Results 1  10
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243
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 1076 (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.
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 758 (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.
Learning probabilistic relational models
 In IJCAI
, 1999
"... A large portion of realworld data is stored in commercial relational database systems. In contrast, most statistical learning methods work only with "flat " data representations. Thus, to apply these methods, we are forced to convert our data into a flat form, thereby losing much ..."
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Cited by 619 (31 self)
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A large portion of realworld data is stored in commercial relational database systems. In contrast, most statistical learning methods work only with &quot;flat &quot; data representations. Thus, to apply these methods, we are forced to convert our data into a flat form, thereby losing much of the relational structure present in our database. This paper builds on the recent work on probabilistic relational models (PRMs), and describes how to learn them from databases. PRMs allow the properties of an object to depend probabilistically both on other properties of that object and on properties of related objects. Although PRMs are significantly more expressive than standard models, such as Bayesian networks, we show how to extend wellknown statistical methods for learning Bayesian networks to learn these models. We describe both parameter estimation and structure learning — the automatic induction of the dependency structure in a model. Moreover, we show how the learning procedure can exploit standard database retrieval techniques for efficient learning from large datasets. We present experimental results on both real and synthetic relational databases. 1
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 291 (4 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.
The maxmin hillclimbing bayesian network structure learning algorithm
 Machine Learning
, 2006
"... Abstract. We present a new algorithm for Bayesian network structure learning, called MaxMin HillClimbing (MMHC). The algorithm combines ideas from local learning, constraintbased, and searchandscore techniques in a principled and effective way. It first reconstructs the skeleton of a Bayesian n ..."
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Cited by 150 (8 self)
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Abstract. We present a new algorithm for Bayesian network structure learning, called MaxMin HillClimbing (MMHC). The algorithm combines ideas from local learning, constraintbased, and searchandscore techniques in a principled and effective way. It first reconstructs the skeleton of a Bayesian network and then performs a Bayesianscoring greedy hillclimbing search to orient the edges. In our extensive empirical evaluation MMHC outperforms on average and in terms of various metrics several prototypical and stateoftheart algorithms, namely the PC, Sparse Candidate, Three Phase Dependency Analysis, Optimal Reinsertion, Greedy Equivalence Search, and Greedy Search. These are the first empirical results simultaneously comparing most of the major Bayesian network algorithms against each other. MMHC offers certain theoretical advantages, specifically over the Sparse Candidate algorithm, corroborated by our experiments. MMHC and detailed results of our study are publicly available at
On Schema Matching with Opaque Column Names and Data Values
 In SIGMOD
, 2003
"... Most previous solutions to the schema matching problem rely in some fashion upon identifying "similar " column names in the schemas to be matched, or by recognizing common domains in the data stored in the schemas. While each of these approaches is valuable in many cases, they are ..."
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Cited by 113 (2 self)
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Most previous solutions to the schema matching problem rely in some fashion upon identifying &quot;similar &quot; column names in the schemas to be matched, or by recognizing common domains in the data stored in the schemas. While each of these approaches is valuable in many cases, they are not infallible, and there exist instances of the schema matching problem for which they do not even apply. Such problem instances typically arise when the column names in the schemas and the data in the columns are &quot;opaque &quot; or very difficult to interpret. In this paper we propose a twostep technique that works even in the presence of opaque column names and data values. In the first step, we measure the pairwise attribute correlations in the tables to be matched and construct a dependency graph using mutual information as a measure of the dependency between attributes. In the second stage, we find matching node pairs in the dependency graphs by running a graph matching algorithm. We validate our approach with an experimental study, the results of which suggest that such an approach can be a useful addition to a set of (semi) automatic schema matching techniques. 1.
Inferring Networks of Diffusion and Influence
, 2010
"... Information diffusion and virus propagation are fundamental processes talking place in networks. While it is often possible to directly observe when nodes become infected, observing individual transmissions (i.e., who infects whom or who influences whom) is typically very difficult. Furthermore, in ..."
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Cited by 112 (13 self)
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Information diffusion and virus propagation are fundamental processes talking place in networks. While it is often possible to directly observe when nodes become infected, observing individual transmissions (i.e., who infects whom or who influences whom) is typically very difficult. Furthermore, in many applications, the underlying network over which the diffusions and propagations spread is actually unobserved. We tackle these challenges by developing a method for tracing paths of diffusion and influence through networks and inferring the networks over which contagions propagate. Given the times when nodes adopt pieces of information or become infected, we identify the optimal network that best explains the observed infection times. Since the optimization problem is NPhard to solve exactly, we develop an efficient approximation algorithm that scales to large datasets and in practice gives provably nearoptimal performance. We demonstrate the effectiveness of our approach by tracing information cascades in a set of 170 million blogs and news articles over a one year period to infer how information flows through the online media space. We find that the diffusion network of news tends to have a coreperiphery structure with a small set of core media sites that diffuse information to the rest of the Web. These sites tend to have stable circles of influence with more general news media sites acting as connectors between them.
Orderingbased search: A simple and effective algorithm for learning Bayesian networks
 In UAI
, 2005
"... One of the basic tasks for Bayesian networks (BNs) is that of learning a network structure from data. The BNlearning problem is NPhard, so the standard solution is heuristic search. Many approaches have been proposed for this task, but only a very small number outperform the baseline of greedy hill ..."
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Cited by 77 (0 self)
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One of the basic tasks for Bayesian networks (BNs) is that of learning a network structure from data. The BNlearning problem is NPhard, so the standard solution is heuristic search. Many approaches have been proposed for this task, but only a very small number outperform the baseline of greedy hillclimbing with tabu lists; moreover, many of the proposed algorithms are quite complex and hard to implement. In this paper, we propose a very simple and easytoimplement method for addressing this task. Our approach is based on the wellknown fact that the best network (of bounded indegree) consistent with a given node ordering can be found very efficiently. We therefore propose a search not over the space of structures, but over the space of orderings, selecting for each ordering the best network consistent with it. This search space is much smaller, makes more global search steps, has a lower branching factor, and avoids costly acyclicity checks. We present results for this algorithm on both synthetic and real data sets, evaluating both the score of the network found and in the running time. We show that orderingbased search outperforms the standard baseline, and is competitive with recent algorithms that are much harder to implement. 1
Active Learning for Structure in Bayesian Networks
 IN INTERNATIONAL JOINT CONFERENCE ON ARTIFICIAL INTELLIGENCE
, 2001
"... The task of causal structure discovery from empirical data is a fundamental problem in many areas. Experimental data is crucial for accomplishing this task. However, experiments are typically expensive, and must be selected with great care. This paper ..."
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Cited by 76 (3 self)
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The task of causal structure discovery from empirical data is a fundamental problem in many areas. Experimental data is crucial for accomplishing this task. However, experiments are typically expensive, and must be selected with great care. This paper
Dynamic Bayesian Multinets
, 2000
"... In this work, dynamic Bayesian multinets are introduced where a Markov chain state at time t determines conditional independence patterns between random variables lying within a local time window surrounding t. It is shown how informationtheoretic criterion functions can be used to induce spa ..."
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Cited by 63 (18 self)
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In this work, dynamic Bayesian multinets are introduced where a Markov chain state at time t determines conditional independence patterns between random variables lying within a local time window surrounding t. It is shown how informationtheoretic criterion functions can be used to induce sparse, discriminative, and classconditional network structures that yield an optimal approximation to the class posterior probability, and therefore are useful for the classification task. Using a new structure learning heuristic, the resulting models are tested on a mediumvocabulary isolatedword speech recognition task. It is demonstrated that these discriminatively structured dynamic Bayesian multinets, when trained in a maximum likelihood setting using EM, can outperform both HMMs and other dynamic Bayesian networks with a similar number of parameters. 1 Introduction While Markov chains are sometimes a useful model for sequences, such simple independence assumptions can lead...