Potential Maximal Clique Algorithms for Perfect Phylogeny Problems

Kloks, Kratsch, and Spinrad showed how treewidth and minimum-fill, NP-hard combinatorial optimization problems related to minimal triangulations, are broken into subproblems by block subgraphs defined by minimal separators. These ideas were expanded on by Bouchitt\'e and Todinca, who used potential maximal cliques to solve these problems using a dynamic programming approach in time polynomial in the number of minimal separators of a graph. It is known that solutions to the perfect phylogeny problem, maximum compatibility problem, and unique perfect phylogeny problem are characterized by minimal triangulations of the partition intersection graph. In this paper, we show that techniques similar to those proposed by Bouchitt\'e and Todinca can be used to solve the perfect phylogeny problem with missing data, the two- state maximum compatibility problem with missing data, and the unique perfect phylogeny problem with missing data in time polynomial in the number of minimal separators of the partition intersection graph

Polynomial-time algorithm for Maximum Weight Independent Set on P6P_6-free graphs

In the classic Maximum Weight Independent Set problem we are given a graph $G$ with a nonnegative weight function on vertices, and the goal is to find an independent set in $G$ of maximum possible weight. While the problem is NP-hard in general, we give a polynomial-time algorithm working on any $P_6$-free graph, that is, a graph that has no path on $6$ vertices as an induced subgraph. This improves the polynomial-time algorithm on $P_5$-free graphs of Lokshtanov et al. (SODA 2014), and the quasipolynomial-time algorithm on $P_6$-free graphs of Lokshtanov et al (SODA 2016). The main technical contribution leading to our main result is enumeration of a polynomial-size family $\mathcal{F}$ of vertex subsets with the following property: for every maximal independent set $I$ in the graph, $\mathcal{F}$ contains all maximal cliques of some minimal chordal completion of $G$ that does not add any edge incident to a vertex of $I$

Fixed-Parameter Tractability of Directed Multiway Cut Parameterized by the Size of the Cutset

Given a directed graph $G$, a set of $k$ terminals and an integer $p$, the \textsc{Directed Vertex Multiway Cut} problem asks if there is a set $S$ of at most $p$ (nonterminal) vertices whose removal disconnects each terminal from all other terminals. \textsc{Directed Edge Multiway Cut} is the analogous problem where $S$ is a set of at most $p$ edges. These two problems indeed are known to be equivalent. A natural generalization of the multiway cut is the \emph{multicut} problem, in which we want to disconnect only a set of $k$ given pairs instead of all pairs. Marx (Theor. Comp. Sci. 2006) showed that in undirected graphs multiway cut is fixed-parameter tractable (FPT) parameterized by $p$. Marx and Razgon (STOC 2011) showed that undirected multicut is FPT and directed multicut is W[1]-hard parameterized by $p$. We complete the picture here by our main result which is that both \textsc{Directed Vertex Multiway Cut} and \textsc{Directed Edge Multiway Cut} can be solved in time $2^{2^{O(p)}}n^{O(1)}$, i.e., FPT parameterized by size $p$ of the cutset of the solution. This answers an open question raised by Marx (Theor. Comp. Sci. 2006) and Marx and Razgon (STOC 2011). It follows from our result that \textsc{Directed Multicut} is FPT for the case of $k=2$ terminal pairs, which answers another open problem raised in Marx and Razgon (STOC 2011)

Fast Algorithms for Parameterized Problems with Relaxed Disjointness Constraints

In parameterized complexity, it is a natural idea to consider different generalizations of classic problems. Usually, such generalization are obtained by introducing a "relaxation" variable, where the original problem corresponds to setting this variable to a constant value. For instance, the problem of packing sets of size at most $p$ into a given universe generalizes the Maximum Matching problem, which is recovered by taking $p=2$. Most often, the complexity of the problem increases with the relaxation variable, but very recently Abasi et al. have given a surprising example of a problem --- $r$-Simple $k$-Path --- that can be solved by a randomized algorithm with running time $O^*(2^{O(k \frac{\log r}{r})})$. That is, the complexity of the problem decreases with $r$. In this paper we pursue further the direction sketched by Abasi et al. Our main contribution is a derandomization tool that provides a deterministic counterpart of the main technical result of Abasi et al.: the $O^*(2^{O(k \frac{\log r}{r})})$ algorithm for $(r,k)$-Monomial Detection, which is the problem of finding a monomial of total degree $k$ and individual degrees at most $r$ in a polynomial given as an arithmetic circuit. Our technique works for a large class of circuits, and in particular it can be used to derandomize the result of Abasi et al. for $r$-Simple $k$-Path. On our way to this result we introduce the notion of representative sets for multisets, which may be of independent interest. Finally, we give two more examples of problems that were already studied in the literature, where the same relaxation phenomenon happens. The first one is a natural relaxation of the Set Packing problem, where we allow the packed sets to overlap at each element at most $r$ times. The second one is Degree Bounded Spanning Tree, where we seek for a spanning tree of the graph with a small maximum degree

A Backtracking-Based Algorithm for Computing Hypertree-Decompositions

Hypertree decompositions of hypergraphs are a generalization of tree decompositions of graphs. The corresponding hypertree-width is a measure for the cyclicity and therefore tractability of the encoded computation problem. Many NP-hard decision and computation problems are known to be tractable on instances whose structure corresponds to hypergraphs of bounded hypertree-width. Intuitively, the smaller the hypertree-width, the faster the computation problem can be solved. In this paper, we present the new backtracking-based algorithm det-k-decomp for computing hypertree decompositions of small width. Our benchmark evaluations have shown that det-k-decomp significantly outperforms opt-k-decomp, the only exact hypertree decomposition algorithm so far. Even compared to the best heuristic algorithm, we obtained competitive results as long as the hypergraphs are not too large.Comment: 19 pages, 6 figures, 3 table

The succinctness of first-order logic on linear orders

Succinctness is a natural measure for comparing the strength of different logics. Intuitively, a logic L_1 is more succinct than another logic L_2 if all properties that can be expressed in L_2 can be expressed in L_1 by formulas of (approximately) the same size, but some properties can be expressed in L_1 by (significantly) smaller formulas. We study the succinctness of logics on linear orders. Our first theorem is concerned with the finite variable fragments of first-order logic. We prove that: (i) Up to a polynomial factor, the 2- and the 3-variable fragments of first-order logic on linear orders have the same succinctness. (ii) The 4-variable fragment is exponentially more succinct than the 3-variable fragment. Our second main result compares the succinctness of first-order logic on linear orders with that of monadic second-order logic. We prove that the fragment of monadic second-order logic that has the same expressiveness as first-order logic on linear orders is non-elementarily more succinct than first-order logic