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14
Complexity and Algorithms for Reasoning About Time: A GraphTheoretic Approach
, 1992
"... Temporal events are regarded here as intervals on a time line. This paper deals with problems in reasoning about such intervals when the precise topological relationship between them is unknown or only partially specified. This work unifies notions of interval algebras in artificial intelligence ..."
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Cited by 100 (11 self)
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Temporal events are regarded here as intervals on a time line. This paper deals with problems in reasoning about such intervals when the precise topological relationship between them is unknown or only partially specified. This work unifies notions of interval algebras in artificial intelligence with those of interval orders and interval graphs in combinatorics. The satisfiability, minimal labeling, all solutions and all realizations problems are considered for temporal (interval) data. Several versions are investigated by restricting the possible interval relationships yielding different complexity results. We show that even when the temporal data comprises of subsets of relations based on intersection and precedence only, the satisfiability question is NPcomplete. On the positive side, we give efficient algorithms for several restrictions of the problem. In the process, the interval graph sandwich problem is introduced, and is shown to be NPcomplete. This problem is als...
Four Strikes against Physical Mapping of DNA
 JOURNAL OF COMPUTATIONAL BIOLOGY
, 1993
"... Physical Mapping is a central problem in molecular biology ... and the human genome project. The problem is to reconstruct the relative position of fragments of DNA along the genome from information on their pairwise overlaps. We show that four simplified models of the problem lead to NPcomplete ..."
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Cited by 68 (8 self)
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Physical Mapping is a central problem in molecular biology ... and the human genome project. The problem is to reconstruct the relative position of fragments of DNA along the genome from information on their pairwise overlaps. We show that four simplified models of the problem lead to NPcomplete decision problems: Colored unit interval graph completion, the maximum interval (or unit interval) subgraph, the pathwidth of a bipartite graph, and the kconsecutive ones problem for k >= 2. These models have been chosen to reflect various features typical in biological data, including false negative and positive errors, small width of the map and chimericism.
Pathwidth, Bandwidth and Completion Problems to Proper Interval Graphs with Small Cliques
 SIAM Journal on Computing
, 1996
"... We study two related problems motivated by molecular biology: ffl Given a graph G and a constant k, does there exist a supergraph G of G which is a unit interval graph and has clique size at most k? ffl Given a graph G and a proper kcoloring c of G, does there exist a supergraph We show th ..."
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Cited by 32 (6 self)
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We study two related problems motivated by molecular biology: ffl Given a graph G and a constant k, does there exist a supergraph G of G which is a unit interval graph and has clique size at most k? ffl Given a graph G and a proper kcoloring c of G, does there exist a supergraph We show that those problems are polynomial for fixed k. On the other hand we prove that the first problem is equivalent to deciding if the bandwidth of G is at most k \Gamma 1. Hence, it is NPhard, and W [t]hard for all t. We also show that the second problem is W [1]hard. This implies that for fixed k, both of the problems are unlikely to have an O(n ) algorithm, where ff is a constant independent of k.
RangeFree Ranking in Sensors Networks and Its Applications to Localization
 Proceedings of 3 rdAdHoc, Mobile, and Wireless Networks
, 2004
"... Abstract. We address the question of finding sensors ’ coordinates, or at least an approximation of them, when the sensors ’ abilities are very weak. In a d dimensional space, we define an extremely relaxed notion of coordinates along dimension i. The ranki of a sensor s is the number of sensors wit ..."
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Cited by 10 (0 self)
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Abstract. We address the question of finding sensors ’ coordinates, or at least an approximation of them, when the sensors ’ abilities are very weak. In a d dimensional space, we define an extremely relaxed notion of coordinates along dimension i. The ranki of a sensor s is the number of sensors with ithcoordinate less than the icoordinate of s. In this paper we provide a theoretical foundation for sensor ranking, when one assumes that a few anchor sensors know their locations and that the others determine their rank only by exchanging information. We show that the rank problem can be solved in linear time in R and that it is NPHard in R 2. We also study the usual localization problem and show that in general one cannot solve it; unless one knows a priori information on the sensors distribution. 1
Inferring Ordered Trees from Local Constraints
"... We consider a problem of inferring an ordered tree from a set of local constraints on its leaves which we term as the ordered local consensus tree problem. Using our efficient decremental interval union algorithm, we show that the ordered local consensus tree problem for m constraints on n leaves ..."
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Cited by 7 (4 self)
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We consider a problem of inferring an ordered tree from a set of local constraints on its leaves which we term as the ordered local consensus tree problem. Using our efficient decremental interval union algorithm, we show that the ordered local consensus tree problem for m constraints on n leaves can be deterministically solved in time O((m+n) log n): We also show that the related optimization problem of constructing an ordered local consensus tree for the maximum number of 3leaf constraints is solvable in cubic time.
Satisfiability Problems on Intervals and Unit Intervals
 Theoretical Computer Science
, 1997
"... For an interval graph with some additional order constraints between pairs of nonintersecting intervals, we give a linear time algorithm to determine if there exists a realization which respects the order constraints. Previous algorithms for this problem (known also as seriation with side constrain ..."
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Cited by 5 (1 self)
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For an interval graph with some additional order constraints between pairs of nonintersecting intervals, we give a linear time algorithm to determine if there exists a realization which respects the order constraints. Previous algorithms for this problem (known also as seriation with side constraints) required quadratic time. This problem contains as subproblems interval graph and interval order recognition. On the other hand, it is a special case of the interval satisfiability problem, which is concerned with the realizability of a set of intervals along a line, subject to precedence and intersection constraints. We study such problems for all possible restrictions on the types of constraints, when all intervals must have the same length. We give efficient algorithms for several restrictions of the problem, and show the NPcompleteness of another restriction. 1 Introduction Two intervals x; y on the real line may either intersect or one of them is completely to the left of the othe...
Interval Graphs with Side (and Size) Constraints
 In Proc. of the Third Annual European Symp. on Algorithms, (ESA 95) Corfu, Greece
, 1995
"... . We study problems of determining whether a given interval graph has a realization which satisfies additional given constraints. Such problems occur frequently in applications where entities are modeled as intervals along a line (events along a time line, DNA segments along a chromosome, etc.). ..."
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Cited by 3 (1 self)
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. We study problems of determining whether a given interval graph has a realization which satisfies additional given constraints. Such problems occur frequently in applications where entities are modeled as intervals along a line (events along a time line, DNA segments along a chromosome, etc.). When the additional information is order constraints on pairs of disjoint intervals, we give a linear time algorithm. Extant algorithms for this problem (known also as seriation with side constraints) required quadratic time. When the constraints are bounds on distances between endpoints, and the graph admits a unique clique order, we show that the problem is polynomial. However, we show that even when the lengths of all intervals are precisely predetermined, the problem is NPcomplete. We also study unit interval satisfiability problems, which are concerned with the realizability of a set of unit intervals along a line, subject to precedence and intersection constraints. For all po...
Realizing Interval Graphs With Size And Distance Constraints
 SIAM Journal on Discrete Mathematics
, 1997
"... . We study the following problem: Given an interval graph, does it have a realization which satisfies additional constraints on the distances between interval endpoints? This problem arises in numerous applications in which topological information on intersection of pairs of intervals is accompanied ..."
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Cited by 3 (0 self)
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. We study the following problem: Given an interval graph, does it have a realization which satisfies additional constraints on the distances between interval endpoints? This problem arises in numerous applications in which topological information on intersection of pairs of intervals is accompanied by additional metric information on their order, distance or sizes. An important application is physical mapping, a central challenge in the human genome project. Our results are: (1) A polynomial algorithm for the problem on interval graphs which admit a unique clique order (UCO graphs). This class of graphs properly contains all prime interval graphs. (2) In case all constraints are upper and lower bounds on individual interval lengths, the problem on UCO graphs is linearly equivalent to deciding if a system of difference inequalities is feasible. (3) Even if all the constraints are prescribed lengths of individual intervals, the problem is NPcomplete. Hence, problems (1) and (2) are als...