Algorithmic and Hardness Results for the Colorful Components Problems

In this paper we investigate the colorful components framework, motivated by applications emerging from comparative genomics. The general goal is to remove a collection of edges from an undirected vertex-colored graph $G$ such that in the resulting graph $G'$ all the connected components are colorful (i.e., any two vertices of the same color belong to different connected components). We want $G'$ to optimize an objective function, the selection of this function being specific to each problem in the framework. We analyze three objective functions, and thus, three different problems, which are believed to be relevant for the biological applications: minimizing the number of singleton vertices, maximizing the number of edges in the transitive closure, and minimizing the number of connected components. Our main result is a polynomial time algorithm for the first problem. This result disproves the conjecture of Zheng et al. that the problem is $NP$-hard (assuming $P \neq NP$). Then, we show that the second problem is $APX$-hard, thus proving and strengthening the conjecture of Zheng et al. that the problem is $NP$-hard. Finally, we show that the third problem does not admit polynomial time approximation within a factor of $|V|^{1/14 - \epsilon}$ for any $\epsilon > 0$, assuming $P \neq NP$ (or within a factor of $|V|^{1/2 - \epsilon}$, assuming $ZPP \neq NP$).Comment: 18 pages, 3 figure

Approximating the Minimum Equivalent Digraph

The MEG (minimum equivalent graph) problem is, given a directed graph, to find a small subset of the edges that maintains all reachability relations between nodes. The problem is NP-hard. This paper gives an approximation algorithm with performance guarantee of pi^2/6 ~ 1.64. The algorithm and its analysis are based on the simple idea of contracting long cycles. (This result is strengthened slightly in ``On strongly connected digraphs with bounded cycle length'' (1996).) The analysis applies directly to 2-Exchange, a simple ``local improvement'' algorithm, showing that its performance guarantee is 1.75.Comment: conference version in ACM-SIAM Symposium on Discrete Algorithms (1994

Computing the Similarity Between Moving Curves

In this paper we study similarity measures for moving curves which can, for example, model changing coastlines or retreating glacier termini. Points on a moving curve have two parameters, namely the position along the curve as well as time. We therefore focus on similarity measures for surfaces, specifically the Fr\'echet distance between surfaces. While the Fr\'echet distance between surfaces is not even known to be computable, we show for variants arising in the context of moving curves that they are polynomial-time solvable or NP-complete depending on the restrictions imposed on how the moving curves are matched. We achieve the polynomial-time solutions by a novel approach for computing a surface in the so-called free-space diagram based on max-flow min-cut duality

The Complexity Landscape of Fixed-Parameter Directed Steiner Network Problems

Given a directed graph G and a list (s_1, t_1), ..., (s_k, t_k) of terminal pairs, the Directed Steiner Network problem asks for a minimum-cost subgraph of G that contains a directed s_i -> t_i path for every 1 <= i <= k. The special case Directed Steiner Tree (when we ask for paths from a root r to terminals t_1, . . .t_k) is known to be fixed-parameter tractable parameterized by the number of terminals, while the special case Strongly Connected Steiner Subgraph (when we ask for a path from every t_i to every other t_j ) is known to be W[1]-hard parameterized by the number of terminals. We systematically explore the complexity landscape of directed Steiner problems to fully understand which other special cases are FPT or W[1]-hard. Formally, if H is a class of directed graphs, then we look at the special case of Directed Steiner Network where the list (s_1, t_1), ..., (s_k, t_k) of requests form a directed graph that is a member of H. Our main result is a complete characterization of the classes H resulting in fixed-parameter tractable special cases: we show that if every pattern in H has the combinatorial property of being "transitively equivalent to a bounded-length caterpillar with a bounded number of extra edges," then the problem is FPT, and it is W[1]-hard for every recursively enumerable H not having this property. This complete dichotomy unifies and generalizes the known results showing that Directed Steiner Tree is FPT [Dreyfus and Wagner, Networks 1971], Strongly Connected Steiner Subgraph is W[1]-hard [Guo et al., SIAM J. Discrete Math. 2011], and Directed Steiner Network is solvable in polynomial-time for constant number of terminals [Feldman and Ruhl, SIAM J. Comput. 2006], and moreover reveals a large continent of tractable cases that were not known before