Results 1  10
of
123
Parameterized Complexity: A Framework for Systematically Confronting Computational Intractability
 DIMACS Series in Discrete Mathematics and Theoretical Computer Science
, 1997
"... In this paper we give a programmatic overview of parameterized computational complexity in the broad context of the problem of coping with computational intractability. We give some examples of how fixedparameter tractability techniques can deliver practical algorithms in two different ways: (1) by ..."
Abstract

Cited by 87 (16 self)
 Add to MetaCart
In this paper we give a programmatic overview of parameterized computational complexity in the broad context of the problem of coping with computational intractability. We give some examples of how fixedparameter tractability techniques can deliver practical algorithms in two different ways: (1) by providing useful exact algorithms for small parameter ranges, and (2) by providing guidance in the design of heuristic algorithms. In particular, we describe an improved FPT kernelization algorithm for Vertex Cover, a practical FPT algorithm for the Maximum Agreement Subtree (MAST) problem parameterized by the number of species to be deleted, and new general heuristics for these problems based on FPT techniques. In the course of making this overview, we also investigate some structural and hardness issues. We prove that an important naturally parameterized problem in artificial intelligence, STRIPS Planning (where the parameter is the size of the plan) is complete for W [1]. As a corollary, this implies that kStep Reachability for Petri Nets is complete for W [1]. We describe how the concept of treewidth can be applied to STRIPS Planning and other problems of logic to obtain FPT results. We describe a surprising structural result concerning the top end of the parameterized complexity hierarchy: the naturally parameterized Graph kColoring problem cannot be resolved with respect to XP either by showing membership in XP, or by showing hardness for XP without settling the P = NP question one way or the other.
A Robust Model for Finding Optimal Evolutionary Trees
, 1993
"... Constructing evolutionary trees for species sets is a fundamental problem in computational biology. One of the standard models assumes the ability to compute distances between every pair of species and seeks to find an edgeweighted tree T in which the distance d T ij in the tree between the leaves ..."
Abstract

Cited by 83 (14 self)
 Add to MetaCart
(Show Context)
Constructing evolutionary trees for species sets is a fundamental problem in computational biology. One of the standard models assumes the ability to compute distances between every pair of species and seeks to find an edgeweighted tree T in which the distance d T ij in the tree between the leaves of T corresponding to the species i and j exactly equals the observed distance, d ij . When such a tree exists, this is expressed in the biological literature by saying that the distance function or matrix is additive, and trees can be constructed from additive distance matrices in O(n 2 ) time. Real distance data is hardly ever additive, and we therefore need ways of modeling the problem of finding the bestfit tree as an optimization problem. In this paper we present several natural and realistic ways of modeling the inaccuracies in the distance data. In one model we assume that we have upper and lower bounds for the distances between pairs of species and try to find an additive distanc...
Parameterized Computational Feasibility
 Feasible Mathematics II
, 1994
"... Many natural computational problems have input consisting of two or more parts. For example, the input might consist of a graph and a positive integer. For many natural problems we may view one of the inputs as a parameter and study how the complexity of the problem varies if the parameter is he ..."
Abstract

Cited by 65 (22 self)
 Add to MetaCart
Many natural computational problems have input consisting of two or more parts. For example, the input might consist of a graph and a positive integer. For many natural problems we may view one of the inputs as a parameter and study how the complexity of the problem varies if the parameter is held fixed. For many applications of computational problems involving such a parameter, only a small range of parameter values is of practical significance, so that fixedparameter complexity is a natural concern. In studying the complexity of such problems, it is therefore important to have a framework in which we can make qualitative distinctions about the contribution of the parameter to the complexity of the problem. In this paper we survey one such framework for investigating parameterized computational complexity and present a number of new results for this theory.
Graph Sandwich Problems
, 1994
"... The graph sandwich problem for property \Pi is defined as follows: Given two graphs G ) such that E ` E , is there a graph G = (V; E) such that E which satisfies property \Pi? Such problems generalize recognition problems and arise in various applications. Concentrating mainly o ..."
Abstract

Cited by 65 (8 self)
 Add to MetaCart
The graph sandwich problem for property \Pi is defined as follows: Given two graphs G ) such that E ` E , is there a graph G = (V; E) such that E which satisfies property \Pi? Such problems generalize recognition problems and arise in various applications. Concentrating mainly on properties characterizing subfamilies of perfect graphs, we give polynomial algorithms for several properties and prove the NPcompleteness of others. We describe
Subexponential parameterized algorithms on graphs of boundedgenus and Hminorfree Graphs
"... ... Building on these results, we develop subexponential fixedparameter algorithms for dominating set, vertex cover, and set cover in any class of graphs excluding a fixed graph H as a minor. Inparticular, this general category of graphs includes planar graphs, boundedgenus graphs, singlecrossing ..."
Abstract

Cited by 63 (22 self)
 Add to MetaCart
... Building on these results, we develop subexponential fixedparameter algorithms for dominating set, vertex cover, and set cover in any class of graphs excluding a fixed graph H as a minor. Inparticular, this general category of graphs includes planar graphs, boundedgenus graphs, singlecrossingminorfree graphs, and anyclass of graphs that is closed under taking minors. Specifically, the running time is 2O(pk)nh, where h is a constant depending onlyon H, which is polynomial for k = O(log² n). We introducea general approach for developing algorithms on Hminorfreegraphs, based on structural results about Hminorfree graphs at the
A PolynomialTime Algorithm for the Perfect Phylogeny Problem when the Number of Character States Is Fixed
 SIAM JOURNAL ON COMPUTING
, 1994
"... We present a polynomialtime algorithm for determining whether a set of species, described by the characters they exhibit, has a perfect phylogeny, assuming the maximum number of possible states for a character is fixed. This solves a longstanding open problem. Our result should be contrasted with ..."
Abstract

Cited by 62 (4 self)
 Add to MetaCart
We present a polynomialtime algorithm for determining whether a set of species, described by the characters they exhibit, has a perfect phylogeny, assuming the maximum number of possible states for a character is fixed. This solves a longstanding open problem. Our result should be contrasted with the proof by Steel and Bodlaender, Fellows, and Warnow that the perfect phylogeny problem is NPcomplete in general.
Beyond NPCompleteness for Problems of Bounded Width: Hardness for the W Hierarchy (Extended Abstract)
 In Proceedings of the 26th Annual ACM Symposium on the Theory of Computing
, 1994
"... The parameterized computational complexity of a collection of wellknown problems including: Bandwidth, Precedence constrained kprocessor scheduling, Longest Common Subsequence, DNA physical mapping (or Intervalizing colored graphs), Perfect phylogeny (or Triangulating colored graphs), Colored cutw ..."
Abstract

Cited by 60 (20 self)
 Add to MetaCart
(Show Context)
The parameterized computational complexity of a collection of wellknown problems including: Bandwidth, Precedence constrained kprocessor scheduling, Longest Common Subsequence, DNA physical mapping (or Intervalizing colored graphs), Perfect phylogeny (or Triangulating colored graphs), Colored cutwidth, and Feasible register assignment is explored. It is shown that these problems are hard for various levels of the W hierarchy. In the case of Precedence constrained kprocessor scheduling the results can be interpreted as providing substantial new complexity lower bounds on the outcome of [OPEN 8] of the Garey and Johnson list. We also obtain the conjectured "third strike" against Perfect phylogeny.
A Fast Algorithm for the Computation and Enumeration of Perfect Phylogenies
 SIAM JOURNAL ON COMPUTING
, 1995
"... The Perfect Phylogeny Problem is a classical problem in computational evolutionary biology, in which a set of species/taxa is described by a set of qualitative characters. In recent years, the problem has been shown to be NPComplete in general, while the different fixed parameter versions can e ..."
Abstract

Cited by 49 (8 self)
 Add to MetaCart
The Perfect Phylogeny Problem is a classical problem in computational evolutionary biology, in which a set of species/taxa is described by a set of qualitative characters. In recent years, the problem has been shown to be NPComplete in general, while the different fixed parameter versions can each be solved in polynomial time. In particular, Agarwala and FernandezBaca have developed an O(2 3r (nk 3 +k 4 )) algorithm for the perfect phylogeny problem for n species defined by k rstate characters. Since commonly the character data is drawn from alignments of molecular sequences, k is the length of the sequences and can thus be very large (in the hundreds or thousands). Thus, it is imperative to develop algorithms which run efficiently for large values of k. In this paper we make additional observations about the structure of the problem and produce an algorithm for the problem that runs in time O(2 2r k 2 n). We also show how it is possible to efficiently build a...
On the Complexity of DNA Physical Mapping
, 1994
"... The Physical Mapping Problem is to reconstruct the relative position of fragments (clones) of DNA along the genome from information on their pairwise overlaps. We show that two simplified versions of the problem belong to the class of NPcomplete problems, which are conjectured to be computationa ..."
Abstract

Cited by 47 (7 self)
 Add to MetaCart
The Physical Mapping Problem is to reconstruct the relative position of fragments (clones) of DNA along the genome from information on their pairwise overlaps. We show that two simplified versions of the problem belong to the class of NPcomplete problems, which are conjectured to be computationally intractable. In one version all clones have equal length, and in another, clone lengths may be arbitrary. The proof uses tools from graph theory and complexity.
A survey of computational methods for determining haplotypes
 Lecture Notes in Computer Science (2983): Computational Methods for SNPs and Haplotype Inference
, 2004
"... Abstract. It is widely anticipated that the study of variation in the human genome will provide a means of predicting risk of a variety of complex diseases. Single nucleotide polymorphisms (SNPs) are the most common form of genomic variation. Haplotypes have been suggested as one means for reducing ..."
Abstract

Cited by 38 (4 self)
 Add to MetaCart
(Show Context)
Abstract. It is widely anticipated that the study of variation in the human genome will provide a means of predicting risk of a variety of complex diseases. Single nucleotide polymorphisms (SNPs) are the most common form of genomic variation. Haplotypes have been suggested as one means for reducing the complexity of studying SNPs. In this paper we review some of the computational approaches that have been taking for determining haplotypes and suggest new approaches. 1