arXiv subjects

Venkatesh Raman

Publications and source records attributed to Venkatesh Raman.

At least 37 records · Page 2Linked to original sources

arXiv2017

Revisiting Connected Vertex Cover: FPT Algorithms and Lossy Kernels

The CONNECTED VERTEX COVER problem asks for a vertex cover in a graph that induces a connected subgraph. The problem is known to be fixed-parameter tractable (FPT), and is unlikely to have a polynomial sized kernel (under complexity theoretic assumptions) when parameterized by the solution size. In a recent paper, Lokshtanov et al.[STOC 2017], have shown an $α$-approximate kernel for the problem for every $α> 1$, in the framework of approximate or lossy kernelization. In this work, we exhibit lossy kernels and FPT algorithms for CONNECTED VERTEX COVER for parameters that are more natural and functions of the input, and in some cases, smaller than the solution size. The parameters we consider are the sizes of a split deletion set, clique deletion set, clique cover, cluster deletion set and chordal deletion set.

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arXiv2017

Improved Space efficient linear time algorithms for BFS, DFS and applications

Recent work by Elmasry et al. (STACS 2015) and Asano et al. (ISAAC 2014), reconsidered classical fundamental graph algorithms focusing on improving the space complexity. We continue this line of work focusing on space. Our first result is a simple data structure that can maintain any subset $S$ of a universe of $n$ elements using $n+o(n)$ bits and support in constant time, apart from the standard insert, delete and membership queries, the operation {\it findany} that finds and returns any element of the set (or outputs that the set is empty). Using this we give a BFS implementation that takes $O(m+n)$ time using at most $2n+o(n)$ bits. Later, we further improve the space requirement of BFS to at most $1.585n + o(n)$ bits. We demonstrate the use of our data structure by developing another data structure using it that can represent a sequence of $n$ non-negative integers $x_1, x_2, \ldots x_n$ using at most $\sum_{i=1}^n x_i + 2n + o(\sum_{i=1}^n x_i+n)$ bits and, in constant time, determine whether the $i$-th element is $0$ or decrement it otherwise. We also discuss an algorithm for finding a minimum weight spanning tree of a weighted undirected graph using at most $n+o(n)$ bits. We also provide an implementation for DFS that takes $O(m+n)$ time and $O(n \lg(m/n))$ bits. Using this DFS algorithm and other careful implementations, we can test biconnectivity, 2-edge connectivity, and determine cut vertices, bridges etc among others, essentially within the same time and space bounds required for DFS. These improve the space required for earlier implementations from $Ω(n\lg n)$ bits.

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arXiv2017

Biconnectivity, $st$-numbering and other applications of DFS using $O(n)$ bits

We consider space efficient implementations of some classical applications of DFS including the problem of testing biconnectivity and $2$-edge connectivity, finding cut vertices and cut edges, computing chain decomposition and $st$-numbering of a given undirected graph $G$ on $n$ vertices and $m$ edges. Classical algorithms for them typically use DFS and some $Ω(\lg n)$ bits\footnote{We use $\lg$ to denote logarithm to the base $2$.} of information at each vertex. Building on a recent $O(n)$-bits implementation of DFS due to Elmasry et al. (STACS 2015) we provide $O(n)$-bit implementations for all these applications of DFS. Our algorithms take $O(m \lg^c n \lg\lg n)$ time for some small constant $c$ (where $c \leq 2$). Central to our implementation is a succinct representation of the DFS tree and a space efficient partitioning of the DFS tree into connected subtrees, which maybe of independent interest for designing other space efficient graph algorithms.

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arXiv2015

Parameterized Algorithms on Perfect Graphs for deletion to $(r,\ell)$-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}

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arXiv2015

SAT-based Analysis of Large Real-world Feature Models is Easy

Modern conflict-driven clause-learning (CDCL) Boolean SAT solvers provide efficient automatic analysis of real-world feature models (FM) of systems ranging from cars to operating systems. It is well-known that solver-based analysis of real-world FMs scale very well even though SAT instances obtained from such FMs are large, and the corresponding analysis problems are known to be NP-complete. To better understand why SAT solvers are so effective, we systematically studied many syntactic and semantic characteristics of a representative set of large real-world FMs. We discovered that a key reason why large real-world FMs are easy-to-analyze is that the vast majority of the variables in these models are unrestricted, i.e., the models are satisfiable for both true and false assignments to such variables under the current partial assignment. Given this discovery and our understanding of CDCL SAT solvers, we show that solvers can easily find satisfying assignments for such models without too many backtracks relative to the model size, explaining why solvers scale so well. Further analysis showed that the presence of unrestricted variables in these real-world models can be attributed to their high-degree of variability. Additionally, we experimented with a series of well-known non-backtracking simplifications that are particularly effective in solving FMs. The remaining variables/clauses after simplifications, called the core, are so few that they are easily solved even with backtracking, further strengthening our conclusions.

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arXiv2014

Reconfiguration over tree decompositions

A vertex-subset graph problem $Q$ defines which subsets of the vertices of an input graph are feasible solutions. The reconfiguration version of a vertex-subset problem $Q$ asks whether it is possible to transform one feasible solution for $Q$ into another in at most $\ell$ steps, where each step is a vertex addition or deletion, and each intermediate set is also a feasible solution for $Q$ of size bounded by $k$. Motivated by recent results establishing W[1]-hardness of the reconfiguration versions of most vertex-subset problems parameterized by $\ell$, we investigate the complexity of such problems restricted to graphs of bounded treewidth. We show that the reconfiguration versions of most vertex-subset problems remain PSPACE-complete on graphs of treewidth at most $t$ but are fixed-parameter tractable parameterized by $\ell + t$ for all vertex-subset problems definable in monadic second-order logic (MSOL). To prove the latter result, we introduce a technique which allows us to circumvent cardinality constraints and define reconfiguration problems in MSOL.

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arXiv2014

Shortest reconfiguration paths in the solution space of Boolean formulas

Given a Boolean formula and a satisfying assignment, a flip is an operation that changes the value of a variable in the assignment so that the resulting assignment remains satisfying. We study the problem of computing the shortest sequence of flips (if one exists) that transforms a given satisfying assignment $s$ to another satisfying assignment $t$ of a Boolean formula. Earlier work characterized the complexity of finding any (not necessarily the shortest) sequence of flips from one satisfying assignment to another using Schaefer's framework for classification of Boolean formulas. We build on it to provide a trichotomy for the complexity of finding the shortest sequence of flips and show that it is either in P, NP-complete, or PSPACE-complete. Our result adds to the small set of complexity results known for shortest reconfiguration sequence problems by providing an example where the shortest sequence can be found in polynomial time even though its length is not equal to the symmetric difference of the values of the variables in $s$ and $t$. This is in contrast to all reconfiguration problems studied so far, where polynomial time algorithms for computing the shortest path were known only for cases where the path modified the symmetric difference only.

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arXiv2013

Evolution and Controllability of Cancer Networks: a Boolean Perspective

Cancer forms a robust system and progresses as stages over time typically with increasing aggressiveness and worsening prognosis. Characterizing these stages and identifying the genes driving transitions between them is critical to understand cancer progression and to develop effective anti-cancer therapies. Here, we propose a novel model of the 'cancer system' as a Boolean state space in which a Boolean network, built from protein interaction and gene-expression data from different stages of cancer, transits between Boolean satisfiability states by "editing" interactions and "flipping" genes. The application of our model (called BoolSpace) on three case studies - pancreatic and breast tumours in human and post spinal-cord injury in rats - reveals valuable insights into the phenomenon of cancer progression. In particular, we notice that several of the genes flipped are serine/threonine kinases which act as natural cellular switches and that different sets of genes are flipped during the initial and final stages indicating a pattern to tumour progression. We hypothesize that robustness of cancer partly stems from "passing of the baton" between genes at different stages, and therefore an effective therapy should target a "cover set" of these genes. A C/C++ implementation of BoolSpace is freely available at: http://www.bioinformatics.org.au/tools-data

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arXiv2013

On the Parameterized Complexity of Reconfiguration Problems

We present the first results on the parameterized complexity of reconfiguration problems, where a reconfiguration version of an optimization problem $Q$ takes as input two feasible solutions $S$ and $T$ and determines if there is a sequence of {\em reconfiguration steps} that can be applied to transform $S$ into $T$ such that each step results in a feasible solution to $Q$. For most of the results in this paper, $S$ and $T$ are subsets of vertices of a given graph and a reconfiguration step adds or deletes a vertex. Our study is motivated by recent results establishing that for most NP-hard problems, the classical complexity of reconfiguration is PSPACE-complete. We address the question for several important graph properties under two natural parameterizations: $k$, the size of the solutions, and $\ell$, the length of the sequence of steps. Our first general result is an algorithmic paradigm, the {\em reconfiguration kernel}, used to obtain fixed-parameter algorithms for the reconfiguration versions of {\sc Vertex Cover} and, more generally, {\sc Bounded Hitting Set} and {\sc Feedback Vertex Set}, all parameterized by $k$. In contrast, we show that reconfiguring {\sc Unbounded Hitting Set} is $W[2]$-hard when parameterized by $k+\ell$. We also demonstrate the $W[1]$-hardness of the reconfiguration versions of a large class of maximization problems parameterized by $k+\ell$, and of their corresponding deletion problems parameterized by $\ell$; in doing so, we show that there exist problems in FPT when parameterized by $k$, but whose reconfiguration versions are $W[1]$-hard when parameterized by $k+\ell$.

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arXiv2013

Succinct data structures for representing equivalence classes

Given a partition of an n element set into equivalence classes, we consider time-space tradeoffs for representing it to support the query that asks whether two given elements are in the same equivalence class. This has various applications including for testing whether two vertices are in the same component in an undirected graph or in the same strongly connected component in a directed graph. We consider the problem in several models. -- Concerning labeling schemes where we assign labels to elements and the query is to be answered just by examining the labels of the queried elements (without any extra space): if each vertex is required to have a unique label, then we show that a label space of (\sum_{i=1}^n \lfloor {n \over i} \rfloor) is necessary and sufficient. In other words, \lg n + \lg \lg n + O(1) bits of space are necessary and sufficient for representing each of the labels. This slightly strengthens the known lower bound and is in contrast to the known necessary and sufficient bound of \lceil \lg n \rceil for the label length, if each vertex need not get a unique label. --Concerning succinct data structures for the problem when the n elements are to be uniquely assigned labels from label set {1, 2, ...n}, we first show that Θ(\sqrt n) bits are necessary and sufficient to represent the equivalence class information. This space includes the space for implicitly encoding the vertex labels. We can support the query in such a structure in O(\lg n) time in the standard word RAM model. We then develop structures resulting in one where the queries can be supported in constant time using O({\sqrt n} \lg n) bits of space. We also develop space efficient structures where union operation along with the equivalence query can be answered fast.

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arXiv2013

Upper and Lower Bounds for Weak Backdoor Set Detection

We obtain upper and lower bounds for running times of exponential time algorithms for the detection of weak backdoor sets of 3CNF formulas, considering various base classes. These results include (omitting polynomial factors), (i) a 4.54^k algorithm to detect whether there is a weak backdoor set of at most k variables into the class of Horn formulas; (ii) a 2.27^k algorithm to detect whether there is a weak backdoor set of at most k variables into the class of Krom formulas. These bounds improve an earlier known bound of 6^k. We also prove a 2^k lower bound for these problems, subject to the Strong Exponential Time Hypothesis.

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arXiv2012

Faster Parameterized Algorithms using Linear Programming

We investigate the parameterized complexity of Vertex Cover parameterized by the difference between the size of the optimal solution and the value of the linear programming (LP) relaxation of the problem. By carefully analyzing the change in the LP value in the branching steps, we argue that combining previously known preprocessing rules with the most straightforward branching algorithm yields an $O^*((2.618)^k)$ algorithm for the problem. Here $k$ is the excess of the vertex cover size over the LP optimum, and we write $O^*(f(k))$ for a time complexity of the form $O(f(k)n^{O(1)})$, where $f (k)$ grows exponentially with $k$. We proceed to show that a more sophisticated branching algorithm achieves a runtime of $O^*(2.3146^k)$. Following this, using known and new reductions, we give $O^*(2.3146^k)$ algorithms for the parameterized versions of Above Guarantee Vertex Cover, Odd Cycle Transversal, Split Vertex Deletion and Almost 2-SAT, and an $O^*(1.5214^k)$ algorithm for Konig Vertex Deletion, Vertex Cover Param by OCT and Vertex Cover Param by KVD. These algorithms significantly improve the best known bounds for these problems. The most notable improvement is the new bound for Odd Cycle Transversal - this is the first algorithm which beats the dependence on $k$ of the seminal $O^*(3^k)$ algorithm of Reed, Smith and Vetta. Finally, using our algorithm, we obtain a kernel for the standard parameterization of Vertex Cover with at most $2k - c \log k$ vertices. Our kernel is simpler than previously known kernels achieving the same size bound.

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arXiv2011

Parameterized Complexity of MaxSat Above Average

In MaxSat, we are given a CNF formula $F$ with $n$ variables and $m$ clauses and asked to find a truth assignment satisfying the maximum number of clauses. Let $r_1,..., r_m$ be the number of literals in the clauses of $F$. Then $asat(F)=\sum_{i=1}^m (1-2^{-r_i})$ is the expected number of clauses satisfied by a random truth assignment (the truth values to the variables are distributed uniformly and independently). It is well-known that, in polynomial time, one can find a truth assignment satisfying at least $asat(F)$ clauses. In the parameterized problem MaxSat-AA, we are to decide whether there is a truth assignment satisfying at least $asat(F)+k$ clauses, where $k$ is the parameter. We prove that MaxSat-AA is para-NP-complete and, thus, MaxSat-AA is not fixed-parameter tractable unless P$=$NP. This is in sharp contrast to MaxLin2-AA which was recently proved to be fixed-parameter tractable by Crowston et al. (arXiv:1104.1135v3). In fact, we consider a more refined version of {\sc MaxSat-AA}, {\sc Max-$r(n)$-Sat-AA}, where $r_j\le r(n)$ for each $j$. Alon {\em et al.} (SODA 2010) proved that if $r=r(n)$ is a constant, then {\sc Max-$r$-Sat-AA} is fixed-parameter tractable. We prove that {\sc Max-$r(n)$-Sat-AA} is para-NP-complete for $r(n)=\lceil \log n\rceil.$ We also prove that assuming the exponential time hypothesis, {\sc Max-$r(n)$-Sat-AA} is not in XP already for any $r(n)\ge \log \log n +ϕ(n)$, where $ϕ(n)$ is any unbounded strictly increasing function. This lower bound on $r(n)$ cannot be decreased much further as we prove that {\sc Max-$r(n)$-Sat-AA} is (i) in XP for any $r(n)\le \log \log n - \log \log \log n$ and (ii) fixed-parameter tractable for any $r(n)\le \log \log n - \log \log \log n - ϕ(n)$, where $ϕ(n)$ is any unbounded strictly increasing function. The proof uses some results on {\sc MaxLin2-AA}.

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arXiv2011

Bidimensionality and EPTAS

Bidimensionality theory is a powerful framework for the development of metaalgorithmic techniques. It was introduced by Demaine et al. as a tool to obtain sub-exponential time parameterized algorithms for problems on H-minor free graphs. Demaine and Hajiaghayi extended the theory to obtain PTASs for bidimensional problems, and subsequently improved these results to EPTASs. Fomin et. al related the theory to the existence of linear kernels for parameterized problems. In this paper we revisit bidimensionality theory from the perspective of approximation algorithms and redesign the framework for obtaining EPTASs to be more powerful, easier to apply and easier to understand. Two of the most widely used approaches to obtain PTASs on planar graphs are the Lipton-Tarjan separator based approach, and Baker's approach. Demaine and Hajiaghayi strengthened both approaches using bidimensionality and obtained EPTASs for a multitude of problems. We unify the two strenghtened approaches to combine the best of both worlds. At the heart of our framework is a decomposition lemma which states that for "most" bidimensional problems, there is a polynomial time algorithm which given an H-minor-free graph G as input and an e > 0 outputs a vertex set X of size e * OPT such that the treewidth of G n X is f(e). Here, OPT is the objective function value of the problem in question and f is a function depending only on e. This allows us to obtain EPTASs on (apex)-minor-free graphs for all problems covered by the previous framework, as well as for a wide range of packing problems, partial covering problems and problems that are neither closed under taking minors, nor contractions. To the best of our knowledge for many of these problems including cycle packing, vertex-h-packing, maximum leaf spanning tree, and partial r-dominating set no EPTASs on planar graphs were previously known.

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arXiv2011

Succinct Representations of Permutations and Functions

We investigate the problem of succinctly representing an arbitrary permutation, π, on {0,...,n-1} so that π^k(i) can be computed quickly for any i and any (positive or negative) integer power k. A representation taking (1+ε) n lg n + O(1) bits suffices to compute arbitrary powers in constant time, for any positive constant ε<= 1. A representation taking the optimal \ceil{\lg n!} + o(n) bits can be used to compute arbitrary powers in O(lg n / lg lg n) time. We then consider the more general problem of succinctly representing an arbitrary function, f: [n] \rightarrow [n] so that f^k(i) can be computed quickly for any i and any integer power k. We give a representation that takes (1+ε) n lg n + O(1) bits, for any positive constant ε<= 1, and computes arbitrary positive powers in constant time. It can also be used to compute f^k(i), for any negative integer k, in optimal O(1+|f^k(i)|) time. We place emphasis on the redundancy, or the space beyond the information-theoretic lower bound that the data structure uses in order to support operations efficiently. A number of lower bounds have recently been shown on the redundancy of data structures. These lower bounds confirm the space-time optimality of some of our solutions. Furthermore, the redundancy of one of our structures "surpasses" a recent lower bound by Golynski [Golynski, SODA 2009], thus demonstrating the limitations of this lower bound.

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arXiv2010

A Quartic Kernel for Pathwidth-One Vertex Deletion

The pathwidth of a graph is a measure of how path-like the graph is. Given a graph G and an integer k, the problem of finding whether there exist at most k vertices in G whose deletion results in a graph of pathwidth at most one is NP- complete. We initiate the study of the parameterized complexity of this problem, parameterized by k. We show that the problem has a quartic vertex-kernel: We show that, given an input instance (G = (V, E), k); |V| = n, we can construct, in polynomial time, an instance (G', k') such that (i) (G, k) is a YES instance if and only if (G', k') is a YES instance, (ii) G' has O(k^{4}) vertices, and (iii) k' \leq k. We also give a fixed parameter tractable (FPT) algorithm for the problem that runs in O(7^{k} k \cdot n^{2}) time.

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arXiv2010

Beyond Bidimensionality: Parameterized Subexponential Algorithms on Directed Graphs

We develop two different methods to achieve subexponential time parameterized algorithms for problems on sparse directed graphs. We exemplify our approaches with two well studied problems. For the first problem, {\sc $k$-Leaf Out-Branching}, which is to find an oriented spanning tree with at least $k$ leaves, we obtain an algorithm solving the problem in time $2^{O(\sqrt{k} \log k)} n+ n^{O(1)}$ on directed graphs whose underlying undirected graph excludes some fixed graph $H$ as a minor. For the special case when the input directed graph is planar, the running time can be improved to $2^{O(\sqrt{k})}n + n^{O(1)}$. The second example is a generalization of the {\sc Directed Hamiltonian Path} problem, namely {\sc $k$-Internal Out-Branching}, which is to find an oriented spanning tree with at least $k$ internal vertices. We obtain an algorithm solving the problem in time $2^{O(\sqrt{k} \log k)} + n^{O(1)}$ on directed graphs whose underlying undirected graph excludes some fixed apex graph $H$ as a minor. Finally, we observe that for any $ε>0$, the {\sc $k$-Directed Path} problem is solvable in time $O((1+ε)^k n^{f(ε)})$, where $f$ is some function of $\ve$. Our methods are based on non-trivial combinations of obstruction theorems for undirected graphs, kernelization, problem specific combinatorial structures and a layering technique similar to the one employed by Baker to obtain PTAS for planar graphs.

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arXiv2009

Faster Algorithms for Finding and Counting Subgraphs

In this paper we study a natural generalization of both {\sc $k$-Path} and {\sc $k$-Tree} problems, namely, the {\sc Subgraph Isomorphism} problem. In the {\sc Subgraph Isomorphism} problem we are given two graphs $F$ and $G$ on $k$ and $n$ vertices respectively as an input, and the question is whether there exists a subgraph of $G$ isomorphic to $F$. We show that if the treewidth of $F$ is at most $t$, then there is a randomized algorithm for the {\sc Subgraph Isomorphism} problem running in time $\cO^*(2^k n^{2t})$. To do so, we associate a new multivariate {Homomorphism polynomial} of degree at most $k$ with the {\sc Subgraph Isomorphism} problem and construct an arithmetic circuit of size at most $n^{\cO(t)}$ for this polynomial. Using this polynomial, we also give a deterministic algorithm to count the number of homomorphisms from $F$ to $G$ that takes $n^{\cO(t)}$ time and uses polynomial space. For the counting version of the {\sc Subgraph Isomorphism} problem, where the objective is to count the number of distinct subgraphs of $G$ that are isomorphic to $F$, we give a deterministic algorithm running in time and space $\cO^*({n \choose k/2}n^{2p})$ or ${n\choose k/2}n^{\cO(t \log k)}$. We also give an algorithm running in time $\cO^{*}(2^{k}{n \choose k/2}n^{5p})$ and taking space polynomial in $n$. Here $p$ and $t$ denote the pathwidth and the treewidth of $F$, respectively. Thus our work not only improves on known results on {\sc Subgraph Isomorphism} but it also extends and generalize most of the known results on {\sc $k$-Path} and {\sc $k$-Tree}.

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