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37,118
Exact algorithms and applications for Treelike Weighted Set Cover
 JOURNAL OF DISCRETE ALGORITHMS
, 2006
"... We introduce an NPcomplete special case of the Weighted Set Cover problem and show its fixedparameter tractability with respect to the maximum subset size, a parameter that appears to be small in relevant applications. More precisely, in this practically relevant variant we require that the given ..."
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Cited by 10 (5 self)
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to the problem of finding a minimum edge cover in an edgeweighted acyclic hypergraph. Our main result is an algorithm running in O(3 k ·mn) time where k denotes the maximum subset size, n: = S, and m: = C. The algorithm also implies a fixedparameter tractability result for the NPcomplete Multicut in Trees
Graphical models, exponential families, and variational inference
, 2008
"... The formalism of probabilistic graphical models provides a unifying framework for capturing complex dependencies among random variables, and building largescale multivariate statistical models. Graphical models have become a focus of research in many statistical, computational and mathematical fiel ..."
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Cited by 800 (26 self)
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The formalism of probabilistic graphical models provides a unifying framework for capturing complex dependencies among random variables, and building largescale multivariate statistical models. Graphical models have become a focus of research in many statistical, computational and mathematical fields, including bioinformatics, communication theory, statistical physics, combinatorial optimization, signal and image processing, information retrieval and statistical machine learning. Many problems that arise in specific instances — including the key problems of computing marginals and modes of probability distributions — are best studied in the general setting. Working with exponential family representations, and exploiting the conjugate duality between the cumulant function and the entropy for exponential families, we develop general variational representations of the problems of computing likelihoods, marginal probabilities and most probable configurations. We describe how a wide varietyof algorithms — among them sumproduct, cluster variational methods, expectationpropagation, mean field methods, maxproduct and linear programming relaxation, as well as conic programming relaxations — can all be understood in terms of exact or approximate forms of these variational representations. The variational approach provides a complementary alternative to Markov chain Monte Carlo as a general source of approximation methods for inference in largescale statistical models.
Community detection in graphs
, 2009
"... The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of th ..."
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Cited by 801 (1 self)
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The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices
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 "flat " 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
A Framework for Dynamic Graph Drawing
 CONGRESSUS NUMERANTIUM
, 1992
"... Drawing graphs is an important problem that combines flavors of computational geometry and graph theory. Applications can be found in a variety of areas including circuit layout, network management, software engineering, and graphics. The main contributions of this paper can be summarized as follows ..."
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Cited by 627 (44 self)
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Drawing graphs is an important problem that combines flavors of computational geometry and graph theory. Applications can be found in a variety of areas including circuit layout, network management, software engineering, and graphics. The main contributions of this paper can be summarized as follows: ffl We devise a model for dynamic graph algorithms, based on performing queries and updates on an implicit representation of the drawing, and we show its applications. ffl We present several efficient dynamic drawing algorithms for trees, seriesparallel digraphs, planar stdigraphs, and planar graphs. These algorithms adopt a variety of representations (e.g., straightline, polyline, visibility), and update the drawing in a smooth way.
Constraint Networks
, 1992
"... Constraintbased reasoning is a paradigm for formulating knowledge as a set of constraints without specifying the method by which these constraints are to be satisfied. A variety of techniques have been developed for finding partial or complete solutions for different kinds of constraint expression ..."
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Cited by 1149 (43 self)
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Constraintbased reasoning is a paradigm for formulating knowledge as a set of constraints without specifying the method by which these constraints are to be satisfied. A variety of techniques have been developed for finding partial or complete solutions for different kinds of constraint expressions. These have been successfully applied to diverse tasks such as design, diagnosis, truth maintenance, scheduling, spatiotemporal reasoning, logic programming and user interface. Constraint networks are graphical representations used to guide strategies for solving constraint satisfaction problems (CSPs).
An introduction to variational methods for graphical models
 TO APPEAR: M. I. JORDAN, (ED.), LEARNING IN GRAPHICAL MODELS
"... ..."
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 729 (15 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.
Bayesian Network Classifiers
, 1997
"... Recent work in supervised learning has shown that a surprisingly simple Bayesian classifier with strong assumptions of independence among features, called naive Bayes, is competitive with stateoftheart classifiers such as C4.5. This fact raises the question of whether a classifier with less restr ..."
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Cited by 788 (23 self)
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Recent work in supervised learning has shown that a surprisingly simple Bayesian classifier with strong assumptions of independence among features, called naive Bayes, is competitive with stateoftheart classifiers such as C4.5. This fact raises the question of whether a classifier with less restrictive assumptions can perform even better. In this paper we evaluate approaches for inducing classifiers from data, based on the theory of learning Bayesian networks. These networks are factored representations of probability distributions that generalize the naive Bayesian classifier and explicitly represent statements about independence. Among these approaches we single out a method we call Tree Augmented Naive Bayes (TAN), which outperforms naive Bayes, yet at the same time maintains the computational simplicity (no search involved) and robustness that characterize naive Bayes. We experimentally tested these approaches, using problems from the University of California at Irvine repository, and compared them to C4.5, naive Bayes, and wrapper methods for feature selection.
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