Inapproximability of maximal strip recovery

In comparative genomic, the first step of sequence analysis is usually to decompose two or more genomes into syntenic blocks that are segments of homologous chromosomes. For the reliable recovery of syntenic blocks, noise and ambiguities in the genomic maps need to be removed first. Maximal Strip Recovery (MSR) is an optimization problem proposed by Zheng, Zhu, and Sankoff for reliably recovering syntenic blocks from genomic maps in the midst of noise and ambiguities. Given $d$ genomic maps as sequences of gene markers, the objective of \msr{d} is to find $d$ subsequences, one subsequence of each genomic map, such that the total length of syntenic blocks in these subsequences is maximized. For any constant $d \ge 2$, a polynomial-time 2d-approximation for \msr{d} was previously known. In this paper, we show that for any $d \ge 2$, \msr{d} is APX-hard, even for the most basic version of the problem in which all gene markers are distinct and appear in positive orientation in each genomic map. Moreover, we provide the first explicit lower bounds on approximating \msr{d} for all $d \ge 2$. In particular, we show that \msr{d} is NP-hard to approximate within $\Omega(d/\log d)$. From the other direction, we show that the previous 2d-approximation for \msr{d} can be optimized into a polynomial-time algorithm even if $d$ is not a constant but is part of the input. We then extend our inapproximability results to several related problems including \cmsr{d}, \gapmsr{\delta}{d}, and \gapcmsr{\delta}{d}.Comment: A preliminary version of this paper appeared in two parts in the Proceedings of the 20th International Symposium on Algorithms and Computation (ISAAC 2009) and the Proceedings of the 4th International Frontiers of Algorithmics Workshop (FAW 2010

Distributed Approximation of Maximum Independent Set and Maximum Matching

We present a simple distributed $\Delta$-approximation algorithm for maximum weight independent set (MaxIS) in the $\mathsf{CONGEST}$ model which completes in $O(\texttt{MIS}(G)\cdot \log W)$ rounds, where $\Delta$ is the maximum degree, $\texttt{MIS}(G)$ is the number of rounds needed to compute a maximal independent set (MIS) on $G$, and $W$ is the maximum weight of a node. %Whether our algorithm is randomized or deterministic depends on the \texttt{MIS} algorithm used as a black-box. Plugging in the best known algorithm for MIS gives a randomized solution in $O(\log n \log W)$ rounds, where $n$ is the number of nodes. We also present a deterministic $O(\Delta +\log^* n)$-round algorithm based on coloring. We then show how to use our MaxIS approximation algorithms to compute a $2$-approximation for maximum weight matching without incurring any additional round penalty in the $\mathsf{CONGEST}$ model. We use a known reduction for simulating algorithms on the line graph while incurring congestion, but we show our algorithm is part of a broad family of \emph{local aggregation algorithms} for which we describe a mechanism that allows the simulation to run in the $\mathsf{CONGEST}$ model without an additional overhead. Next, we show that for maximum weight matching, relaxing the approximation factor to ($2+\varepsilon$) allows us to devise a distributed algorithm requiring $O(\frac{\log \Delta}{\log\log\Delta})$ rounds for any constant $\varepsilon>0$. For the unweighted case, we can even obtain a $(1+\varepsilon)$-approximation in this number of rounds. These algorithms are the first to achieve the provably optimal round complexity with respect to dependency on $\Delta$

On the fine-grained complexity of rainbow coloring

The Rainbow k-Coloring problem asks whether the edges of a given graph can be colored in $k$ colors so that every pair of vertices is connected by a rainbow path, i.e., a path with all edges of different colors. Our main result states that for any $k\ge 2$, there is no algorithm for Rainbow k-Coloring running in time $2^{o(n^{3/2})}$, unless ETH fails. Motivated by this negative result we consider two parameterized variants of the problem. In Subset Rainbow k-Coloring problem, introduced by Chakraborty et al. [STACS 2009, J. Comb. Opt. 2009], we are additionally given a set $S$ of pairs of vertices and we ask if there is a coloring in which all the pairs in $S$ are connected by rainbow paths. We show that Subset Rainbow k-Coloring is FPT when parameterized by $|S|$. We also study Maximum Rainbow k-Coloring problem, where we are additionally given an integer $q$ and we ask if there is a coloring in which at least $q$ anti-edges are connected by rainbow paths. We show that the problem is FPT when parameterized by $q$ and has a kernel of size $O(q)$ for every $k\ge 2$ (thus proving that the problem is FPT), extending the result of Ananth et al. [FSTTCS 2011]

Approximation Algorithms for Polynomial-Expansion and Low-Density Graphs

We study the family of intersection graphs of low density objects in low dimensional Euclidean space. This family is quite general, and includes planar graphs. We prove that such graphs have small separators. Next, we present efficient $(1+\varepsilon)$-approximation algorithms for these graphs, for Independent Set, Set Cover, and Dominating Set problems, among others. We also prove corresponding hardness of approximation for some of these optimization problems, providing a characterization of their intractability in terms of density

Motif Clustering and Overlapping Clustering for Social Network Analysis

Motivated by applications in social network community analysis, we introduce a new clustering paradigm termed motif clustering. Unlike classical clustering, motif clustering aims to minimize the number of clustering errors associated with both edges and certain higher order graph structures (motifs) that represent "atomic units" of social organizations. Our contributions are two-fold: We first introduce motif correlation clustering, in which the goal is to agnostically partition the vertices of a weighted complete graph so that certain predetermined "important" social subgraphs mostly lie within the same cluster, while "less relevant" social subgraphs are allowed to lie across clusters. We then proceed to introduce the notion of motif covers, in which the goal is to cover the vertices of motifs via the smallest number of (near) cliques in the graph. Motif cover algorithms provide a natural solution for overlapping clustering and they also play an important role in latent feature inference of networks. For both motif correlation clustering and its extension introduced via the covering problem, we provide hardness results, algorithmic solutions and community detection results for two well-studied social networks

Approximation Algorithms for Multi-Criteria Traveling Salesman Problems

In multi-criteria optimization problems, several objective functions have to be optimized. Since the different objective functions are usually in conflict with each other, one cannot consider only one particular solution as the optimal solution. Instead, the aim is to compute a so-called Pareto curve of solutions. Since Pareto curves cannot be computed efficiently in general, we have to be content with approximations to them. We design a deterministic polynomial-time algorithm for multi-criteria g-metric STSP that computes (min{1 +g, 2g^2/(2g^2 -2g +1)} + eps)-approximate Pareto curves for all 1/2<=g<=1. In particular, we obtain a (2+eps)-approximation for multi-criteria metric STSP. We also present two randomized approximation algorithms for multi-criteria g-metric STSP that achieve approximation ratios of (2g^3 +2g^2)/(3g^2 -2g +1) + eps and (1 +g)/(1 +3g -4g^2) + eps, respectively. Moreover, we present randomized approximation algorithms for multi-criteria g-metric ATSP (ratio 1/2 + g^3/(1 -3g^2) + eps) for g < 1/sqrt(3)), STSP with weights 1 and 2 (ratio 4/3) and ATSP with weights 1 and 2 (ratio 3/2). To do this, we design randomized approximation schemes for multi-criteria cycle cover and graph factor problems.Comment: To appear in Algorithmica. A preliminary version has been presented at the 4th Workshop on Approximation and Online Algorithms (WAOA 2006

The Minimum Wiener Connector

The Wiener index of a graph is the sum of all pairwise shortest-path distances between its vertices. In this paper we study the novel problem of finding a minimum Wiener connector: given a connected graph $G=(V,E)$ and a set $Q\subseteq V$ of query vertices, find a subgraph of $G$ that connects all query vertices and has minimum Wiener index. We show that The Minimum Wiener Connector admits a polynomial-time (albeit impractical) exact algorithm for the special case where the number of query vertices is bounded. We show that in general the problem is NP-hard, and has no PTAS unless $\mathbf{P} = \mathbf{NP}$. Our main contribution is a constant-factor approximation algorithm running in time $\widetilde{O}(|Q||E|)$. A thorough experimentation on a large variety of real-world graphs confirms that our method returns smaller and denser solutions than other methods, and does so by adding to the query set $Q$ a small number of important vertices (i.e., vertices with high centrality).Comment: Published in Proceedings of the 2015 ACM SIGMOD International Conference on Management of Dat