Fast Biclustering by Dual Parameterization

We study two clustering problems, Starforest Editing, the problem of adding and deleting edges to obtain a disjoint union of stars, and the generalization Bicluster Editing. We show that, in addition to being NP-hard, none of the problems can be solved in subexponential time unless the exponential time hypothesis fails. Misra, Panolan, and Saurabh (MFCS 2013) argue that introducing a bound on the number of connected components in the solution should not make the problem easier: In particular, they argue that the subexponential time algorithm for editing to a fixed number of clusters (p-Cluster Editing) by Fomin et al. (J. Comput. Syst. Sci., 80(7) 2014) is an exception rather than the rule. Here, p is a secondary parameter, bounding the number of components in the solution. However, upon bounding the number of stars or bicliques in the solution, we obtain algorithms which run in time $2^{5 \sqrt{pk}} + O(n+m)$ for p-Starforest Editing and $2^{O(p \sqrt{k} \log(pk))} + O(n+m)$ for p-Bicluster Editing. We obtain a similar result for the more general case of t-Partite p-Cluster Editing. This is subexponential in k for fixed number of clusters, since p is then considered a constant. Our results even out the number of multivariate subexponential time algorithms and give reasons to believe that this area warrants further study.Comment: Accepted for presentation at IPEC 201

From Gap-ETH to FPT-Inapproximability: Clique, Dominating Set, and More

We consider questions that arise from the intersection between the areas of polynomial-time approximation algorithms, subexponential-time algorithms, and fixed-parameter tractable algorithms. The questions, which have been asked several times (e.g., [Marx08, FGMS12, DF13]), are whether there is a non-trivial FPT-approximation algorithm for the Maximum Clique (Clique) and Minimum Dominating Set (DomSet) problems parameterized by the size of the optimal solution. In particular, letting $\text{OPT}$ be the optimum and $N$ be the size of the input, is there an algorithm that runs in $t(\text{OPT})\text{poly}(N)$ time and outputs a solution of size $f(\text{OPT})$, for any functions $t$ and $f$ that are independent of $N$ (for Clique, we want $f(\text{OPT})=\omega(1)$)? In this paper, we show that both Clique and DomSet admit no non-trivial FPT-approximation algorithm, i.e., there is no $o(\text{OPT})$-FPT-approximation algorithm for Clique and no $f(\text{OPT})$-FPT-approximation algorithm for DomSet, for any function $f$ (e.g., this holds even if $f$ is the Ackermann function). In fact, our results imply something even stronger: The best way to solve Clique and DomSet, even approximately, is to essentially enumerate all possibilities. Our results hold under the Gap Exponential Time Hypothesis (Gap-ETH) [Dinur16, MR16], which states that no $2^{o(n)}$-time algorithm can distinguish between a satisfiable 3SAT formula and one which is not even $(1 - \epsilon)$-satisfiable for some constant $\epsilon > 0$. Besides Clique and DomSet, we also rule out non-trivial FPT-approximation for Maximum Balanced Biclique, Maximum Subgraphs with Hereditary Properties, and Maximum Induced Matching in bipartite graphs. Additionally, we rule out $k^{o(1)}$-FPT-approximation algorithm for Densest $k$-Subgraph although this ratio does not yet match the trivial $O(k)$-approximation algorithm.Comment: 43 pages. To appear in FOCS'1

Assessing the Computational Complexity of Multi-Layer Subgraph Detection

Multi-layer graphs consist of several graphs (layers) over the same vertex set. They are motivated by real-world problems where entities (vertices) are associated via multiple types of relationships (edges in different layers). We chart the border of computational (in)tractability for the class of subgraph detection problems on multi-layer graphs, including fundamental problems such as maximum matching, finding certain clique relaxations (motivated by community detection), or path problems. Mostly encountering hardness results, sometimes even for two or three layers, we can also spot some islands of tractability

Mod/Resc Parsimony Inference

We address in this paper a new computational biology problem that aims at understanding a mechanism that could potentially be used to genetically manipulate natural insect populations infected by inherited, intra-cellular parasitic bacteria. In this problem, that we denote by \textsc{Mod/Resc Parsimony Inference}, we are given a boolean matrix and the goal is to find two other boolean matrices with a minimum number of columns such that an appropriately defined operation on these matrices gives back the input. We show that this is formally equivalent to the \textsc{Bipartite Biclique Edge Cover} problem and derive some complexity results for our problem using this equivalence. We provide a new, fixed-parameter tractability approach for solving both that slightly improves upon a previously published algorithm for the \textsc{Bipartite Biclique Edge Cover}. Finally, we present experimental results where we applied some of our techniques to a real-life data set.Comment: 11 pages, 3 figure

Reconfiguration on sparse graphs

A vertex-subset graph problem Q defines which subsets of the vertices of an input graph are feasible solutions. A reconfiguration variant of a vertex-subset problem asks, given two feasible solutions S and T of size k, whether it is possible to transform S into T by a sequence of vertex additions and deletions such that each intermediate set is also a feasible solution of size bounded by k. We study reconfiguration variants of two classical vertex-subset problems, namely Independent Set and Dominating Set. We denote the former by ISR and the latter by DSR. Both ISR and DSR are PSPACE-complete on graphs of bounded bandwidth and W[1]-hard parameterized by k on general graphs. We show that ISR is fixed-parameter tractable parameterized by k when the input graph is of bounded degeneracy or nowhere-dense. As a corollary, we answer positively an open question concerning the parameterized complexity of the problem on graphs of bounded treewidth. Moreover, our techniques generalize recent results showing that ISR is fixed-parameter tractable on planar graphs and graphs of bounded degree. For DSR, we show the problem fixed-parameter tractable parameterized by k when the input graph does not contain large bicliques, a class of graphs which includes graphs of bounded degeneracy and nowhere-dense graphs