34,030 research outputs found

    Parallelization of the PC Algorithm

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    This paper describes a parallel version of the PC algorithm for learning the structure of a Bayesian network from data. The PC algorithm is a constraint-based algorithm consisting of fi ve steps where the first step is to perform a set of (conditional) independence tests while the remaining four steps relate to identifying the structure of the Bayesian network using the results of the (conditional) independence tests. In this paper, we describe a new approach to parallelization of the (conditional) independence testing as experiments illustrate that this is by far the most time consuming step. The proposed parallel PC algorithm is evaluated on data sets generated at random from five different real- world Bayesian networks. The results demonstrate that signi cant time performance improvements are possible using the proposed algorithm

    Reasoning about Independence in Probabilistic Models of Relational Data

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    We extend the theory of d-separation to cases in which data instances are not independent and identically distributed. We show that applying the rules of d-separation directly to the structure of probabilistic models of relational data inaccurately infers conditional independence. We introduce relational d-separation, a theory for deriving conditional independence facts from relational models. We provide a new representation, the abstract ground graph, that enables a sound, complete, and computationally efficient method for answering d-separation queries about relational models, and we present empirical results that demonstrate effectiveness.Comment: 61 pages, substantial revisions to formalisms, theory, and related wor

    Application of new probabilistic graphical models in the genetic regulatory networks studies

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    This paper introduces two new probabilistic graphical models for reconstruction of genetic regulatory networks using DNA microarray data. One is an Independence Graph (IG) model with either a forward or a backward search algorithm and the other one is a Gaussian Network (GN) model with a novel greedy search method. The performances of both models were evaluated on four MAPK pathways in yeast and three simulated data sets. Generally, an IG model provides a sparse graph but a GN model produces a dense graph where more information about gene-gene interactions is preserved. Additionally, we found two key limitations in the prediction of genetic regulatory networks using DNA microarray data, the first is the sufficiency of sample size and the second is the complexity of network structures may not be captured without additional data at the protein level. Those limitations are present in all prediction methods which used only DNA microarray data.Comment: 38 pages, 3 figure

    Bayesian Networks for Max-linear Models

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    We study Bayesian networks based on max-linear structural equations as introduced in Gissibl and Kl\"uppelberg [16] and provide a summary of their independence properties. In particular we emphasize that distributions for such networks are generally not faithful to the independence model determined by their associated directed acyclic graph. In addition, we consider some of the basic issues of estimation and discuss generalized maximum likelihood estimation of the coefficients, using the concept of a generalized likelihood ratio for non-dominated families as introduced by Kiefer and Wolfowitz [21]. Finally we argue that the structure of a minimal network asymptotically can be identified completely from observational data.Comment: 18 page
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