Long Circuits and Large Euler Subgraphs

An undirected graph is Eulerian if it is connected and all its vertices are of even degree. Similarly, a directed graph is Eulerian, if for each vertex its in-degree is equal to its out-degree. It is well known that Eulerian graphs can be recognized in polynomial time while the problems of finding a maximum Eulerian subgraph or a maximum induced Eulerian subgraph are NP-hard. In this paper, we study the parameterized complexity of the following Euler subgraph problems: - Large Euler Subgraph: For a given graph G and integer parameter k, does G contain an induced Eulerian subgraph with at least k vertices? - Long Circuit: For a given graph G and integer parameter k, does G contain an Eulerian subgraph with at least k edges? Our main algorithmic result is that Large Euler Subgraph is fixed parameter tractable (FPT) on undirected graphs. We find this a bit surprising because the problem of finding an induced Eulerian subgraph with exactly k vertices is known to be W[1]-hard. The complexity of the problem changes drastically on directed graphs. On directed graphs we obtained the following complexity dichotomy: Large Euler Subgraph is NP-hard for every fixed k>3 and is solvable in polynomial time for k<=3. For Long Circuit, we prove that the problem is FPT on directed and undirected graphs

A simpler and more efficient algorithm for the next-to-shortest path problem

Given an undirected graph $G=(V,E)$ with positive edge lengths and two vertices $s$ and $t$, the next-to-shortest path problem is to find an $st$-path which length is minimum amongst all $st$-paths strictly longer than the shortest path length. In this paper we show that the problem can be solved in linear time if the distances from $s$ and $t$ to all other vertices are given. Particularly our new algorithm runs in $O(|V|\log |V|+|E|)$ time for general graphs, which improves the previous result of $O(|V|^2)$ time for sparse graphs, and takes only linear time for unweighted graphs, planar graphs, and graphs with positive integer edge lengths.Comment: Partial result appeared in COCOA201

Parameterization Above a Multiplicative Guarantee

Parameterization above a guarantee is a successful paradigm in Parameterized Complexity. To the best of our knowledge, all fixed-parameter tractable problems in this paradigm share an additive form defined as follows. Given an instance (I,k) of some (parameterized) problem ? with a guarantee g(I), decide whether I admits a solution of size at least (at most) k+g(I). Here, g(I) is usually a lower bound (resp. upper bound) on the maximum (resp. minimum) size of a solution. Since its introduction in 1999 for Max SAT and Max Cut (with g(I) being half the number of clauses and half the number of edges, respectively, in the input), analysis of parameterization above a guarantee has become a very active and fruitful topic of research. We highlight a multiplicative form of parameterization above a guarantee: Given an instance (I,k) of some (parameterized) problem ? with a guarantee g(I), decide whether I admits a solution of size at least (resp. at most) k ? g(I). In particular, we study the Long Cycle problem with a multiplicative parameterization above the girth g(I) of the input graph, and provide a parameterized algorithm for this problem. Apart from being of independent interest, this exemplifies how parameterization above a multiplicative guarantee can arise naturally. We also show that, for any fixed constant ?>0, multiplicative parameterization above g(I)^(1+?) of Long Cycle yields para-NP-hardness, thus our parameterization is tight in this sense. We complement our main result with the design (or refutation of the existence) of algorithms for other problems parameterized multiplicatively above girth

A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data

We present a new algorithm for enumerating bubbles with length constraints in directed graphs. This problem arises in transcriptomics, where the question is to identify all alternative splicing events present in a sample of mRNAs sequenced by RNA-seq. This is the first polynomial-delay algorithm for this problem and we show that in practice, it is faster than previous approaches. This enables us to deal with larger instances and therefore to discover novel alternative splicing events, especially long ones, that were previously overseen using existing methods.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Distributed Connectivity Decomposition

We present time-efficient distributed algorithms for decomposing graphs with large edge or vertex connectivity into multiple spanning or dominating trees, respectively. As their primary applications, these decompositions allow us to achieve information flow with size close to the connectivity by parallelizing it along the trees. More specifically, our distributed decomposition algorithms are as follows: (I) A decomposition of each undirected graph with vertex-connectivity $k$ into (fractionally) vertex-disjoint weighted dominating trees with total weight $\Omega(\frac{k}{\log n})$, in $\widetilde{O}(D+\sqrt{n})$ rounds. (II) A decomposition of each undirected graph with edge-connectivity $\lambda$ into (fractionally) edge-disjoint weighted spanning trees with total weight $\lceil\frac{\lambda-1}{2}\rceil(1-\varepsilon)$, in $\widetilde{O}(D+\sqrt{n\lambda})$ rounds. We also show round complexity lower bounds of $\tilde{\Omega}(D+\sqrt{\frac{n}{k}})$ and $\tilde{\Omega}(D+\sqrt{\frac{n}{\lambda}})$ for the above two decompositions, using techniques of [Das Sarma et al., STOC'11]. Moreover, our vertex-connectivity decomposition extends to centralized algorithms and improves the time complexity of [Censor-Hillel et al., SODA'14] from $O(n^3)$ to near-optimal $\tilde{O}(m)$. As corollaries, we also get distributed oblivious routing broadcast with $O(1)$-competitive edge-congestion and $O(\log n)$-competitive vertex-congestion. Furthermore, the vertex connectivity decomposition leads to near-time-optimal $O(\log n)$-approximation of vertex connectivity: centralized $\widetilde{O}(m)$ and distributed $\tilde{O}(D+\sqrt{n})$. The former moves toward the 1974 conjecture of Aho, Hopcroft, and Ullman postulating an $O(m)$ centralized exact algorithm while the latter is the first distributed vertex connectivity approximation

Vertex Disjoint Path in Upward Planar Graphs

The $k$-vertex disjoint paths problem is one of the most studied problems in algorithmic graph theory. In 1994, Schrijver proved that the problem can be solved in polynomial time for every fixed $k$ when restricted to the class of planar digraphs and it was a long standing open question whether it is fixed-parameter tractable (with respect to parameter $k$) on this restricted class. Only recently, \cite{CMPP}.\ achieved a major breakthrough and answered the question positively. Despite the importance of this result (and the brilliance of their proof), it is of rather theoretical importance. Their proof technique is both technically extremely involved and also has at least double exponential parameter dependence. Thus, it seems unrealistic that the algorithm could actually be implemented. In this paper, therefore, we study a smaller class of planar digraphs, the class of upward planar digraphs, a well studied class of planar graphs which can be drawn in a plane such that all edges are drawn upwards. We show that on the class of upward planar digraphs the problem (i) remains NP-complete and (ii) the problem is fixed-parameter tractable. While membership in FPT follows immediately from \cite{CMPP}'s general result, our algorithm has only single exponential parameter dependency compared to the double exponential parameter dependence for general planar digraphs. Furthermore, our algorithm can easily be implemented, in contrast to the algorithm in \cite{CMPP}.Comment: 14 page

An Algorithmic Metatheorem for Directed Treewidth

The notion of directed treewidth was introduced by Johnson, Robertson, Seymour and Thomas [Journal of Combinatorial Theory, Series B, Vol 82, 2001] as a first step towards an algorithmic metatheory for digraphs. They showed that some NP-complete properties such as Hamiltonicity can be decided in polynomial time on digraphs of constant directed treewidth. Nevertheless, despite more than one decade of intensive research, the list of hard combinatorial problems that are known to be solvable in polynomial time when restricted to digraphs of constant directed treewidth has remained scarce. In this work we enrich this list by providing for the first time an algorithmic metatheorem connecting the monadic second order logic of graphs to directed treewidth. We show that most of the known positive algorithmic results for digraphs of constant directed treewidth can be reformulated in terms of our metatheorem. Additionally, we show how to use our metatheorem to provide polynomial time algorithms for two classes of combinatorial problems that have not yet been studied in the context of directed width measures. More precisely, for each fixed $k,w \in \mathbb{N}$, we show how to count in polynomial time on digraphs of directed treewidth $w$, the number of minimum spanning strong subgraphs that are the union of $k$ directed paths, and the number of maximal subgraphs that are the union of $k$ directed paths and satisfy a given minor closed property. To prove our metatheorem we devise two technical tools which we believe to be of independent interest. First, we introduce the notion of tree-zig-zag number of a digraph, a new directed width measure that is at most a constant times directed treewidth. Second, we introduce the notion of $z$-saturated tree slice language, a new formalism for the specification and manipulation of infinite sets of digraphs.Comment: 41 pages, 6 figures, Accepted to Discrete Applied Mathematic