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27
Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks
 Bioinformatics
, 2003
"... Motivation: Bayesian networks have been applied to infer genetic regulatory interactions from microarray gene expression data. This inference problem is particularly hard in that interactions between hundreds of genes have to be learned from very small data sets, typically containing only a few doze ..."
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Cited by 109 (3 self)
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Motivation: Bayesian networks have been applied to infer genetic regulatory interactions from microarray gene expression data. This inference problem is particularly hard in that interactions between hundreds of genes have to be learned from very small data sets, typically containing only a few dozen time points during a cell cycle. Most previous studies have assessed the inference results on real gene expression data by comparing predicted genetic regulatory interactions with those known from the biological literature. This approach is controversial due to the absence of known gold standards, which renders the estimation of the sensitivity and specificity, that is, the true and (complementary) false detection rate, unreliable and difficult. The objective of the present study is to test the viability of the Bayesian network paradigm in a realistic simulation study. First, gene expression data are simulated from a realistic biological network involving DNAs, mRNAs, inactive protein monomers and active protein dimers. Then, interaction networks are inferred from these data in a reverse engineering approach, using Bayesian networks and Bayesian learning with Markov chain Monte Carlo.
Results: The simulation results are presented as receiver operator characteristics curves. This allows estimating the proportion of spurious gene interactions incurred for a specified target proportion of recovered true interactions. The findings demonstrate how the network inference performance varies with the training set size, the degree of inadequacy of prior assumptions, the experimental sampling strategy and the inclusion of further, sequencebased information.
Learning Bayesian Networks from Data: An InformationTheory Based Approach
"... This paper provides algorithms that use an informationtheoretic analysis to learn Bayesian network structures from data. Based on our threephase learning framework, we develop efficient algorithms that can effectively learn Bayesian networks, requiring only polynomial numbers of conditional indepe ..."
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Cited by 92 (5 self)
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This paper provides algorithms that use an informationtheoretic analysis to learn Bayesian network structures from data. Based on our threephase learning framework, we develop efficient algorithms that can effectively learn Bayesian networks, requiring only polynomial numbers of conditional independence (CI) tests in typical cases. We provide precise conditions that specify when these algorithms are guaranteed to be correct as well as empirical evidence (from real world applications and simulation tests) that demonstrates that these systems work efficiently and reliably in practice.
Graphical models and automatic speech recognition
 Mathematical Foundations of Speech and Language Processing
, 2003
"... Graphical models provide a promising paradigm to study both existing and novel techniques for automatic speech recognition. This paper first provides a brief overview of graphical models and their uses as statistical models. It is then shown that the statistical assumptions behind many pattern recog ..."
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Cited by 67 (13 self)
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Graphical models provide a promising paradigm to study both existing and novel techniques for automatic speech recognition. This paper first provides a brief overview of graphical models and their uses as statistical models. It is then shown that the statistical assumptions behind many pattern recognition techniques commonly used as part of a speech recognition system can be described by a graph – this includes Gaussian distributions, mixture models, decision trees, factor analysis, principle component analysis, linear discriminant analysis, and hidden Markov models. Moreover, this paper shows that many advanced models for speech recognition and language processing can also be simply described by a graph, including many at the acoustic, pronunciation, and languagemodeling levels. A number of speech recognition techniques born directly out of the graphicalmodels paradigm are also surveyed. Additionally, this paper includes a novel graphical analysis regarding why derivative (or delta) features improve hidden Markov modelbased speech recognition by improving structural discriminability. It also includes an example where a graph can be used to represent language model smoothing constraints. As will be seen, the space of models describable by a graph is quite large. A thorough exploration of this space should yield techniques that ultimately will supersede the hidden Markov model.
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 59 (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...
Building LargeScale Bayesian Networks
, 1999
"... Bayesian Networks (BNs) model problems that involve uncertainty. A BN is a directed graph, whose nodes are the uncertain variables and whose edges are the causal or influential links between the variables. Associated with each node is a set of conditional probability functions that model the unce ..."
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Cited by 40 (15 self)
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Bayesian Networks (BNs) model problems that involve uncertainty. A BN is a directed graph, whose nodes are the uncertain variables and whose edges are the causal or influential links between the variables. Associated with each node is a set of conditional probability functions that model the uncertain relationship between the node and its parents. The benefits of using BNs to model uncertain domains are well known, especially since the recent breakthroughs in algorithms and tools to implement them. However, there have been serious problems for practitioners trying to use BNs to solve realistic problems. This is because, although the tools make it possible to execute largescale BNs efficiently, there have been no guidelines on building BNs. Specifically, practitioners face two significant barriers. The first barrier is that of specifying the graph structure such that it is a sensible model of the types of reasoning being applied. The second barrier is that of eliciting the conditional probability values, from a domain expert, for a graph containing many combinations of nodes, where each may have a large number of discrete or continuous values. We have tackled both of these practical problems in recent research projects and have produced partial solutions for both that have been applied extensively on a number of reallife applications. In this paper we shall concentrate on this first problem, that of specifying a sensible BN graph structure. Our solution is based on the notion of generally applicable `building blocks', called idioms, which can be combined together into modular subnets. These can then in turn be combined into larger BNs, using simple combination rules and by exploiting recent ideas on modular and Object Oriented BNs (OOBNs). This appr...
Learning Bayesian Networks from Data: An Efficient Approach Based on Information Theory
, 1997
"... This paper addresses the problem of learning Bayesian network structures from data by using an information theoretic dependency analysis approach. Based on our threephase construction mechanism, two efficient algorithms have been developed. One of our algorithms deals with a special case where the ..."
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Cited by 35 (0 self)
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This paper addresses the problem of learning Bayesian network structures from data by using an information theoretic dependency analysis approach. Based on our threephase construction mechanism, two efficient algorithms have been developed. One of our algorithms deals with a special case where the node ordering is given, the algorithm only require ) ( 2 N O CI tests and is correct given that the underlying model is DAGFaithful [Spirtes et. al., 1996]. The other algorithm deals with the general case and requires ) ( 4 N O conditional independence (CI) tests. It is correct given that the underlying model is monotone DAGFaithful (see Section 4.4). A system based on these algorithms has been developed and distributed through the Internet. The empirical results show that our approach is efficient and reliable. 1 Introduction The Bayesian network is a powerful knowledge representation and reasoning tool under conditions of uncertainty. A Bayesian network is a directed acyclic graph ...
A Probabilistic Model for Software Defect Prediction
, 2001
"... Although a number of approaches have been taken to quality prediction for software, none have achieved widespread applicability. Our aim here is to produce a single model to combine the diverse forms of, often causal, evidence available in software development in a more natural and efficient way tha ..."
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Cited by 14 (2 self)
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Although a number of approaches have been taken to quality prediction for software, none have achieved widespread applicability. Our aim here is to produce a single model to combine the diverse forms of, often causal, evidence available in software development in a more natural and efficient way than done previously. We use graphical probability models (also known as Bayesian Belief Networks) as the appropriate formalism for representing this evidence. We can use the subjective judgements of experienced project managers to build the probability model and use this model to produce forecasts about the software quality throughout the development life cycle. Moreover, the causal or influence structure of the model more naturally mirrors the real world sequence of events and relations than can be achieved with other formalisms. The paper focuses on the particular model that has been developed for Philips Software Centre (PSC), using expert knowledge from Philips Research Labs. The model is used especially to predict defect rates at various testing and operational phases. To make the model usable by software quality managers we have developed a tool (AID) and have used it to validate the model on 28 diverse projects at PSC. In each of these projects, extensive historical records were available. The results of the validation are encouraging. In most cases the model provides accurate predictions of defect rates even on projects whose size was outside the original scope of the model.
Learning Bayes net structure from sparse data sets
, 2001
"... There are essentially two kinds of approaches for learning the structure of Bayesian Networks (BNs) from data. The first approach tries to find a graph which satis es all the constraints implied by the empirical conditional independencies measured in the data [PV91, SGS00a, Shi00]. The second approa ..."
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Cited by 12 (2 self)
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There are essentially two kinds of approaches for learning the structure of Bayesian Networks (BNs) from data. The first approach tries to find a graph which satis es all the constraints implied by the empirical conditional independencies measured in the data [PV91, SGS00a, Shi00]. The second approach searches through the space of models (either DAGs or PDAGs), and uses some scoring metric (typically Bayesian or some approximation, such as BIC/MDL) to evaluate the models [CH92, Hec95, Hec98, Kra98], typically returning the highest scoring model found. Our main interest is in learning BN structure from gene expression data [FLNP00, HGJY01, MM99, SGS00b]. In domains such as this, where the ratio of the number of observations to the number of variables is low (i.e., when we have sparse data), selecting a threshold for the conditional independence (CI) tests can be tricky, and repeated use of such tests can lead to inconsistencies [DD99]. Bayesian s...
Bayesian Networks and INEX
"... We present a bayesian framework for XML document retrieval. This framework allows us to consider content only and structure and content queries. We perform the retrieval task using inference in our network. Our model can adapt to a specific corpora through parameter learning. ..."
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Cited by 10 (2 self)
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We present a bayesian framework for XML document retrieval. This framework allows us to consider content only and structure and content queries. We perform the retrieval task using inference in our network. Our model can adapt to a specific corpora through parameter learning.
Fusion of Domain Knowledge with Data for Structural Learning in Object Oriented Domains
, 2003
"... When constructing a Bayesian network, it can be advantageous to employ structural learning algorithms to combine knowledge captured in databases with prior information provided by domain experts. Unfortunately, conventional learning algorithms do not easily incorporate prior information, if this inf ..."
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Cited by 9 (0 self)
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When constructing a Bayesian network, it can be advantageous to employ structural learning algorithms to combine knowledge captured in databases with prior information provided by domain experts. Unfortunately, conventional learning algorithms do not easily incorporate prior information, if this information is too vague to be encoded as properties that are local to families of variables. For instance, conventional algorithms do not exploit prior information about repetitive structures, which are often found in object oriented domains such as computer networks, large pedigrees and genetic analysis.