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Parameterized Complexity
, 1998
"... the rapidly developing systematic connections between FPT and useful heuristic algorithms  a new and exciting bridge between the theory of computing and computing in practice. The organizers of the seminar strongly believe that knowledge of parameterized complexity techniques and results belongs ..."
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Cited by 1218 (75 self)
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the rapidly developing systematic connections between FPT and useful heuristic algorithms  a new and exciting bridge between the theory of computing and computing in practice. The organizers of the seminar strongly believe that knowledge of parameterized complexity techniques and results belongs into the toolkit of every algorithm designer. The purpose of the seminar was to bring together leading experts from all over the world, and from the diverse areas of computer science that have been attracted to this new framework. The seminar was intended as the rst larger international meeting with a specic focus on parameterized complexity, and it hopefully serves as a driving force in the development of the eld. 1 We had 49 participants from Australia, Canada, India, Israel, New Zealand, USA, and various European countries. During the workshop 25 lectures were given. Moreover, one night session was devoted to open problems and Thursday was basically used for problem discussion
A Partial KArboretum of Graphs With Bounded Treewidth
 J. Algorithms
, 1998
"... The notion of treewidth has seen to be a powerful vehicle for many graph algorithmic studies. This survey paper wants to give an overview of many classes of graphs that can be seen to have a uniform upper bound on the treewidth of graphs in the class. Also, some mutual relations between such classes ..."
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Cited by 328 (34 self)
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The notion of treewidth has seen to be a powerful vehicle for many graph algorithmic studies. This survey paper wants to give an overview of many classes of graphs that can be seen to have a uniform upper bound on the treewidth of graphs in the class. Also, some mutual relations between such classes are discussed.
Discovering Statistically Significant Biclusters in Gene Expression Data
 In Proceedings of ISMB 2002
, 2002
"... In gene expression data, a bicluster is a subset of the genes exhibiting consistent patterns over a subset of the conditions. We propose a new method to detect significant biclusters in large expression datasets. Our approach is graph theoretic coupled with statistical modelling of the data. Under p ..."
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Cited by 299 (4 self)
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In gene expression data, a bicluster is a subset of the genes exhibiting consistent patterns over a subset of the conditions. We propose a new method to detect significant biclusters in large expression datasets. Our approach is graph theoretic coupled with statistical modelling of the data. Under plausible assumptions, our algorithm is polynomial and is guaranteed to find the most significant biclusters. We tested our method on a collection of yeast expression profiles and on a human cancer dataset. Cross validation results show high specificity in assigning function to genes based on their biclusters, and we are able to annotate in this way 196 uncharacterized yeast genes. We also demonstrate how the biclusters lead to detecting new concrete biological associations. In cancer data we are able to detect and relate finer tissue types than was previously possible. We also show that the method outperforms the biclustering algorithm of Cheng and Church (2000).
The NPcompleteness column: an ongoing guide
 JOURNAL OF ALGORITHMS
, 1987
"... This is the nineteenth edition of a (usually) quarterly column that covers new developments in the theory of NPcompleteness. The presentation is modeled on that used by M. R. Garey and myself in our book "Computers and Intractability: A Guide to the Theory of NPCompleteness," W. H. Freem ..."
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Cited by 242 (0 self)
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This is the nineteenth edition of a (usually) quarterly column that covers new developments in the theory of NPcompleteness. The presentation is modeled on that used by M. R. Garey and myself in our book "Computers and Intractability: A Guide to the Theory of NPCompleteness," W. H. Freeman & Co., New York, 1979 (hereinafter referred to as "[G&J]"; previous columns will be referred to by their dates). A background equivalent to that provided by [G&J] is assumed, and, when appropriate, crossreferences will be given to that book and the list of problems (NPcomplete and harder) presented there. Readers who have results they would like mentioned (NPhardness, PSPACEhardness, polynomialtimesolvability, etc.) or open problems they would like publicized, should
Modelling gene expression data using dynamic bayesian networks
, 1999
"... Recently, there has been much interest in reverse engineering genetic networks from time series data. In this paper, we show that most of the proposed discrete time models — including the boolean network model [Kau93, SS96], the linear model of D’haeseleer et al. [DWFS99], and the nonlinear model of ..."
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Cited by 223 (1 self)
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Recently, there has been much interest in reverse engineering genetic networks from time series data. In this paper, we show that most of the proposed discrete time models — including the boolean network model [Kau93, SS96], the linear model of D’haeseleer et al. [DWFS99], and the nonlinear model of Weaver et al. [WWS99] — are all special cases of a general class of models called Dynamic Bayesian Networks (DBNs). The advantages of DBNs include the ability to model stochasticity, to incorporate prior knowledge, and to handle hidden variables and missing data in a principled way. This paper provides a review of techniques for learning DBNs. Keywords: Genetic networks, boolean networks, Bayesian networks, neural networks, reverse engineering, machine learning. 1
On the desirability of acyclic database schemes
, 1983
"... A class of database schemes, called acychc, was recently introduced. It is shown that this class has a number of desirable properties. In particular, several desirable properties that have been studied by other researchers m very different terms are all shown to be eqmvalent to acydicity. In additi ..."
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Cited by 206 (2 self)
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A class of database schemes, called acychc, was recently introduced. It is shown that this class has a number of desirable properties. In particular, several desirable properties that have been studied by other researchers m very different terms are all shown to be eqmvalent to acydicity. In addition, several equivalent charactenzauons of the class m terms of graphs and hypergraphs are given, and a smaple algorithm for determining acychclty is presented. Also given are several eqmvalent characterizations of those sets M of multivalued dependencies such that M is the set of muRlvalued dependencies that are the consequences of a given join dependency. Several characterizations for a conflictfree (in the sense of Lien) set of muluvalued dependencies are provided.
Axioms for probability and belieffunction propagation
 Uncertainty in Artificial Intelligence
, 1990
"... In this paper, we describe an abstract framework and axioms under which exact local computation of marginals is possible. The primitive objects of the framework are variables and valuations. The primitive operators of the framework are combination and marginalization. These operate on valuations. We ..."
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Cited by 162 (24 self)
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In this paper, we describe an abstract framework and axioms under which exact local computation of marginals is possible. The primitive objects of the framework are variables and valuations. The primitive operators of the framework are combination and marginalization. These operate on valuations. We state three axioms for these operators and we derive the possibility of local computation from the axioms. Next, we describe a propagation scheme for computing marginals of a valuation when we have a factorization of the valuation on a hypertree. Finally we show how the problem of computing marginals of joint probability distributions and joint belief functions fits the general framework. 1.
A unified approach to approximating resource allocation and scheduling
 Journal of the ACM
, 2000
"... We present a general framework for solving resource allocation and scheduling problems. Given a resource of fixed size, we present algorithms that approximate the maximum throughput or the minimum loss by a constant factor. Our approximation factors apply to many problems, among which are: (i) real ..."
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Cited by 157 (23 self)
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We present a general framework for solving resource allocation and scheduling problems. Given a resource of fixed size, we present algorithms that approximate the maximum throughput or the minimum loss by a constant factor. Our approximation factors apply to many problems, among which are: (i) realtime scheduling of jobs on parallel machines, (ii) bandwidth allocation for sessions between two endpoints, (iii) general caching, (iv) dynamic storage allocation, and (v) bandwidth allocation on optical line and ring topologies. For some of these problems we provide the first constant factor approximation algorithm. Our algorithms are simple and efficient and are based on the localratio technique. We note that they can equivalently be interpreted within the primaldual schema.
Register Allocation via Graph Coloring
, 1992
"... Chaitin and his colleagues at IBM in Yorktown Heights built the first global register allocator based on graph coloring. This thesis describes a series of improvements and extensions to the Yorktown allocator. There are four primary results: Optimistic coloring Chaitin's coloring heuristic pes ..."
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Cited by 157 (4 self)
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Chaitin and his colleagues at IBM in Yorktown Heights built the first global register allocator based on graph coloring. This thesis describes a series of improvements and extensions to the Yorktown allocator. There are four primary results: Optimistic coloring Chaitin's coloring heuristic pessimistically assumes any node of high degree will not be colored and must therefore be spilled. By optimistically assuming that nodes of high degree will receive colors, I often achieve lower spill costs and faster code; my results are never worse. Coloring pairs The pessimism of Chaitin's coloring heuristic is emphasized when trying to color register pairs. My heuristic handles pairs as a natural consequence of its optimism. Rematerialization Chaitin et al. introduced the idea of rematerialization to avoid the expense of spilling and reloading certain simple values. By propagating rematerialization information around the SSA graph using a simple variation of Wegman and Zadeck's constant propag...