Some results on more flexible versions of Graph Motif

The problems studied in this paper originate from Graph Motif, a problem introduced in 2006 in the context of biological networks. Informally speaking, it consists in deciding if a multiset of colors occurs in a connected subgraph of a vertex-colored graph. Due to the high rate of noise in the biological data, more flexible definitions of the problem have been outlined. We present in this paper two inapproximability results for two different optimization variants of Graph Motif: one where the size of the solution is maximized, the other when the number of substitutions of colors to obtain the motif from the solution is minimized. We also study a decision version of Graph Motif where the connectivity constraint is replaced by the well known notion of graph modularity. While the problem remains NP-complete, it allows algorithms in FPT for biologically relevant parameterizations

Fast Witness Extraction Using a Decision Oracle

The gist of many (NP-)hard combinatorial problems is to decide whether a universe of $n$ elements contains a witness consisting of $k$ elements that match some prescribed pattern. For some of these problems there are known advanced algebra-based FPT algorithms which solve the decision problem but do not return the witness. We investigate techniques for turning such a YES/NO-decision oracle into an algorithm for extracting a single witness, with an objective to obtain practical scalability for large values of $n$. By relying on techniques from combinatorial group testing, we demonstrate that a witness may be extracted with $O(k\log n)$ queries to either a deterministic or a randomized set inclusion oracle with one-sided probability of error. Furthermore, we demonstrate through implementation and experiments that the algebra-based FPT algorithms are practical, in particular in the setting of the $k$-path problem. Also discussed are engineering issues such as optimizing finite field arithmetic.Comment: Journal version, 16 pages. Extended abstract presented at ESA'1

Quasipolynomial Representation of Transversal Matroids with Applications in Parameterized Complexity

Deterministic polynomial-time computation of a representation of a transversal matroid is a longstanding open problem. We present a deterministic computation of a so-called union representation of a transversal matroid in time quasipolynomial in the rank of the matroid. More precisely, we output a collection of linear matroids such that a set is independent in the transversal matroid if and only if it is independent in at least one of them. Our proof directly implies that if one is interested in preserving independent sets of size at most r, for a given rinmathbb{N}, but does not care whether larger independent sets are preserved, then a union representation can be computed deterministically in time quasipolynomial in r. This consequence is of independent interest, and sheds light on the power of union~representation. Our main result also has applications in Parameterized Complexity. First, it yields a fast computation of representative sets, and due to our relaxation in the context of r, this computation also extends to (standard) truncations. In turn, this computation enables to efficiently solve various problems, such as subcases of subgraph isomorphism, motif search and packing problems, in the presence of color lists. Such problems have been studied to model scenarios where pairs of elements to be matched may not be identical but only similar, and color lists aim to describe the set of compatible elements associated with each element

Univariate Ideal Membership Parameterized by Rank, Degree, and Number of Generators

Let F[X] be the polynomial ring over the variables X={x_1,x_2, ..., x_n}. An ideal I= generated by univariate polynomials {p_i(x_i)}_{i=1}^n is a univariate ideal. We study the ideal membership problem for the univariate ideals and show the following results. - Let f(X) in F[l_1, ..., l_r] be a (low rank) polynomial given by an arithmetic circuit where l_i : 1 be a univariate ideal. Given alpha in F^n, the (unique) remainder f(X) mod I can be evaluated at alpha in deterministic time d^{O(r)} * poly(n), where d=max {deg(f),deg(p_1)...,deg(p_n)}. This yields a randomized n^{O(r)} algorithm for minimum vertex cover in graphs with rank-r adjacency matrices. It also yields an n^{O(r)} algorithm for evaluating the permanent of a n x n matrix of rank r, over any field F. Over Q, an algorithm of similar run time for low rank permanent is due to Barvinok [Barvinok, 1996] via a different technique. - Let f(X)in F[X] be given by an arithmetic circuit of degree k (k treated as fixed parameter) and I=. We show that in the special case when I=, we obtain a randomized O^*(4.08^k) algorithm that uses poly(n,k) space. - Given f(X)in F[X] by an arithmetic circuit and I=, membership testing is W[1]-hard, parameterized by k. The problem is MINI[1]-hard in the special case when I=

The Graph Motif problem parameterized by the structure of the input graph

The Graph Motif problem was introduced in 2006 in the context of biological networks. It consists of deciding whether or not a multiset of colors occurs in a connected subgraph of a vertex-colored graph. Graph Motif has been mostly analyzed from the standpoint of parameterized complexity. The main parameters which came into consideration were the size of the multiset and the number of colors. Though, in the many applications of Graph Motif, the input graph originates from real-life and has structure. Motivated by this prosaic observation, we systematically study its complexity relatively to graph structural parameters. For a wide range of parameters, we give new or improved FPT algorithms, or show that the problem remains intractable. For the FPT cases, we also give some kernelization lower bounds as well as some ETH-based lower bounds on the worst case running time. Interestingly, we establish that Graph Motif is W[1]-hard (while in W[P]) for parameter max leaf number, which is, to the best of our knowledge, the first problem to behave this way.Comment: 24 pages, accepted in DAM, conference version in IPEC 201

The Graph Motif Problem Parameterized by the Structure of the Input Graph

The Graph Motif problem was introduced in 2006 in the context of biological networks. It consists of deciding whether or not a multiset of colors occurs in a connected subgraph of a vertex-colored graph. Graph Motif has been analyzed from the standpoint of parameterized complexity. The main parameters which came into consideration were the size of the multiset and the number of colors. Though, in the many applications of Graph Motif, the input graph originates from real-life and has structure. Motivated by this prosaic observation, we systematically study its complexity relatively to graph structural parameters. For a wide range of parameters, we give new or improved FPT algorithms, or show that the problem remains intractable. Interestingly, we establish that Graph Motif is W[1]-hard (while in W[P]) for parameter max leaf number, which is, to the best of our knowledge, the first problem to behave this way