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753
Using Bayesian networks to analyze expression data
 Journal of Computational Biology
, 2000
"... DNA hybridization arrays simultaneously measure the expression level for thousands of genes. These measurements provide a “snapshot ” of transcription levels within the cell. A major challenge in computational biology is to uncover, from such measurements, gene/protein interactions and key biologica ..."
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Cited by 1013 (18 self)
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DNA hybridization arrays simultaneously measure the expression level for thousands of genes. These measurements provide a “snapshot ” of transcription levels within the cell. A major challenge in computational biology is to uncover, from such measurements, gene/protein interactions and key biological features of cellular systems. In this paper, we propose a new framework for discovering interactions between genes based on multiple expression measurements. This framework builds on the use of Bayesian networks for representing statistical dependencies. A Bayesian network is a graphbased model of joint multivariate probability distributions that captures properties of conditional independence between variables. Such models are attractive for their ability to describe complex stochastic processes and because they provide a clear methodology for learning from (noisy) observations. We start by showing how Bayesian networks can describe interactions between genes. We then describe a method for recovering gene interactions from microarray data using tools for learning Bayesian networks. Finally, we demonstrate this method on the S. cerevisiae cellcycle measurements of Spellman et al. (1998). Key words: gene expression, microarrays, Bayesian methods. 1.
A Bayesian approach to filtering junk Email
 PAPERS FROM THE 1998 WORKSHOP, AAAI
, 1998
"... In addressing the growing problem of junk Email on the Internet, we examine methods for the automated construction of filters to eliminate such unwanted messages from a user’s mail stream. By casting this problem in a decision theoretic framework, we are able to make use of probabilistic learning m ..."
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Cited by 508 (5 self)
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In addressing the growing problem of junk Email on the Internet, we examine methods for the automated construction of filters to eliminate such unwanted messages from a user’s mail stream. By casting this problem in a decision theoretic framework, we are able to make use of probabilistic learning methods in conjunction with a notion of differential misclassification cost to produce filters Which are especially appropriate for the nuances of this task. While this may appear, at first, to be a straightforward text classification problem, we show that by considering domainspecific features of this problem in addition to the raw text of Email messages, we can produce much more accurate filters. Finally, we show the efficacy of such filters in a real world usage scenario, arguing that this technology is mature enough for deployment.
Correlating Instrumentation Data to System States: A Building Block for Automated Diagnosis and Control
 In OSDI
, 2004
"... building block for automated diagnosis and control ..."
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Cited by 241 (18 self)
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building block for automated diagnosis and control
Adaptive Probabilistic Networks with Hidden Variables
 Machine Learning
, 1997
"... . Probabilistic networks (also known as Bayesian belief networks) allow a compact description of complex stochastic relationships among several random variables. They are rapidly becoming the tool of choice for uncertain reasoning in artificial intelligence. In this paper, we investigate the problem ..."
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Cited by 179 (10 self)
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. Probabilistic networks (also known as Bayesian belief networks) allow a compact description of complex stochastic relationships among several random variables. They are rapidly becoming the tool of choice for uncertain reasoning in artificial intelligence. In this paper, we investigate the problem of learning probabilistic networks with known structure and hidden variables. This is an important problem, because structure is much easier to elicit from experts than numbers, and the world is rarely fully observable. We present a gradientbased algorithmand show that the gradient can be computed locally, using information that is available as a byproduct of standard probabilistic network inference algorithms. Our experimental results demonstrate that using prior knowledge about the structure, even with hidden variables, can significantly improve the learning rate of probabilistic networks. We extend the method to networks in which the conditional probability tables are described using a ...
Facial Expression Recognition from Video Sequences: Temporal and Static Modelling
 Computer Vision and Image Understanding
, 2003
"... Humancomputer intelligent interaction (HCII) is an emerging field of science aimed at providing natural ways for humans to use computers as aids. It is argued that for the computer to be able to interact with humans, it needs to have the communication skills of humans. One of these skills is the ab ..."
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Cited by 175 (20 self)
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Humancomputer intelligent interaction (HCII) is an emerging field of science aimed at providing natural ways for humans to use computers as aids. It is argued that for the computer to be able to interact with humans, it needs to have the communication skills of humans. One of these skills is the ability to understand the emotional state of the person. The most expressive way humans display emotions is through facial expressions. In this work we report on several advances we have made in building a system for classification of facial expressions from continuous video input. We introduce and test different architectures, focusing on changes in distribution assumptions and feature dependency structures. We also introduce a facial expression recognition from live video input using temporal cues. Methods for using temporal information have been extensively explored for speech recognition applications. Among these methods are template matching using dynamic programming methods and hidden Markov models (HMM). This work exploits existing methods and proposes a new architecture of HMMs for automatically segmenting and recognizing human facial expression from video sequences. The architecture performs both segmentation and recognition of the facial expressions automatically using an multilevel architecture composed of an HMM layer and a Markov model layer. We explore both persondependent and personindependent recognition of expressions and compare the different methods.
An empirical study of the naive bayes classifier
, 2001
"... The naive Bayes classifier greatly simplify learning by assuming that features are independent given class. Although independence is generally a poor assumption, in practice naive Bayes often competes well with more sophisticated classifiers. Our broad goal is to understand the data characteristics ..."
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Cited by 169 (0 self)
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The naive Bayes classifier greatly simplify learning by assuming that features are independent given class. Although independence is generally a poor assumption, in practice naive Bayes often competes well with more sophisticated classifiers. Our broad goal is to understand the data characteristics which affect the performance of naive Bayes. Our approach uses Monte Carlo simulations that allow a systematic study of classification accuracy for several classes of randomly generated problems. We analyze the impact of the distribution entropy on the classification error, showing that lowentropy feature distributions yield good performance of naive Bayes. We also demonstrate that naive Bayes works well for certain nearlyfunctional feature dependencies, thus reaching its best performance in two opposite cases: completely independent features (as expected) and functionally dependent features (which is surprising). Another surprising result is that the accuracy of naive Bayes is not directly correlated with the degree of feature dependencies measured as the classconditional mutual information between the features. Instead, a better predictor of naive Bayes accuracy is the amount of information about the class that is lost because of the independence assumption. 1
Learning with mixtures of trees
 Journal of Machine Learning Research
, 2000
"... This paper describes the mixturesoftrees model, a probabilistic model for discrete multidimensional domains. Mixturesoftrees generalize the probabilistic trees of Chow and Liu [6] in a different and complementary direction to that of Bayesian networks. We present efficient algorithms for learnin ..."
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Cited by 140 (2 self)
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This paper describes the mixturesoftrees model, a probabilistic model for discrete multidimensional domains. Mixturesoftrees generalize the probabilistic trees of Chow and Liu [6] in a different and complementary direction to that of Bayesian networks. We present efficient algorithms for learning mixturesoftrees models in maximum likelihood and Bayesian frameworks. We also discuss additional efficiencies that can be obtained when data are “sparse, ” and we present data structures and algorithms that exploit such sparseness. Experimental results demonstrate the performance of the model for both density estimation and classification. We also discuss the sense in which treebased classifiers perform an implicit form of feature selection, and demonstrate a resulting insensitivity to irrelevant attributes.
Object recognition with informative features and linear classification
 In ICCV
, 2003
"... In this paper we show that efficient object recognition can be obtained by combining informative features with linear classification. The results demonstrate the superiority of informative classspecific features, as compared with generic type features such as wavelets, for the task of object recogn ..."
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Cited by 135 (5 self)
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In this paper we show that efficient object recognition can be obtained by combining informative features with linear classification. The results demonstrate the superiority of informative classspecific features, as compared with generic type features such as wavelets, for the task of object recognition. We show that information rich features can reach optimal performance with simple linear separation rules, while generic feature based classifiers require more complex classification schemes. This is significant because efficient and optimal methods have been developed for spaces that allow linear separation. To compare different strategies for feature extraction, we trained and compared classifiers working in feature spaces of the same low dimensionality, using two feature types (image fragments vs. wavelets) and two classification rules (linear hyperplane and a Bayesian Network). The results show that by maximizing the individual information of the features, it is possible to obtain efficient classification by a simple linear separating rule, as well as more efficient learning. 1.
An Experimental Comparison of Naive Bayesian and KeywordBased AntiSpam Filtering with Personal Email Messages
 In Proceedings of the 23rd annual international ACM SIGIR conference on Research and development in information retrieval
, 2000
"... The growing problem of unsolicited bulk email, also known as "spare", has generated a need for reliable antispam email filters. Filters of this type have so far been based mostly on manually constructed keyword patterns. An alternative approach has recently been proposed, whereb ..."
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Cited by 130 (2 self)
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The growing problem of unsolicited bulk email, also known as &quot;spare&quot;, has generated a need for reliable antispam email filters. Filters of this type have so far been based mostly on manually constructed keyword patterns. An alternative approach has recently been proposed, whereby a Naive Bayesian classifier is trained automatically to detect spam messages. We test this approach on a large collection of personal email messages, which we make publicly available in &quot;encrypted &quot; form contributing towards standard benchmarks. We introduce appropriate costsensitive measures, investigating at the same time the effect of attributeset size, trainingcorpus size, lemmatization, and stop lists, issues that have not been explored in previous experiments. Finally, the Naive Bayesian filter is compared, in terms of performance, to a filter that uses keyword patterns, and which is part of a widely used email reader. Keywords filtering/routing; text categorization; machine learning and IR; evaluation (general); test collections I.
CentroidBased Document Classification: Analysis Experimental Results
, 2000
"... . In this paper we present a simple lineartime centroidbased document classification algorithm, that despite its simplicity and robust performance, has not been extensively studied and analyzed. Our experiments show that this centroidbased classifier consistently and substantially outperforms ..."
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Cited by 127 (1 self)
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. In this paper we present a simple lineartime centroidbased document classification algorithm, that despite its simplicity and robust performance, has not been extensively studied and analyzed. Our experiments show that this centroidbased classifier consistently and substantially outperforms other algorithms such as Naive Bayesian, knearestneighbors, and C4.5, on a wide range of datasets. Our analysis shows that the similarity measure used by the centroidbased scheme allows it to classify a new document based on how closely its behavior matches the behavior of the documents belonging to different classes. This matching allows it to dynamically adjust for classes with different densities and accounts for dependencies between the terms in the different classes. 1 Introduction We have seen a tremendous growth in the volume of online text documents available on the Internet, digital libraries, news sources, and companywide intranets. It has been forecasted that these docu...