Parameterized Algorithms on Perfect Graphs for deletion to (r,ℓ)(r,\ell)-graphs

For fixed integers $r,\ell \geq 0$, a graph $G$ is called an {\em $(r,\ell)$-graph} if the vertex set $V(G)$ can be partitioned into $r$ independent sets and $\ell$ cliques. The class of $(r, \ell)$ graphs generalizes $r$-colourable graphs (when $\ell =0)$ and hence not surprisingly, determining whether a given graph is an $(r, \ell)$-graph is \NP-hard even when $r \geq 3$ or $\ell \geq 3$ in general graphs. When $r$ and $\ell$ are part of the input, then the recognition problem is NP-hard even if the input graph is a perfect graph (where the {\sc Chromatic Number} problem is solvable in polynomial time). It is also known to be fixed-parameter tractable (FPT) on perfect graphs when parameterized by $r$ and $\ell$. I.e. there is an f(r+\ell) \cdot n^{\Oh(1)} algorithm on perfect graphs on $n$ vertices where $f$ is some (exponential) function of $r$ and $\ell$. In this paper, we consider the parameterized complexity of the following problem, which we call {\sc Vertex Partization}. Given a perfect graph $G$ and positive integers $r,\ell,k$ decide whether there exists a set $S\subseteq V(G)$ of size at most $k$ such that the deletion of $S$ from $G$ results in an $(r,\ell)$-graph. We obtain the following results: \begin{enumerate} \item {\sc Vertex Partization} on perfect graphs is FPT when parameterized by $k+r+\ell$. \item The problem does not admit any polynomial sized kernel when parameterized by $k+r+\ell$. In other words, in polynomial time, the input graph can not be compressed to an equivalent instance of size polynomial in $k+r+\ell$. In fact, our result holds even when $k=0$. \item When $r,\ell$ are universal constants, then {\sc Vertex Partization} on perfect graphs, parameterized by $k$, has a polynomial sized kernel. \end{enumerate

A practical fpt algorithm for Flow Decomposition and transcript assembly

The Flow Decomposition problem, which asks for the smallest set of weighted paths that "covers" a flow on a DAG, has recently been used as an important computational step in transcript assembly. We prove the problem is in FPT when parameterized by the number of paths by giving a practical linear fpt algorithm. Further, we implement and engineer a Flow Decomposition solver based on this algorithm, and evaluate its performance on RNA-sequence data. Crucially, our solver finds exact solutions while achieving runtimes competitive with a state-of-the-art heuristic. Finally, we contextualize our design choices with two hardness results related to preprocessing and weight recovery. Specifically, $k$-Flow Decomposition does not admit polynomial kernels under standard complexity assumptions, and the related problem of assigning (known) weights to a given set of paths is NP-hard.Comment: Introduces software package Toboggan: Version 1.0. http://dx.doi.org/10.5281/zenodo.82163

Parameterized Algorithms on Perfect Graphs for Deletion to (r,l)-Graphs

For fixed integers r,l >= 0, a graph G is called an (r,l)-graph if the vertex set V(G) can be partitioned into r independent sets and l cliques. Such a graph is also said to have cochromatic number r+l. The class of (r,l) graphs generalizes r-colourable graphs (when l=0) and hence not surprisingly, determining whether a given graph is an (r,l)-graph is NP-hard even when r >= 3 or l >= 3 in general graphs. When r and ell are part of the input, then the recognition problem is NP-hard even if the input graph is a perfect graph (where the Chromatic Number problem is solvable in polynomial time). It is also known to be fixed-parameter tractable (FPT) on perfect graphs when parameterized by r and l. I.e. there is an f(r+l) n^O(1) algorithm on perfect graphs on n vertices where f is a function of r and l. Observe that such an algorithm is unlikely on general graphs as the problem is NP-hard even for constant r and l. In this paper, we consider the parameterized complexity of the following problem, which we call Vertex Partization. Given a perfect graph G and positive integers r,l,k decide whether there exists a set S subset or equal to V(G) of size at most k such that the deletion of S from G results in an (r,l)-graph. This problem generalizes well studied problems such as Vertex Cover (when r=1 and l=0), Odd Cycle Transversal (when r=2, l=0) and Split Vertex Deletion (when r=1=l). 1. Vertex Partization on perfect graphs is FPT when parameterized by k+r+l. 2. The problem, when parameterized by k+r+l, does not admit any polynomial sized kernel, under standard complexity theoretic assumptions. In other words, in polynomial time, the input graph cannot be compressed to an equivalent instance of size polynomial in k+r+l. In fact, our result holds even when k=0. 3. When r,ell are universal constants, then Vertex Partization on perfect graphs, parameterized by k, has a polynomial sized kernel

Human Performance on Hard Non-Euclidean Graph Problems: Vertex Cover

Recent studies on a computationally hard visual optimization problem, the Traveling Salesperson Problem (TSP), indicate that humans are capable of finding close to optimal solutions in near-linear time. The current study is a preliminary step in investigating human performance on another hard problem, the Minimum Vertex Cover Problem, in which solvers attempt to find a smallest set of vertices that ensures that every edge in an undirected graph is incident with at least one of the selected vertices. We identify appropriate measures of performance, examine features of problem instances that impact performance, and describe strategies typically employed by participants to solve instances of the Vertex Cover problem

Evaluating Datalog via Tree Automata and Cycluits

We investigate parameterizations of both database instances and queries that make query evaluation fixed-parameter tractable in combined complexity. We show that clique-frontier-guarded Datalog with stratified negation (CFG-Datalog) enjoys bilinear-time evaluation on structures of bounded treewidth for programs of bounded rule size. Such programs capture in particular conjunctive queries with simplicial decompositions of bounded width, guarded negation fragment queries of bounded CQ-rank, or two-way regular path queries. Our result is shown by translating to alternating two-way automata, whose semantics is defined via cyclic provenance circuits (cycluits) that can be tractably evaluated.Comment: 56 pages, 63 references. Journal version of "Combined Tractability of Query Evaluation via Tree Automata and Cycluits (Extended Version)" at arXiv:1612.04203. Up to the stylesheet, page/environment numbering, and possible minor publisher-induced changes, this is the exact content of the journal paper that will appear in Theory of Computing Systems. Update wrt version 1: latest reviewer feedbac

Grid Recognition: Classical and Parameterized Computational Perspectives

Grid graphs, and, more generally, $k\times r$ grid graphs, form one of the most basic classes of geometric graphs. Over the past few decades, a large body of works studied the (in)tractability of various computational problems on grid graphs, which often yield substantially faster algorithms than general graphs. Unfortunately, the recognition of a grid graph is particularly hard -- it was shown to be NP-hard even on trees of pathwidth 3 already in 1987. Yet, in this paper, we provide several positive results in this regard in the framework of parameterized complexity (additionally, we present new and complementary hardness results). Specifically, our contribution is threefold. First, we show that the problem is fixed-parameter tractable (FPT) parameterized by $k+\mathsf {mcc}$ where $\mathsf{mcc}$ is the maximum size of a connected component of $G$. This also implies that the problem is FPT parameterized by $\mathtt{td}+k$ where $\mathtt{td}$ is the treedepth of $G$ (to be compared with the hardness for pathwidth 2 where $k=3$). Further, we derive as a corollary that strip packing is FPT with respect to the height of the strip plus the maximum of the dimensions of the packed rectangles, which was previously only known to be in XP. Second, we present a new parameterization, denoted $a_G$, relating graph distance to geometric distance, which may be of independent interest. We show that the problem is para-NP-hard parameterized by $a_G$, but FPT parameterized by $a_G$ on trees, as well as FPT parameterized by $k+a_G$. Third, we show that the recognition of $k\times r$ grid graphs is NP-hard on graphs of pathwidth 2 where $k=3$. Moreover, when $k$ and $r$ are unrestricted, we show that the problem is NP-hard on trees of pathwidth 2, but trivially solvable in polynomial time on graphs of pathwidth 1