Results 1  10
of
26
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.
Nonprojective dependency parsing using spanning tree algorithms
 In Proceedings of Human Language Technology Conference and Conference on Empirical Methods in Natural Language Processing
, 2005
"... We formalize weighted dependency parsing as searching for maximum spanning trees (MSTs) in directed graphs. Using this representation, the parsing algorithm of Eisner (1996) is sufficient for searching over all projective trees in O(n 3) time. More surprisingly, the representation is extended natura ..."
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Cited by 271 (10 self)
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We formalize weighted dependency parsing as searching for maximum spanning trees (MSTs) in directed graphs. Using this representation, the parsing algorithm of Eisner (1996) is sufficient for searching over all projective trees in O(n 3) time. More surprisingly, the representation is extended naturally to nonprojective parsing using ChuLiuEdmonds (Chu and Liu, 1965; Edmonds, 1967) MST algorithm, yielding an O(n 2) parsing algorithm. We evaluate these methods on the Prague Dependency Treebank using online largemargin learning techniques (Crammer et al., 2003; McDonald et al., 2005) and show that MST parsing increases efficiency and accuracy for languages with nonprojective dependencies. 1
The Power of Amnesia: Learning Probabilistic Automata with Variable Memory Length
 Machine Learning
, 1996
"... . We propose and analyze a distribution learning algorithm for variable memory length Markov processes. These processes can be described by a subclass of probabilistic finite automata which we name Probabilistic Suffix Automata (PSA). Though hardness results are known for learning distributions gene ..."
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Cited by 173 (16 self)
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. We propose and analyze a distribution learning algorithm for variable memory length Markov processes. These processes can be described by a subclass of probabilistic finite automata which we name Probabilistic Suffix Automata (PSA). Though hardness results are known for learning distributions generated by general probabilistic automata, we prove that the algorithm we present can efficiently learn distributions generated by PSAs. In particular, we show that for any target PSA, the KLdivergence between the distribution generated by the target and the distribution generated by the hypothesis the learning algorithm outputs, can be made small with high confidence in polynomial time and sample complexity. The learning algorithm is motivated by applications in humanmachine interaction. Here we present two applications of the algorithm. In the first one we apply the algorithm in order to construct a model of the English language, and use this model to correct corrupted text. In the second ...
A Guide to the Literature on Learning Probabilistic Networks From Data
, 1996
"... This literature review discusses different methods under the general rubric of learning Bayesian networks from data, and includes some overlapping work on more general probabilistic networks. Connections are drawn between the statistical, neural network, and uncertainty communities, and between the ..."
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Cited by 172 (0 self)
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This literature review discusses different methods under the general rubric of learning Bayesian networks from data, and includes some overlapping work on more general probabilistic networks. Connections are drawn between the statistical, neural network, and uncertainty communities, and between the different methodological communities, such as Bayesian, description length, and classical statistics. Basic concepts for learning and Bayesian networks are introduced and methods are then reviewed. Methods are discussed for learning parameters of a probabilistic network, for learning the structure, and for learning hidden variables. The presentation avoids formal definitions and theorems, as these are plentiful in the literature, and instead illustrates key concepts with simplified examples. Keywords Bayesian networks, graphical models, hidden variables, learning, learning structure, probabilistic networks, knowledge discovery. I. Introduction Probabilistic networks or probabilistic gra...
Learning Bayesian Networks is NPComplete
, 1996
"... Algorithms for learning Bayesian networks from data havetwo components: a scoring metric and a search procedure. The scoring metric computes a score reflecting the goodnessoffit of the structure to the data. The search procedure tries to identify network structures with high scores. Heckerman e ..."
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Cited by 159 (8 self)
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Algorithms for learning Bayesian networks from data havetwo components: a scoring metric and a search procedure. The scoring metric computes a score reflecting the goodnessoffit of the structure to the data. The search procedure tries to identify network structures with high scores. Heckerman et al. (1995) introduce a Bayesian metric, called the BDe metric, that computes the relative posterior probabilityofanetwork structure given data. In this paper, we show that the search problem of identifying a Bayesian networkamong those where each node has at most K parentsthat has a relative posterior probability greater than a given constant is NPcomplete, when the BDe metric is used. 12.1
Learning Bayesian Networks is NPHard
, 1994
"... Algorithms for learning Bayesian networks from data have two components: a scoring metric and a search procedure. The scoring metric computes a score reflecting the goodnessoffit of the structure to the data. The search procedure tries to identify network structures with high scores. Heckerman et ..."
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Cited by 130 (2 self)
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Algorithms for learning Bayesian networks from data have two components: a scoring metric and a search procedure. The scoring metric computes a score reflecting the goodnessoffit of the structure to the data. The search procedure tries to identify network structures with high scores. Heckerman et al. (1994) introduced a Bayesian metric, called the BDe metric, that computes the relative posterior probability of a network structure given data. They show that the metric has a property desireable for inferring causal structure from data. In this paper, we show that the problem of deciding whether there is a Bayesian networkamong those where each node has at most k parentsthat has a relative posterior probability greater than a given constant is NPcomplete, when the BDe metric is used. 1 Introduction Recently, many researchers have begun to investigate methods for learning Bayesian networks, including Bayesian methods [Cooper and Herskovits, 1991, Buntine, 1991, York 1992, Spiegel...
Exact Bayesian structure discovery in Bayesian networks
 J. of Machine Learning Research
, 2004
"... We consider a Bayesian method for learning the Bayesian network structure from complete data. Recently, Koivisto and Sood (2004) presented an algorithm that for any single edge computes its marginal posterior probability in O(n2 n) time, where n is the number of attributes; the number of parents per ..."
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Cited by 55 (8 self)
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We consider a Bayesian method for learning the Bayesian network structure from complete data. Recently, Koivisto and Sood (2004) presented an algorithm that for any single edge computes its marginal posterior probability in O(n2 n) time, where n is the number of attributes; the number of parents per attribute is bounded by a constant. In this paper we show that the posterior probabilities for all the n(n−1) potential edges can be computed in O(n2 n) total time. This result is achieved by a forward–backward technique and fast Möbius transform algorithms, which are of independent interest. The resulting speedup by a factor of about n 2 allows us to experimentally study the statistical power of learning moderatesize networks. We report results from a simulation study that covers data sets with 20 to 10,000 records over 5 to 25 discrete attributes. 1
Learning Bayesian Nets that Perform Well
 In UAI97
, 1997
"... A Bayesian net (BN) is more than a succinct way to encode a probabilistic distribution; it also corresponds to a function used to answer queries. A BN can therefore be evaluated by the accuracy of the answers it returns. Many algorithms for learning BNs, however, attempt to optimize another criterio ..."
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Cited by 48 (17 self)
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A Bayesian net (BN) is more than a succinct way to encode a probabilistic distribution; it also corresponds to a function used to answer queries. A BN can therefore be evaluated by the accuracy of the answers it returns. Many algorithms for learning BNs, however, attempt to optimize another criterion (usually likelihood, possibly augmented with a regularizing term), which is independent of the distribution of queries that are posed. This paper takes the "performance criteria" seriously, and considers the challenge of computing the BN whose performance  read "accuracy over the distribution of queries"  is optimal. We show that many aspects of this learning task are more difficult than the corresponding subtasks in the standard model. To appear in Proceedings of the Thirteenth Conference on Uncertainty in Artificial Intelligence (UAI97), Providence, RI, August 1997. 1 INTRODUCTION Many tasks require answering questions; this model applies, for example, to both expert systems th...
Learning factor graphs in polynomial time and sample complexity. JMLR
, 2006
"... We study the computational and sample complexity of parameter and structure learning in graphical models. Our main result shows that the class of factor graphs with bounded degree can be learned in polynomial time and from a polynomial number of training examples, assuming that the data is generated ..."
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Cited by 47 (0 self)
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We study the computational and sample complexity of parameter and structure learning in graphical models. Our main result shows that the class of factor graphs with bounded degree can be learned in polynomial time and from a polynomial number of training examples, assuming that the data is generated by a network in this class. This result covers both parameter estimation for a known network structure and structure learning. It implies as a corollary that we can learn factor graphs for both Bayesian networks and Markov networks of bounded degree, in polynomial time and sample complexity. Importantly, unlike standard maximum likelihood estimation algorithms, our method does not require inference in the underlying network, and so applies to networks where inference is intractable. We also show that the error of our learned model degrades gracefully when the generating distribution is not a member of the target class of networks. In addition to our main result, we show that the sample complexity of parameter learning in graphical models has an O(1) dependence on the number of variables in the model when using the KLdivergence normalized by the number of variables as the performance criterion. 1
On the Sample Complexity of Learning Bayesian Networks
, 1996
"... In recent years there has been an increasing interest in learning Bayesian networks from data. One of the most effective methods for learning such networks is based on the minimum description length (MDL) principle. Previous work has shown that this learning procedure is asymptotically successful: w ..."
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Cited by 45 (2 self)
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In recent years there has been an increasing interest in learning Bayesian networks from data. One of the most effective methods for learning such networks is based on the minimum description length (MDL) principle. Previous work has shown that this learning procedure is asymptotically successful: with probability one, it will converge to the target distribution, given a sufficient number of samples. However, the rate of this convergence has been hitherto unknown. In this work we examine the sample complexity of MDL based learning procedures for Bayesian networks. We show that the number of samples needed to learn an fflclose approximation (in terms of entropy distance) with confidence ffi is O i ( 1 ffl ) 4 3 log 1 ffl log 1 ffi log log 1 ffi j . This means that the sample complexity is a loworder polynomial in the error threshold and sublinear in the confidence bound. We also discuss how the constants in this term depend on the complexity of the target distribution. F...