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895
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 250 (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 191 (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
, 1985
"... 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 ..."
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Cited by 189 (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 161 (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
Reasoning about Qualitative Temporal Information
 Artificial Intelligence
, 1992
"... Representing and reasoning about incomplete and indefinite qualitative temporal information is an essential part of many artificial intelligence tasks. An intervalbased framework and a pointbased framework have been proposed for representing such temporal information. In this paper, we address ..."
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Cited by 137 (5 self)
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Representing and reasoning about incomplete and indefinite qualitative temporal information is an essential part of many artificial intelligence tasks. An intervalbased framework and a pointbased framework have been proposed for representing such temporal information. In this paper, we address two fundamental reasoning tasks that arise in applications of these frameworks: Given possibly indefinite and incomplete knowledge of the relationships between some intervals or points, (i) find a scenario that is consistent with the information provided, and (ii) find the feasible relations between all pairs of intervals or points. For the pointbased framework and a restricted version of the intervalbased framework, we give computationally efficient procedures for finding a consistent scenario and for finding the feasible relations. Our algorithms are marked improvements over the previously known algorithms. In particular, we develop an O(n 2 ) time algorithm for finding one co...
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 pessimis ..."
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Cited by 136 (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...
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 135 (17 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.
Simple heuristics for unit disk graphs
 NETWORKS
, 1995
"... Unit disk graphs are intersection graphs of circles of unit radius in the plane. We present simple and provably good heuristics for a number of classical NPhard optimization problems on unit disk graphs. The problems considered include maximum independent set, minimum vertex cover, minimum coloring ..."
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Cited by 125 (6 self)
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Unit disk graphs are intersection graphs of circles of unit radius in the plane. We present simple and provably good heuristics for a number of classical NPhard optimization problems on unit disk graphs. The problems considered include maximum independent set, minimum vertex cover, minimum coloring and minimum dominating set. We also present an online coloring heuristic which achieves a competitive ratio of 6 for unit disk graphs. Our heuristics do not need a geometric representation of unit disk graphs. Geometric representations are used only in establishing the performance guarantees of the heuristics. Several of our approximation algorithms can be extended to intersection graphs of circles of arbitrary radii in the plane, intersection graphs of regular polygons, and to intersection graphs of higher dimensional regular objects.
Energy minimization using multiple supply voltages
 In International Symposium on Low Power Electronics and Design
, 1996
"... AbstractWe present a dynamic programming technique for solving the multiple supply voltage scheduling problem in both nonpipelined and functionally pipelined datapaths. The scheduling problem refers to the assignment of a supply voltage level (selected from a xed and known number of voltage level ..."
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Cited by 121 (5 self)
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AbstractWe present a dynamic programming technique for solving the multiple supply voltage scheduling problem in both nonpipelined and functionally pipelined datapaths. The scheduling problem refers to the assignment of a supply voltage level (selected from a xed and known number of voltage levels) to each operation in a data ow graph so as to minimize the average energy consumption for given computation time or throughput constraints or both. The energy model is accurate and accounts for the input pattern dependencies, reconvergent fanout induced dependencies, and the energy cost of level shifters. Experimental results show that using three supply voltage levels on a number of standard benchmarks, an average energy saving of 40.19% (with a computation time constraint of 1.5 times the critical path delay) can be obtained compared to using a single supply voltage level.