeling choices. Many of these approaches can be viewed as m ..."
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Cited by 33 (0 self)
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Abstract. We present a unified view of matrix factorization that frames the differences among popular methods, such as NMF, Weighted SVD, EPCA, MMMF, pLSI, pLSIpHITS, Bregman coclustering, and many others, in terms of a small number of modeling choices. Many of these approaches can be viewed as minimizing a generalized Bregman divergence, and we show that (i) a straightforward alternating projection algorithm can be applied to almost any model in our unified view; (ii) the Hessian for each projection has special structure that makes a Newton projection feasible, even when there are equality constraints on the factors, which allows for matrix coclustering; and (iii) alternating projections can be generalized to simultaneously factor a set of matrices that share dimensions. These observations immediately yield new optimization algorithms for the above factorization methods, and suggest novel generalizations of these methods such as incorporating row and column biases, and adding or relaxing clustering constraints. 1
The discrete basis problem
, 2005
"... We consider the Discrete Basis Problem, which can be described as follows: given a collection of Boolean vectors find a collection of k Boolean basis vectors such that the original vectors can be represented using disjunctions of these basis vectors. We show that the decision version of this problem ..."
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Cited by 26 (9 self)
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We consider the Discrete Basis Problem, which can be described as follows: given a collection of Boolean vectors find a collection of k Boolean basis vectors such that the original vectors can be represented using disjunctions of these basis vectors. We show that the decision version of this problem is NPcomplete and that the optimization version cannot be approximated within any finite ratio. We also study two variations of this problem, where the Boolean basis vectors must be mutually otrhogonal. We show that the other variation is closely related with the wellknown Metric kmedian Problem in Boolean space. To solve these problems, two algorithms will be presented. One is designed for the variations mentioned above, and it is solely based on solving the kmedian problem, while another is a heuristic intended to solve the general Discrete Basis Problem. We will also study the results of extensive experiments made with these two algorithms with both synthetic and realworld data. The results are twofold: with the synthetic data, the algorithms did rather well, but with the realworld data the results were not as good.
Bayesian Exponential Family PCA
"... Principal Components Analysis (PCA) has become established as one of the key tools for dimensionality reduction when dealing with real valued data. Approaches such as exponential family PCA and nonnegative matrix factorisation have successfully extended PCA to nonGaussian data types, but these tec ..."
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Cited by 12 (3 self)
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Principal Components Analysis (PCA) has become established as one of the key tools for dimensionality reduction when dealing with real valued data. Approaches such as exponential family PCA and nonnegative matrix factorisation have successfully extended PCA to nonGaussian data types, but these techniques fail to take advantage of Bayesian inference and can suffer from problems of overfitting and poor generalisation. This paper presents a fully probabilistic approach to PCA, which is generalised to the exponential family, based on Hybrid Monte Carlo sampling. We describe the model which is based on a factorisation of the observed data matrix, and show performance of the model on both synthetic and real data. 1
Estimating likelihoods for topic models
 in Asian Conference on Machine Learning
, 2009
"... Abstract. Topic models are a discrete analogue to principle component analysis and independent component analysis that model topic at the word level within a document. They have many variants such as NMF, PLSI and LDA, and are used in many fields such as genetics, text and the web, image analysis an ..."
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Cited by 6 (0 self)
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Abstract. Topic models are a discrete analogue to principle component analysis and independent component analysis that model topic at the word level within a document. They have many variants such as NMF, PLSI and LDA, and are used in many fields such as genetics, text and the web, image analysis and recommender systems. However, only recently have reasonable methods for estimating the likelihood of unseen documents, for instance to perform testing or model comparison, become available. This paper explores a number of recent methods, and improves their theory, performance, and testing. 1
Relative Performance Guarantees for Approximate Inference in Latent Dirichlet Allocation
"... Hierarchical probabilistic modeling of discrete data has emerged as a powerful tool for text analysis. Posterior inference in such models is intractable, and practitioners rely on approximate posterior inference methods such as variational inference or Gibbs sampling. There has been much research in ..."
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Cited by 3 (0 self)
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Hierarchical probabilistic modeling of discrete data has emerged as a powerful tool for text analysis. Posterior inference in such models is intractable, and practitioners rely on approximate posterior inference methods such as variational inference or Gibbs sampling. There has been much research in designing better approximations, but there is yet little theoretical understanding of which of the available techniques are appropriate, and in which data analysis settings. In this paper we provide the beginnings of such understanding. We analyze the improvement that the recently proposed collapsed variational inference (CVB) provides over mean field variational inference (VB) in latent Dirichlet allocation. We prove that the difference in the tightness of the bound on the likelihood of a document decreases as O(k −1)+ √ log m/m, where k is the number of topics in the model and m is the number of words in a document. As a consequence, the advantage of CVB over VB is lost for long documents but increases with the number of topics. We demonstrate empirically that the theory holds, using simulated text data and two text corpora. We provide practical guidelines for choosing an approximation. 1
M.: Asynchronous distributed estimation of topic models for document analysis
 Statistical Methodology
, 2011
"... Given the prevalence of large data sets and the availability of inexpensive parallel computing hardware, there is significant motivation to explore distributed implementations of statistical learning algorithms. In this paper, we present a distributed learning framework for Latent Dirichlet Allocati ..."
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Cited by 3 (0 self)
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Given the prevalence of large data sets and the availability of inexpensive parallel computing hardware, there is significant motivation to explore distributed implementations of statistical learning algorithms. In this paper, we present a distributed learning framework for Latent Dirichlet Allocation (LDA), a wellknown Bayesian latent variable model for sparse matrices of count data. In the proposed approach, data are distributed across P processors, and processors independently perform inference on their local data and communicate their sufficient statistics in a local asynchronous manner with other processors. We apply two different approximate inference techniques for LDA, collapsed Gibbs sampling and collapsed variational inference, within a distributed framework. The results show significant improvements in computation time and memory when running the algorithms on very large text corpora using parallel hardware. Despite the approximate nature of the proposed approach, simulations suggest that asynchronous distributed algorithms are able to learn models that are nearly as accurate as those learned by the standard nondistributed approaches. We also find that our distributed algorithms converge rapidly to good solutions.