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185
Empirical Analysis of Predictive Algorithm for Collaborative Filtering
 Proceedings of the 14 th Conference on Uncertainty in Artificial Intelligence
, 1998
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Bayesian Network Classifiers
, 1997
"... Recent work in supervised learning has shown that a surprisingly simple Bayesian classifier with strong assumptions of independence among features, called naive Bayes, is competitive with stateoftheart classifiers such as C4.5. This fact raises the question of whether a classifier with less restr ..."
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Cited by 638 (23 self)
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Recent work in supervised learning has shown that a surprisingly simple Bayesian classifier with strong assumptions of independence among features, called naive Bayes, is competitive with stateoftheart classifiers such as C4.5. This fact raises the question of whether a classifier with less restrictive assumptions can perform even better. In this paper we evaluate approaches for inducing classifiers from data, based on the theory of learning Bayesian networks. These networks are factored representations of probability distributions that generalize the naive Bayesian classifier and explicitly represent statements about independence. Among these approaches we single out a method we call Tree Augmented Naive Bayes (TAN), which outperforms naive Bayes, yet at the same time maintains the computational simplicity (no search involved) and robustness that characterize naive Bayes. We experimentally tested these approaches, using problems from the University of California at Irvine repository, and compared them to C4.5, naive Bayes, and wrapper methods for feature selection.
Dynamic Bayesian Networks: Representation, Inference and Learning
, 2002
"... Modelling sequential data is important in many areas of science and engineering. Hidden Markov models (HMMs) and Kalman filter models (KFMs) are popular for this because they are simple and flexible. For example, HMMs have been used for speech recognition and biosequence analysis, and KFMs have bee ..."
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Cited by 598 (3 self)
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Modelling sequential data is important in many areas of science and engineering. Hidden Markov models (HMMs) and Kalman filter models (KFMs) are popular for this because they are simple and flexible. For example, HMMs have been used for speech recognition and biosequence analysis, and KFMs have been used for problems ranging from tracking planes and missiles to predicting the economy. However, HMMs
and KFMs are limited in their “expressive power”. Dynamic Bayesian Networks (DBNs) generalize HMMs by allowing the state space to be represented in factored form, instead of as a single discrete random variable. DBNs generalize KFMs by allowing arbitrary probability distributions, not just (unimodal) linearGaussian. In this thesis, I will discuss how to represent many different kinds of models as DBNs, how to perform exact and approximate inference in DBNs, and how to learn DBN models from sequential data.
In particular, the main novel technical contributions of this thesis are as follows: a way of representing
Hierarchical HMMs as DBNs, which enables inference to be done in O(T) time instead of O(T 3), where T is the length of the sequence; an exact smoothing algorithm that takes O(log T) space instead of O(T); a simple way of using the junction tree algorithm for online inference in DBNs; new complexity bounds on exact online inference in DBNs; a new deterministic approximate inference algorithm called factored frontier; an analysis of the relationship between the BK algorithm and loopy belief propagation; a way of
applying RaoBlackwellised particle filtering to DBNs in general, and the SLAM (simultaneous localization
and mapping) problem in particular; a way of extending the structural EM algorithm to DBNs; and a variety of different applications of DBNs. However, perhaps the main value of the thesis is its catholic presentation of the field of sequential data modelling.
How many clusters? Which clustering method? Answers via modelbased cluster analysis
 THE COMPUTER JOURNAL
, 1998
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The Bayesian Structural EM Algorithm
, 1998
"... In recent years there has been a flurry of works on learning Bayesian networks from data. One of the hard problems in this area is how to effectively learn the structure of a belief network from incomplete datathat is, in the presence of missing values or hidden variables. In a recent paper, I in ..."
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Cited by 223 (12 self)
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In recent years there has been a flurry of works on learning Bayesian networks from data. One of the hard problems in this area is how to effectively learn the structure of a belief network from incomplete datathat is, in the presence of missing values or hidden variables. In a recent paper, I introduced an algorithm called Structural EM that combines the standard Expectation Maximization (EM) algorithm, which optimizes parameters, with structure search for model selection. That algorithm learns networks based on penalized likelihood scores, which include the BIC/MDL score and various approximations to the Bayesian score. In this paper, I extend Structural EM to deal directly with Bayesian model selection. I prove the convergence of the resulting algorithm and show how to apply it for learning a large class of probabilistic models, including Bayesian networks and some variants thereof.
Trust management for the semantic web
 In ISWC
, 2003
"... Abstract. Though research on the Semantic Web has progressed at a steady pace, its promise has yet to be realized. One major difficulty is that, by its very nature, the Semantic Web is a large, uncensored system to which anyone may contribute. This raises the question of how much credence to give ea ..."
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Cited by 206 (3 self)
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Abstract. Though research on the Semantic Web has progressed at a steady pace, its promise has yet to be realized. One major difficulty is that, by its very nature, the Semantic Web is a large, uncensored system to which anyone may contribute. This raises the question of how much credence to give each source. We cannot expect each user to know the trustworthiness of each source, nor would we want to assign topdown or global credibility values due to the subjective nature of trust. We tackle this problem by employing a web of trust, in which each user provides personal trust values for a small number of other users. We compose these trusts to compute the trust a user should place in any other user in the network. A user is not assigned a single trust rank. Instead, different users may have different trust values for the same user. We define properties for combination functions which merge such trusts, and define a class of functions for which merging may be done locally while maintaining these properties. We give examples of specific functions and apply them to data from Epinions and our BibServ bibliography server. Experiments confirm that the methods are robust to noise, and do not put unreasonable expectations on users. We hope that these methods will help move the Semantic Web closer to fulfilling its promise. 1.
Consensus clustering  A resamplingbased method for class discovery and visualization of gene expression microarray data
 MACHINE LEARNING 52 (2003) 91–118 FUNCTIONAL GENOMICS SPECIAL ISSUE
, 2003
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Learning Belief Networks in the Presence of Missing Values and Hidden Variables
 Proceedings of the Fourteenth International Conference on Machine Learning
, 1997
"... In recent years there has been a flurry of works on learning probabilistic belief networks. Current state of the art methods have been shown to be successful for two learning scenarios: learning both network structure and parameters from complete data, and learning parameters for a fixed network fr ..."
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Cited by 131 (14 self)
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In recent years there has been a flurry of works on learning probabilistic belief networks. Current state of the art methods have been shown to be successful for two learning scenarios: learning both network structure and parameters from complete data, and learning parameters for a fixed network from incomplete datathat is, in the presence of missing values or hidden variables. However, no method has yet been demonstrated to effectively learn network structure from incomplete data. In this paper, we propose a new method for learning network structure from incomplete data. This method is based on an extension of the ExpectationMaximization (EM) algorithm for model selection problems that performs search for the best structure inside the EM procedure. We prove the convergence of this algorithm, and adapt it for learning belief networks. We then describe how to learn networks in two scenarios: when the data contains missing values, and in the presence of hidden variables. We provide...
Modeling Dependencies in ProteinDNA Binding Sites
, 2003
"... The availability of whole genome sequences and highthroughput genomic assays opens the door for in silico analysis of transcription regulation. This includes methods for discovering and characterizing the binding sites of DNAbinding proteins, such as transcription factors. A common representation ..."
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Cited by 92 (2 self)
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The availability of whole genome sequences and highthroughput genomic assays opens the door for in silico analysis of transcription regulation. This includes methods for discovering and characterizing the binding sites of DNAbinding proteins, such as transcription factors. A common representation of transcription factor binding sites is aposition specific score matrix (PSSM). This representation makes the strong assumption that binding site positions are independent of each other. In this work, we explore Bayesian network representations of binding sites that provide different tradeoffs between complexity (number of parameters) and the richness of dependencies between positions. We develop the formal machinery for learning such models from data and for estimating the statistical significance of putative binding sites. We then evaluate the ramifications of these richer representations in characterizing binding site motifs and predicting their genomic locations. We show that these richer representations improve over the PSSM model in both tasks.