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673
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 731 (16 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.
Robust Monte Carlo Localization for Mobile Robots
, 2001
"... Mobile robot localization is the problem of determining a robot's pose from sensor data. This article presents a family of probabilistic localization algorithms known as Monte Carlo Localization (MCL). MCL algorithms represent a robot's belief by a set of weighted hypotheses (samples), which approxi ..."
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Cited by 608 (83 self)
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Mobile robot localization is the problem of determining a robot's pose from sensor data. This article presents a family of probabilistic localization algorithms known as Monte Carlo Localization (MCL). MCL algorithms represent a robot's belief by a set of weighted hypotheses (samples), which approximate the posterior under a common Bayesian formulation of the localization problem. Building on the basic MCL algorithm, this article develops a more robust algorithm called MixtureMCL, which integrates two complimentary ways of generating samples in the estimation. To apply this algorithm to mobile robots equipped with range finders, a kernel density tree is learned that permits fast sampling. Systematic empirical results illustrate the robustness and computational efficiency of the approach.
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 564 (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.
Modeling and simulation of genetic regulatory systems: A literature review
 Journal of Computational Biology
, 2002
"... In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between ..."
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Cited by 415 (9 self)
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In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between DNA, RNA, proteins, and small molecules. As most genetic regulatory networks of interest involve many components connected through interlocking positive and negative feedback loops, an intuitive understanding of their dynamics is hard to obtain. As a consequence, formal methods and computer tools for the modeling and simulation of genetic regulatory networks will be indispensable. This paper reviews formalisms that have been employed in mathematical biology and bioinformatics to describe genetic regulatory systems, in particular directed graphs, Bayesian networks, Boolean networks and their generalizations, ordinary and partial differential equations, qualitative differential equations, stochastic equations, and rulebased formalisms. In addition, the paper discusses how these formalisms have been used in the simulation of the behavior of actual regulatory systems. Key words: genetic regulatory networks, mathematical modeling, simulation, computational biology.
A Bayesian computer vision system for modeling human interactions
 IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
, 2000
"... We describe a realtime computer vision and machine learning system for modeling and recognizing human behaviors in a visual surveillance task [1]. The system is particularly concerned with detecting when interactions between people occur and classifying the type of interaction. Examples of interes ..."
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Cited by 353 (6 self)
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We describe a realtime computer vision and machine learning system for modeling and recognizing human behaviors in a visual surveillance task [1]. The system is particularly concerned with detecting when interactions between people occur and classifying the type of interaction. Examples of interesting interaction behaviors include following another person, altering one's path to meet another, and so forth. Our system combines topdown with bottomup information in a closed feedback loop, with both components employing a statistical Bayesian approach [2]. We propose and compare two different statebased learning architectures, namely, HMMs and CHMMs for modeling behaviors and interactions. The CHMM model is shown to work much more efficiently and accurately. Finally, to deal with the problem of limited training data, a synthetic ªAlifestyleº training system is used to develop flexible prior models for recognizing human interactions. We demonstrate the ability to use these a priori models to accurately classify real human behaviors and interactions with no additional tuning or training.
Learning and Revising User Profiles: The Identification of Interesting Web Sites
 Machine Learning
, 1997
"... . We discuss algorithms for learning and revising user profiles that can determine which World Wide Web sites on a given topic would be interesting to a user. We describe the use of a naive Bayesian classifier for this task, and demonstrate that it can incrementally learn profiles from user feedback ..."
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Cited by 288 (14 self)
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. We discuss algorithms for learning and revising user profiles that can determine which World Wide Web sites on a given topic would be interesting to a user. We describe the use of a naive Bayesian classifier for this task, and demonstrate that it can incrementally learn profiles from user feedback on the interestingness of Web sites. Furthermore, the Bayesian classifier may easily be extended to revise user provided profiles. In an experimental evaluation we compare the Bayesian classifier to computationally more intensive alternatives, and show that it performs at least as well as these approaches throughout a range of different domains. In addition, we empirically analyze the effects of providing the classifier with background knowledge in form of user defined profiles and examine the use of lexical knowledge for feature selection. We find that both approaches can substantially increase the prediction accuracy. Keywords: Information filtering, intelligent agents, multistrategy lea...
The State of Record Linkage and Current Research Problems
 Statistical Research Division, U.S. Census Bureau
, 1999
"... This paper provides an overview of methods and systems developed for record linkage. Modern record linkage begins with the pioneering work of Newcombe and is especially based on the formal mathematical model of Fellegi and Sunter. In their seminal work, Fellegi and Sunter introduced many powerful id ..."
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Cited by 217 (7 self)
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This paper provides an overview of methods and systems developed for record linkage. Modern record linkage begins with the pioneering work of Newcombe and is especially based on the formal mathematical model of Fellegi and Sunter. In their seminal work, Fellegi and Sunter introduced many powerful ideas for estimating record linkage parameters and other ideas that still influence record linkage today. Record linkage research is characterized by its synergism of statistics, computer science, and operations research. Many difficult algorithms have been developed and put in software systems. Record linkage practice is still very limited. Some limits are due to existing software. Other limits are due to the difficulty in automatically estimating matching parameters and error rates, with current research highlighted by the work of Larsen and Rubin. Keywords: computer matching, modeling, iterative fitting, string comparison, optimization RsSUMs Cet article donne une vue d'ensemble sur les ...
Being Bayesian about network structure
 Machine Learning
, 2000
"... Abstract. 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 sel ..."
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Cited by 202 (5 self)
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Abstract. 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 nonnegligible 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 reallife datasets that compare our approach to full model averaging (when possible), to MCMC over network structures, and to a nonBayesian bootstrap approach.
Learning Bayesian network structure from massive datasets: The “sparse candidate” algorithm
, 1999
"... Learning Bayesian networks is often cast as an optimization problem, where the computational task is to find a structure that maximizes a statistically motivated score. By and large, existing learning tools address this optimization problem using standard heuristic search techniques. Since the searc ..."
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Cited by 181 (10 self)
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Learning Bayesian networks is often cast as an optimization problem, where the computational task is to find a structure that maximizes a statistically motivated score. By and large, existing learning tools address this optimization problem using standard heuristic search techniques. Since the search space is extremely large, such search procedures can spend most of the time examining candidates that are extremely unreasonable. This problem becomes critical when we deal with data sets that are large either in the number of instances, or the number of attributes. In this paper, we introduce an algorithm that achieves faster learning by restricting the search space. This iterative algorithm restricts the parents of each variable to belong to a small subset of candidates. We then search for a network that satisfies these constraints. The learned network is then used for selecting better candidates for the next iteration. We evaluate this algorithm both on synthetic and reallife data. Our results show that it is significantly faster than alternative search procedures without loss of quality in the learned structures. 1
Probabilistic Algorithms in Robotics
 AI Magazine vol
"... This article describes a methodology for programming robots known as probabilistic robotics. The probabilistic paradigm pays tribute to the inherent uncertainty in robot perception, relying on explicit representations of uncertainty when determining what to do. This article surveys some of the progr ..."
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Cited by 166 (9 self)
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This article describes a methodology for programming robots known as probabilistic robotics. The probabilistic paradigm pays tribute to the inherent uncertainty in robot perception, relying on explicit representations of uncertainty when determining what to do. This article surveys some of the progress in the field, using indepth examples to illustrate some of the nuts and bolts of the basic approach. Our central conjecture is that the probabilistic approach to robotics scales better to complex realworld applications than approaches that ignore a robot’s uncertainty. 1