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 NP-complete decision problems: Colored unit interval graph completion, the maximum interval (or unit interval) subgraph, the pathwidth of a bipartite graph, and the k-consecutive 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.

Various parameters of graphs connected to sparse matrix factorization and other applications can be approximated using an algorithm of Leighton et al. that finds vertex separators of graphs. The approximate values of the parameters, which include minimum front size, treewidth, pathwidth, and minimum elimination tree height, are no more than O(logn) (minimum front size and treewidth) and O(log^2 n) (pathwidth and minimum elimination tree height) times the optimal values. In addition, we show that unless P = NP there are no absolute approximation algorithms for any of the parameters.

In this paper we give, for all constants k, l, explicit algorithms, that given a graph G = (V; E) with a tree-decomposition of G with treewidth at most l, decide whether the treewidth (or pathwidth) of G is at most k, and if so, find a tree-decomposition or (path-decomposition) of G of width at most k, and that use O(|V|) time. In contrast with previous solutions, our algorithms do not rely on non-constructive reasoning, and are single exponential in k and l. This result can be combined with a result of Reed [37], yielding explicit O(n log n) algorithms for the problem, given a graph G, to determine whether the treewidth (or pathwidth) of G is at most k, and if so, to find a tree- (or path-)decomposition of width at most k (k constant). Also, Bodlaender [13] has used the result of this paper to obtain linear time algorithms for these problems. We also show that for all constants k, there exists a polynomial time algorithm, that, when given a graph G = (V; E) with treewidth k, computes the pathwidth of G and a minimum path decomposition of G.

We study the parameterized complexity of three NP-hard graph completion problems. The MINIMUM FILL-IN problem is to decide if a graph can be triangulated by adding at most k edges. We develop O(c m) and O(k mn + f(k)) algorithms for this problem on a graph with n vertices and m edges. Here f(k) is exponential in k and the constants hidden by the big-O notation are small and do not depend on k. In particular, this implies that the problem is fixed-parameter tractable (FPT). The PROPER

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 k-coloring 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 NP-hard, 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.

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This paper addresses memory requirement issues arising in implementations of algorithms on graphs of bounded treewidth. Such dynamic programming algorithms require a large data table for each vertex of a treedecomposition T of the input graph. We give a linear-time algorithm that finds the traversal order of T minimizing the number of tables stored simultaneously. We show that this minimum value is lower-bounded by the pathwidth of T plus one, and upper bounded by twice the pathwidth of T plus one. We also give a linear-time algorithm finding the depth-first traversal order minimizing the sum of the sizes of tables stored simultaneously.

We present a linear time algorithm which, given a tree, computes a linear layout optimal with respect to vertex separation. As a consequence optimal edge search strategies, optimal node search strategies, and optimal interval augmentations can be computed also in O(n) for trees. This improves the running time of former algorithms from O(n log n) to O(n) and answers two related open questions raised in [7] and [15].

Abstract. We prove that finding a rooted subtree with at least k leaves in a digraph is a fixed parameter tractable problem. A similar result holds for finding rooted spanning trees with many leaves in digraphs from a wide family L that includes all strong and acyclic digraphs. This settles completely an open question of Fellows and solves another one for digraphs in L. Our algorithms are based on the following combinatorial result which can be viewed as a generalization of many results for a ‘spanning tree with many leaves ’ in the undirected case, and which is interesting on its own: If a digraph D ∈ L of order n with minimum in-degree at least 3 contains a rooted spanning tree, then D contains one with at least (n/2) 1/5 − 1 leaves. 1

. We introduce the interval order polytope of a digraph D as the convex hull of interval order inducing arc subsets of D. Two general schemes for producing valid inequalities are presented. These schemes have been used implicitly for several polytopes and they are applied here to the interval order polytope. It is shown that almost all known classes of valid inequalities of the linear ordering polytope can be explained by the two classes derived from these schemes. We provide two applications of the interval order polytope to combinatorial optimization problems for which to our knowledge no polyhedral descriptions have been given so far. One of them is related to analysing DNA subsequences. 1 Introduction Interval orders and their cocomparability graphs, the interval graphs, play an important role not only in the theory of partially ordered sets and graph theory (cf., e.g., [Fis85]) but also for combinatorial optimization problems. This is due to the fact that each element is associat...