Parameterized Directed kk-Chinese Postman Problem and kk Arc-Disjoint Cycles Problem on Euler Digraphs

In the Directed $k$-Chinese Postman Problem ($k$-DCPP), we are given a connected weighted digraph $G$ and asked to find $k$ non-empty closed directed walks covering all arcs of $G$ such that the total weight of the walks is minimum. Gutin, Muciaccia and Yeo (Theor. Comput. Sci. 513 (2013) 124--128) asked for the parameterized complexity of $k$-DCPP when $k$ is the parameter. We prove that the $k$-DCPP is fixed-parameter tractable. We also consider a related problem of finding $k$ arc-disjoint directed cycles in an Euler digraph, parameterized by $k$. Slivkins (ESA 2003) showed that this problem is W[1]-hard for general digraphs. Generalizing another result by Slivkins, we prove that the problem is fixed-parameter tractable for Euler digraphs. The corresponding problem on vertex-disjoint cycles in Euler digraphs remains W[1]-hard even for Euler digraphs

Parameterized Rural Postman Problem

The Directed Rural Postman Problem (DRPP) can be formulated as follows: given a strongly connected directed multigraph $D=(V,A)$ with nonnegative integral weights on the arcs, a subset $R$ of $A$ and a nonnegative integer $\ell$, decide whether $D$ has a closed directed walk containing every arc of $R$ and of total weight at most $\ell$. Let $k$ be the number of weakly connected components in the the subgraph of $D$ induced by $R$. Sorge et al. (2012) ask whether the DRPP is fixed-parameter tractable (FPT) when parameterized by $k$, i.e., whether there is an algorithm of running time $O^*(f(k))$ where $f$ is a function of $k$ only and the $O^*$ notation suppresses polynomial factors. Sorge et al. (2012) note that this question is of significant practical relevance and has been open for more than thirty years. Using an algebraic approach, we prove that DRPP has a randomized algorithm of running time $O^*(2^k)$ when $\ell$ is bounded by a polynomial in the number of vertices in $D$. We also show that the same result holds for the undirected version of DRPP, where $D$ is a connected undirected multigraph

Parameterized complexity of the k-arc Chinese Postman Problem

In the Mixed Chinese Postman Problem (MCPP), given an edge-weighted mixed graph $G$ ($G$ may have both edges and arcs), our aim is to find a minimum weight closed walk traversing each edge and arc at least once. The MCPP parameterized by the number of edges was known to be fixed-parameter tractable using a simple argument. Solving an open question of van Bevern et al., we prove that the MCPP parameterized by the number of arcs is also fixed-parameter tractable. Our proof is more involved and, in particular, uses a well-known result of Marx, O'Sullivan and Razgon (2013) on the treewidth of torso graphs with respect to small separators. We obtain a small cut analog of this result, and use it to construct a tree decomposition which, despite not having bounded width, has other properties allowing us to design a fixed-parameter algorithm

Editing to Eulerian Graphs

We investigate the problem of modifying a graph into a connected graph in which the degree of each vertex satisfies a prescribed parity constraint. Let $ea$, $ed$ and $vd$ denote the operations edge addition, edge deletion and vertex deletion respectively. For any $S\subseteq \{ea,ed,vd\}$, we define Connected Degree Parity Editing$(S)$ (CDPE($S$)) to be the problem that takes as input a graph $G$, an integer $k$ and a function $\delta\colon V(G)\rightarrow\{0,1\}$, and asks whether $G$ can be modified into a connected graph $H$ with $d_{H}(v)\equiv\delta(v)~(\bmod~2)$ for each $v\in V(H)$, using at most $k$ operations from $S$. We prove that 1. if $S=\{ea\}$ or $S=\{ea,ed\}$, then CDPE($S$) can be solved in polynomial time; 2. if $\{vd\} \subseteq S\subseteq \{ea,ed,vd\}$, then CDPE($S$) is NP-complete and W[1]-hard when parameterized by $k$, even if $\delta\equiv 0$. Together with known results by Cai and Yang and by Cygan, Marx, Pilipczuk, Pilipczuk and Schlotter, our results completely classify the classical and parameterized complexity of the CDPE($S$) problem for all $S\subseteq \{ea,ed,vd\}$. We obtain the same classification for a natural variant of the CDPE($S$) problem on directed graphs, where the target is a weakly connected digraph in which the difference between the in- and out-degree of every vertex equals a prescribed value. As an important implication of our results, we obtain polynomial-time algorithms for the Eulerian Editing problem and its directed variant.Comment: 33 pages. An extended abstract of this paper will appear in the proceedings of FSTTCS 201

JGraphT -- A Java library for graph data structures and algorithms

Mathematical software and graph-theoretical algorithmic packages to efficiently model, analyze and query graphs are crucial in an era where large-scale spatial, societal and economic network data are abundantly available. One such package is JGraphT, a programming library which contains very efficient and generic graph data-structures along with a large collection of state-of-the-art algorithms. The library is written in Java with stability, interoperability and performance in mind. A distinctive feature of this library is the ability to model vertices and edges as arbitrary objects, thereby permitting natural representations of many common networks including transportation, social and biological networks. Besides classic graph algorithms such as shortest-paths and spanning-tree algorithms, the library contains numerous advanced algorithms: graph and subgraph isomorphism; matching and flow problems; approximation algorithms for NP-hard problems such as independent set and TSP; and several more exotic algorithms such as Berge graph detection. Due to its versatility and generic design, JGraphT is currently used in large-scale commercial, non-commercial and academic research projects. In this work we describe in detail the design and underlying structure of the library, and discuss its most important features and algorithms. A computational study is conducted to evaluate the performance of JGraphT versus a number of similar libraries. Experiments on a large number of graphs over a variety of popular algorithms show that JGraphT is highly competitive with other established libraries such as NetworkX or the BGL.Comment: Major Revisio

Networks, (K)nots, Nucleotides, and Nanostructures

Designing self-assembling DNA nanostructures often requires the identification of a route for a scaffolding strand of DNA through the target structure. When the target structure is modeled as a graph, these scaffolding routes correspond to Eulerian circuits subject to turning restrictions imposed by physical constraints on the strands of DNA. Existence of such Eulerian circuits is an NP-hard problem, which can be approached by adapting solutions to a version of the Traveling Salesperson Problem. However, the author and collaborators have demonstrated that even Eulerian circuits obeying these turning restrictions are not necessarily feasible as scaffolding routes by giving examples of nontrivially knotted circuits which cannot be traced by the unknotted scaffolding strand. Often, targets of DNA nanostructure self-assembly are modeled as graphs embedded on surfaces in space. In this case, Eulerian circuits obeying the turning restrictions correspond to A-trails, circuits which turn immediately left or right at each vertex. In any graph embedded on the sphere, all A-trails are unknotted regardless of the embedding of the sphere in space. We show that this does not hold in general for graphs on the torus. However, we show this property does hold for checkerboard-colorable graphs on the torus, that is, those graphs whose faces can be properly 2-colored, and provide a partial converse to this result. As a consequence, we characterize (with one exceptional family) regular triangulations of the torus containing unknotted A-trails. By developing a theory of sums of A-trails, we lift constructions from the torus to arbitrary n-tori, and by generalizing our work on A-trails to smooth circuit decompositions, we construct all torus links and certain sums of torus links from circuit decompositions of rectangular torus grids. Graphs embedded on surfaces are equivalent to ribbon graphs, which are particularly well-suited to modeling DNA nanostructures, as their boundary components correspond to strands of DNA and their twisted ribbons correspond to double-helices. Every ribbon graph has a corresponding delta-matroid, a combinatorial object encoding the structure of the ribbon-graph\u27s spanning quasi-trees (substructures having exactly one boundary component). We show that interlacement with respect to quasi-trees can be generalized to delta-matroids, and use the resulting structure on delta-matroids to provide feasible-set expansions for a family of delta-matroid polynomials, both recovering well-known expansions of this type (such as the spanning-tree expansion of the Tutte polynnomial) as well as providing several previously unknown expansions. Among these are expansions for the transition polynomial, a version of which has been used to study DNA nanostructure self-assembly, and the interlace polynomial, which solves a problem in DNA recombination