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Infinite Latent Feature Models and the Indian Buffet Process
, 2005
"... We define a probability distribution over equivalence classes of binary matrices with a finite number of rows and an unbounded number of columns. This distribution ..."
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Cited by 270 (45 self)
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We define a probability distribution over equivalence classes of binary matrices with a finite number of rows and an unbounded number of columns. This distribution
Computational Discovery of Gene Modules, Regulatory Networks and Expression Programs
, 2007
"... Highthroughput molecular data are revolutionizing biology by providing massive amounts of information about gene expression and regulation. Such information is applicable both to furthering our understanding of fundamental biology and to developing new diagnostic and treatment approaches for diseas ..."
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Cited by 232 (17 self)
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Highthroughput molecular data are revolutionizing biology by providing massive amounts of information about gene expression and regulation. Such information is applicable both to furthering our understanding of fundamental biology and to developing new diagnostic and treatment approaches for diseases. However, novel mathematical methods are needed for extracting biological knowledge from highdimensional, complex and noisy data sources. In this thesis, I develop and apply three novel computational approaches for this task. The common theme of these approaches is that they seek to discover meaningful groups of genes, which confer robustness to noise and compress complex information into interpretable models. I first present the GRAM algorithm, which fuses information from genomewide expression and in vivo transcription factorDNA binding data to discover regulatory networks of
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 220 (6 self)
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Probabilistic topic models are a suite of algorithms whose aim is to discover the
Topic and role discovery in social networks
 In IJCAI
, 2005
"... Previous work in social network analysis (SNA) has modeled the existence of links from one entity to another, but not the language content or topics on those links. We present the AuthorRecipientTopic (ART) model for social network analysis, which learns topic distributions based on the direction ..."
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Cited by 212 (15 self)
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Previous work in social network analysis (SNA) has modeled the existence of links from one entity to another, but not the language content or topics on those links. We present the AuthorRecipientTopic (ART) model for social network analysis, which learns topic distributions based on the directionsensitive messages sent between entities. The model builds on Latent Dirichlet Allocation (LDA) and the AuthorTopic (AT) model, adding the key attribute that distribution over topics is conditioned distinctly on both the sender and recipient—steering the discovery of topics according to the relationships between people. We give results on both the Enron email corpus and a researcher’s email archive, providing evidence not only that clearly relevant topics are discovered, but that the ART model better predicts people’s roles. 1 Introduction and Related Work Social network analysis (SNA) is the study of mathematical models for interactions among people, organizations and groups. With the recent availability of large datasets of human
Discovering object categories in image collections
, 2004
"... Given a set of images containing multiple object categories, we seek to discover those categories and their image locations without supervision. We achieve this using generative models from the statistical text literature: probabilistic Latent Semantic Analysis (pLSA), and Latent Dirichlet Allocatio ..."
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Cited by 189 (12 self)
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Given a set of images containing multiple object categories, we seek to discover those categories and their image locations without supervision. We achieve this using generative models from the statistical text literature: probabilistic Latent Semantic Analysis (pLSA), and Latent Dirichlet Allocation (LDA). In text analysis these are used to discover topics in a corpus using the bagofwords document representation. Here we discover topics as object categories, so that an image containing instances of several categories is modelled as a mixture of topics. The models are applied to images by using a visual analogue of a word, formed by vector quantizing SIFT like region descriptors. We investigate a set of increasingly demanding scenarios, starting with image sets containing only two object categories through to sets containing multiple categories (including airplanes, cars, faces, motorbikes, spotted cats) and background clutter. The object categories sample both intraclass and scale variation, and both the categories and their approximate spatial layout are found without supervision. We also demonstrate classification of unseen images and images containing multiple objects. Performance of the proposed unsupervised method is compared to the semisupervised approach of [7].
Topics in semantic representation
 Psychological Review
, 2007
"... Accounts of language processing have suggested that it requires retrieving concepts from memory in response to an ongoing stream of information. This can be facilitated by inferring the gist of a sentence, conversation, or document, and using that computational problem underlying the extraction and ..."
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Cited by 171 (14 self)
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Accounts of language processing have suggested that it requires retrieving concepts from memory in response to an ongoing stream of information. This can be facilitated by inferring the gist of a sentence, conversation, or document, and using that computational problem underlying the extraction and use of gist, formulating this problem as a rational statistical inference. This leads us to a novel approach to semantic representation in which word meanings are represented in terms of a set of probabilistic topics. The topic model performs well in predicting word association and the effects of semantic association and ambiguity on a variety of language processing and memory tasks. It also provides a foundation for developing more richly structured statistical models of language, as the generative process assumed in the topic model can easily be extended to incorporate other kinds of semantic and syntactic structure. Many aspects of perception and cognition can be understood by considering the computational problem that is addressed by a particular human capacity (Andersion, 1990; Marr, 1982). Perceptual capacities such as identifying shape from shading (Freeman, 1994), motion perception
A CORRELATED TOPIC MODEL OF SCIENCE
, 2007
"... Topic models, such as latent Dirichlet allocation (LDA), can be useful tools for the statistical analysis of document collections and other discrete data. The LDA model assumes that the words of each document arise from a mixture of topics, each of which is a distribution over the vocabulary. A limi ..."
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Cited by 148 (10 self)
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Topic models, such as latent Dirichlet allocation (LDA), can be useful tools for the statistical analysis of document collections and other discrete data. The LDA model assumes that the words of each document arise from a mixture of topics, each of which is a distribution over the vocabulary. A limitation of LDA is the inability to model topic correlation even though, for example, a document about genetics is more likely to also be about disease than Xray astronomy. This limitation stems from the use of the Dirichlet distribution to model the variability among the topic proportions. In this paper we develop the correlated topic model (CTM), where the topic proportions exhibit correlation via the logistic normal distribution [J. Roy. Statist. Soc. Ser. B 44 (1982) 139–177]. We derive a fast variational inference algorithm for approximate posterior inference in this model, which is complicated by the fact that the logistic normal is not conjugate to the multinomial. We apply the CTM to the articles from Science published from 1990–1999, a data set that comprises 57M words. The CTM gives a better fit of the data than LDA, and we demonstrate its use as an exploratory tool of large document collections.
A hierarchical Bayesian language model based on Pitman–Yor processes
 In Coling/ACL, 2006. 9
, 2006
"... We propose a new hierarchical Bayesian ngram model of natural languages. Our model makes use of a generalization of the commonly used Dirichlet distributions called PitmanYor processes which produce powerlaw distributions more closely resembling those in natural languages. We show that an approxi ..."
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Cited by 143 (10 self)
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We propose a new hierarchical Bayesian ngram model of natural languages. Our model makes use of a generalization of the commonly used Dirichlet distributions called PitmanYor processes which produce powerlaw distributions more closely resembling those in natural languages. We show that an approximation to the hierarchical PitmanYor language model recovers the exact formulation of interpolated KneserNey, one of the best smoothing methods for ngram language models. Experiments verify that our model gives cross entropy results superior to interpolated KneserNey and comparable to modified KneserNey. 1
Hierarchical beta processes and the Indian buffet process. This volume
 In Practical Nonparametric and Semiparametric Bayesian Statistics
, 2007
"... We show that the beta process is the de Finetti mixing distribution underlying the Indian buffet process of [2]. This result shows that the beta process plays the role for the Indian buffet process that the Dirichlet process plays for Chinese restaurant process, a parallel that guides us in deriving ..."
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Cited by 130 (18 self)
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We show that the beta process is the de Finetti mixing distribution underlying the Indian buffet process of [2]. This result shows that the beta process plays the role for the Indian buffet process that the Dirichlet process plays for Chinese restaurant process, a parallel that guides us in deriving analogs for the beta process of the many known extensions of the Dirichlet process. In particular we define Bayesian hierarchies of beta processes and use the connection to the beta process to develop posterior inference algorithms for the Indian buffet process. We also present an application to document classification, exploring a relationship between the hierarchical beta process and smoothed naive Bayes models. 1 1
The nested chinese restaurant process and bayesian inference of topic hierarchies
, 2007
"... We present the nested Chinese restaurant process (nCRP), a stochastic process which assigns probability distributions to infinitelydeep, infinitelybranching trees. We show how this stochastic process can be used as a prior distribution in a Bayesian nonparametric model of document collections. Spe ..."
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Cited by 123 (15 self)
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We present the nested Chinese restaurant process (nCRP), a stochastic process which assigns probability distributions to infinitelydeep, infinitelybranching trees. We show how this stochastic process can be used as a prior distribution in a Bayesian nonparametric model of document collections. Specifically, we present an application to information retrieval in which documents are modeled as paths down a random tree, and the preferential attachment dynamics of the nCRP leads to clustering of documents according to sharing of topics at multiple levels of abstraction. Given a corpus of documents, a posterior inference algorithm finds an approximation to a posterior distribution over trees, topics and allocations of words to levels of the tree. We demonstrate this algorithm on collections of scientific abstracts from several journals. This model exemplifies a recent trend in statistical machine learning—the use of Bayesian nonparametric methods to infer distributions on flexible data structures.