PACE Solver Description: SMS

Peer reviewe

Lower bounds on dynamic programming for maximum weight independent set

Publisher Copyright: © 2021 Tuukka Korhonen.We prove lower bounds on pure dynamic programming algorithms for maximum weight independent set (MWIS). We model such algorithms as tropical circuits, i.e., circuits that compute with max and + operations. For a graph G, an MWIS-circuit of G is a tropical circuit whose inputs correspond to vertices of G and which computes the weight of a maximum weight independent set of G for any assignment of weights to the inputs. We show that if G has treewidth w and maximum degree d, then any MWIS-circuit of G has 2Ω(w/d) gates and that if G is planar, or more generally H-minor-free for any fixed graph H, then any MWIS-circuit of G has 2Ω(w) gates. An MWIS-formula is an MWIScircuit where each gate has fan-out at most one. We show that if G has treedepth t and maximum degree d, then any MWIS-formula of G has 2Ω(t/d) gates. It follows that treewidth characterizes optimal MWIS-circuits up to polynomials for all bounded degree graphs and H-minor-free graphs, and treedepth characterizes optimal MWIS-formulas up to polynomials for all bounded degree graphs.Peer reviewe

Finding Optimal Triangulations Parameterized by Edge Clique Cover

Publisher Copyright: © 2022, The Author(s).We consider problems that can be formulated as a task of finding an optimal triangulation of a graph w.r.t. some notion of optimality. We present algorithms parameterized by the size of a minimum edge clique cover (cc) to such problems. This parameterization occurs naturally in many problems in this setting, e.g., in the perfect phylogeny problem cc is at most the number of taxa, in fractional hypertreewidth cc is at most the number of hyperedges, and in treewidth of Bayesian networks cc is at most the number of non-root nodes. We show that the number of minimal separators of graphs is at most 2 cc, the number of potential maximal cliques is at most 3 cc, and these objects can be listed in times O∗(2 cc) and O∗(3 cc) , respectively, even when no edge clique cover is given as input; the O∗(·) notation omits factors polynomial in the input size. These enumeration algorithms imply O∗(3 cc) time algorithms for problems such as treewidth, weighted minimum fill-in, and feedback vertex set. For generalized and fractional hypertreewidth we give O∗(4 m) time and O∗(3 m) time algorithms, respectively, where m is the number of hyperedges. When an edge clique cover of size cc′ is given as a part of the input we give O∗(2cc′) time algorithms for treewidth, minimum fill-in, and chordal sandwich. This implies an O∗(2 n) time algorithm for perfect phylogeny, where n is the number of taxa. We also give polynomial space algorithms with time complexities O∗(9cc′) and O∗(9cc+O(log2cc)) for problems in this framework.Peer reviewe

Finding Optimal Triangulations Parameterized by Edge Clique Cover

Peer reviewe

Finding Optimal Tree Decompositions

The task of organizing a given graph into a structure called a tree decomposition is relevant in multiple areas of computer science. In particular, many NP-hard problems can be solved in polynomial time if a suitable tree decomposition of a graph describing the problem instance is given as a part of the input. This motivates the task of finding as good tree decompositions as possible, or ideally, optimal tree decompositions. This thesis is about finding optimal tree decompositions of graphs with respect to several notions of optimality. Each of the considered notions measures the quality of a tree decomposition in the context of an application. In particular, we consider a total of seven problems that are formulated as finding optimal tree decompositions: treewidth, minimum fill-in, generalized and fractional hypertreewidth, total table size, phylogenetic character compatibility, and treelength. For each of these problems we consider the BT algorithm of Bouchitté and Todinca as the method of finding optimal tree decompositions. The BT algorithm is well-known on the theoretical side, but to our knowledge the first time it was implemented was only recently for the 2nd Parameterized Algorithms and Computational Experiments Challenge (PACE 2017). The author’s implementation of the BT algorithm took the second place in the minimum fill-in track of PACE 2017. In this thesis we review and extend the BT algorithm and our implementation. In particular, we improve the eciency of the algorithm in terms of both theory and practice. We also implement the algorithm for each of the seven problems considered, introducing a novel adaptation of the algorithm for the maximum compatibility problem of phylogenetic characters. Our implementation outperforms alternative state-of-the-art approaches in terms of numbers of test instances solved on well-known benchmarks on minimum fill-in, generalized hypertreewidth, fractional hypertreewidth, total table size, and the maximum compatibility problem of phylogenetic characters. Furthermore, to our understanding the implementation is the first exact approach for the treelength problem

Finding Most Compatible Phylogenetic Trees over Multi-State Characters

Peer reviewe

An Improved Parameterized Algorithm for Treewidth

We give an algorithm that takes as input an $n$-vertex graph $G$ and an integer $k$, runs in time $2^{O(k^2)} n^{O(1)}$, and outputs a tree decomposition of $G$ of width at most $k$, if such a decomposition exists. This resolves the long-standing open problem of whether there is a $2^{o(k^3)} n^{O(1)}$ time algorithm for treewidth. In particular, our algorithm is the first improvement on the dependency on $k$ in algorithms for treewidth since the $2^{O(k^3)} n^{O(1)}$ time algorithm given by Bodlaender and Kloks [ICALP 1991] and Lagergren and Arnborg [ICALP 1991]. We also give an algorithm that given an $n$-vertex graph $G$, an integer $k$, and a rational $\varepsilon \in (0,1)$, in time $k^{O(k/\varepsilon)} n^{O(1)}$ either outputs a tree decomposition of $G$ of width at most $(1+\varepsilon)k$ or determines that the treewidth of $G$ is larger than $k$. Prior to our work, no approximation algorithms for treewidth with approximation ratio less than $2$, other than the exact algorithms, were known. Both of our algorithms work in polynomial space.Comment: 57 pages, 2 figures. STOC 2023. In version v2 added a conclusion sectio

New Width Parameters for Independent Set: One-sided-mim-width and Neighbor-depth

We study the tractability of the maximum independent set problem from the viewpoint of graph width parameters, with the goal of defining a width parameter that is as general as possible and allows to solve independent set in polynomial-time on graphs where the parameter is bounded. We introduce two new graph width parameters: one-sided maximum induced matching-width (o-mim-width) and neighbor-depth. O-mim-width is a graph parameter that is more general than the known parameters mim-width and tree-independence number, and we show that independent set and feedback vertex set can be solved in polynomial-time given a decomposition with bounded o-mim-width. O-mim-width is the first width parameter that gives a common generalization of chordal graphs and graphs of bounded clique-width in terms of tractability of these problems. The parameter o-mim-width, as well as the related parameters mim-width and sim-width, have the limitation that no algorithms are known to compute bounded-width decompositions in polynomial-time. To partially resolve this limitation, we introduce the parameter neighbor-depth. We show that given a graph of neighbor-depth $k$, independent set can be solved in time $n^{O(k)}$ even without knowing a corresponding decomposition. We also show that neighbor-depth is bounded by a polylogarithmic function on the number of vertices on large classes of graphs, including graphs of bounded o-mim-width, and more generally graphs of bounded sim-width, giving a quasipolynomial-time algorithm for independent set on these graph classes. This resolves an open problem asked by Kang, Kwon, Str{\o}mme, and Telle [TCS 2017].Comment: 26 pages, 1 figure. This is the full version of an extended abstract that will appear in WG202

Tight Lower Bounds for Problems Parameterized by Rank-Width

We show that there is no 2o(k2)nO(1) time algorithm for Independent Set on n-vertex graphs with rank-width k, unless the Exponential Time Hypothesis (ETH) fails. Our lower bound matches the 2O(k2)nO(1) time algorithm given by Bui-Xuan, Telle, and Vatshelle [Discret. Appl. Math., 2010] and it answers the open question of Bergougnoux and Kanté [SIAM J. Discret. Math., 2021]. We also show that the known 2O(k2)nO(1) time algorithms for Weighted Dominating Set, Maximum Induced Matching and Feedback Vertex Set parameterized by rank-width k are optimal assuming ETH. Our results are the first tight ETH lower bounds parameterized by rank-width that do not follow directly from lower bounds for n-vertex graphs