The Maximum Common Subgraph is a computationally challenging problem with countless practical applications. Even if it has been long proven NP-hard, its importance still motivates searching for exact solutions. This work starts by discussing the possibility to extend an existing, very effective branch-and-bound procedure on parallel multi-core and many-core architectures. We analyze a parallel multi-core implementation that exploits a divide-and-conquer approach based on a thread-pool, which does not deteriorate the original algorithmic efficiency and it is not memory bound. We extend the algorithm to parallel many-core GPU architectures adopting the CUDA programming framework, and we show how to handle the heavily workload-unbalance and the massive data dependency. Then, we suggest new heuristics that reorder the adjacency matrix, deal with "dead-ends" and randomize the search with automatic restarts, achieving significant improvements on specific cases. Finally, we propose a portfolio approach, which integrates all the different local search algorithms as component tools. Such portfolio, rather than choosing the best tool for a given instance up-front, takes the decision on-line. The proposed approach drastically limits memory bandwidth constraints and avoids other typical portfolio fragilities as CPU and GPU versions often show a complementary efficiency and run on separated platforms. Experimental results support the claims and motivate further research to better exploit GPUs in embedded task-intensive, and multi-engine parallel applications.
Given a graph $G$, the NP-hard Maximum Planar Subgraph problem asks for a planar subgraph of $G$ with the maximum number of edges. The only known non-trivial exact algorithm utilizes Kuratowski's famous planarity criterion and can be formulated as an integer linear program (ILP) or a pseudo-boolean satisfiability problem (PBS). We examine three alternative characterizations of planarity regarding their applicability to model maximum planar subgraphs. For each, we consider both ILP and PBS variants, investigate diverse formulation aspects, and evaluate their practical performance.
In this paper we study the problem of finding a maximum induced d-degenerate subgraph in a given n-vertex graph from the point of view of exact algorithms. We show that for any fixed d one can find a maximum induced d-degenerate subgraph in randomized (2-eps_d)^n n^O(1) time, for some constant eps_d>0 depending only on d. Moreover, our algorithm can be used to sample inclusion-wise maximal induced d-degenerate subgraphs in such a manner that every such subgraph is output with probability at least (2-eps_d)^-n; hence, we prove that their number is bounded by (2-eps_d)^n.
The NP-hard Maximum Planar Subgraph problem asks for a planar subgraph $H$ of a given graph $G$ such that $H$ has maximum edge cardinality. For more than two decades, the only known non-trivial exact algorithm was based on integer linear programming and Kuratowski's famous planarity criterion. We build upon this approach and present new constraint classes, together with a lifting of the polyhedron, to obtain provably stronger LP-relaxations, and in turn faster algorithms in practice. The new constraints take Euler's polyhedron formula as a starting point and combine it with considering cycles …
Network enrichment analysis methods allow to identify active modules without being biased towards a priori defined pathways. One of mathematical formulations of such analysis is a reduction to a maximum-weight connected subgraph problem. In particular, in analysis of metabolic networks a generalized maximum-weight connected subgraph (GMWCS) problem, where both nodes and edges are scored, naturally arises. Here we present the first to our knowledge practical exact GMWCS solver. We have tested it on real-world instances and compared to similar solvers. First, the results show that on node-weight…
Given an undirected node-weighted graph, the Maximum-Weight Connected Subgraph problem (MWCS) is to identify a subset of nodes of maximalsum of weights that induce a connected subgraph. MWCS is closely related to the well-studied Prize Collecting Steiner Tree problem and has many applications in different areas, including computational biology, network design and computer vision. The problem is NP-hard and even hard to approximate within a constant factor. In this work we describe an algorithmic scheme for solving MWCS to provable optimality, which is based on preprocessing rules, new results …
We propose a new and strengthened Branch-and-Bound (BnB) algorithm for the maximum common (connected) induced subgraph problem based on two new operators, Long-Short Memory (LSM) and Leaf vertex Union Match (LUM). Given two graphs for which we search for the maximum common (connected) induced subgraph, the first operator of LSM maintains a score for the branching node using the short-term reward of each vertex of the first graph and the long-term reward of each vertex pair of the two graphs. In this way, the BnB process learns to reduce the search tree size significantly and improve the algori…
Schietgat, Ramon and Bruynooghe proposed a polynomial-time algorithm for computing a maximum common subgraph under the block-and-bridge preserving subgraph isomorphism (BBP-MCS) for outerplanar graphs. We show that the article contains the following errors: (i) The running time of the presented approach is claimed to be $\mathcal{O}(n^{2.5})$ for two graphs of order $n$. We show that the algorithm of the authors allows no better bound than $\mathcal{O}(n^4)$ when using state-of-the-art general purpose methods to solve the matching instances arising as subproblems. This is even true for the spe…
The Maximum Balanced Subgraph Problem (MBSP) is the problem of finding a subgraph of a signed graph that is balanced and maximizes the cardinality of its vertex set. We are interested in the exact solution of the problem: an improved version of a branch-and-cut algorithm is proposed. Extensive computational experiments are carried out on a set of instances from three applications previously discussed in the literature as well as on a set of random instances.
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…
In this paper, we develop efficient exact and approximate algorithms for computing a maximum independent set in random graphs. In a random graph $G$, each pair of vertices are joined by an edge with a probability $p$, where $p$ is a constant between $0$ and $1$. We show that, a maximum independent set in a random graph that contains $n$ vertices can be computed in expected computation time $2^{O(\log_{2}^{2}{n})}$. Using techniques based on enumeration, we develop an algorithm that can find a largest common subgraph in two random graphs in $n$ and $m$ vertices ($m \leq n$) in expected computat…
The complexity of the maximum common connected subgraph problem in partial $k$-trees is still not fully understood. Polynomial-time solutions are known for degree-bounded outerplanar graphs, a subclass of the partial $2$-trees. On the other hand, the problem is known to be ${\bf NP}$-hard in vertex-labeled partial $11$-trees of bounded degree. We consider series-parallel graphs, i.e., partial $2$-trees. We show that the problem remains ${\bf NP}$-hard in biconnected series-parallel graphs with all but one vertex of degree $3$ or less. A positive complexity result is presented for a related pro…
Given an undirected graph $G$ and integers $c$ and $k$, the Maximum Edge-Colorable Subgraph problem asks whether we can delete at most $k$ edges in $G$ to obtain a graph that has a proper edge coloring with at most $c$ colors. We show that Maximum Edge-Colorable Subgraph admits, for every fixed $c$, a linear-size problem kernel when parameterized by the edge deletion distance of $G$ to a graph with maximum degree $c-1$. This parameterization measures the distance to instances that, due to Vizing's famous theorem, are trivial yes-instances. For $c\le 4$, we also provide a linear-size kernel for…
In the classical Maximum Acyclic Subgraph problem (MAS), given a directed-edge weighted graph, we are required to find an ordering of the nodes that maximizes the total weight of forward-directed edges. MAS admits a 2 approximation, and this approximation is optimal under the Unique Game Conjecture. In this paper we consider a generalization of MAS, the Restricted Maximum Acyclic Subgraph problem (RMAS), where each node is associated with a list of integer labels, and we have to find a labeling of the nodes so as to maximize the weight of edges whose head label is larger than the tail label. T…
We define a proportionally dense subgraph (PDS) as an induced subgraph of a graph with the property that each vertex in the PDS is adjacent to proportionally as many vertices in the subgraph as in the graph. We prove that the problem of finding a PDS of maximum size is APX-hard on split graphs, and NP-hard on bipartite graphs. We also show that deciding if a PDS is inclusion-wise maximal is co-NP-complete on bipartite graphs. Nevertheless, we present a simple polynomial-time $(2-\frac{2}{Δ+1})$-approximation algorithm for the problem, where $Δ$ is the maximum degree of the graph. Finally, we s…
We study the directed maximum common edge subgraph problem (DMCES) for the class of directed graphs that are finite, weakly connected, oriented, and simple. We use DMCES to define a metric on partially ordered sets that can be represented as weakly connected directed acyclic graphs. While most existing metrics assume that the underlying sets of the partial order are identical, and only the relationships between elements can differ, the metric defined here allows the partially ordered sets to be different. The proof that there is a metric based on DMCES involves the extension of the concept of …
We prove that in an n-vertex graph, induced chordal and interval subgraphs with the maximum number of vertices can be found in time $O(2^{λn})$ for some $λ<1$. These are the first algorithms breaking the trivial $2^n n^{O(1)}$ bound of the brute-force search for these problems.
We propose a simple and computationally efficient method for dense subgraph discovery, which is a classic problem both in theory and in practice. It is well known that dense subgraphs can have strong correlation with structures of interest in real-world networks across various domains ranging from social networks to biological systems [Gionis and Tsourakakis `15]. For the densest subgraph problem, Charikar's greedy algorithm [Asashiro `00, Charikar `00] is very simple, and can typically find result of quality much better than the provable factor 2-approximation, which makes it very popular in …
For a graph G with real weights assigned to the vertices (edges), the MAX H-SUBGRAPH problem is to find an H-subgraph of G with maximum total weight, if one exists. The all-pairs MAX H-SUBGRAPH problem is to find for every pair of vertices u,v, a maximum H-subgraph containing both u and v, if one exists. Our main results are new strongly polynomial algorithms for the all-pairs MAX H-SUBGRAPH problem for vertex weighted graphs. We also give improved algorithms for the MAX-H SUBGRAPH problem for edge weighted graphs, and various related problems, including computing the first k most significant …
Given a graph $G$, the NP-hard Maximum Planar Subgraph problem (MPS) asks for a planar subgraph of $G$ with the maximum number of edges. There are several heuristic, approximative, and exact algorithms to tackle the problem, but---to the best of our knowledge---they have never been compared competitively in practice. We report on an exploratory study on the relative merits of the diverse approaches, focusing on practical runtime, solution quality, and implementation complexity. Surprisingly, a seemingly only theoretically strong approximation forms the building block of the strongest choice.
The Balanced Connected Subgraph problem (BCS) was recently introduced by Bhore et al. (CALDAM 2019). In this problem, we are given a graph $G$ whose vertices are colored by red or blue. The goal is to find a maximum connected subgraph of $G$ having the same number of blue vertices and red vertices. They showed that this problem is NP-hard even on planar graphs, bipartite graphs, and chordal graphs. They also gave some positive results: BCS can be solved in $O(n^3)$ time for trees and $O(n + m)$ time for split graphs and properly colored bipartite graphs, where $n$ is the number of vertices and…
The component size of a graph is the maximum number of edges in any connected component of the graph. Given a graph $G$ and two integers $k$ and $c$, $(k,c)$-Decomposition is the problem of deciding whether $G$ admits an edge partition into $k$ subgraphs with component size at most $c$. We prove that for any fixed $k \ge 2$ and $c \ge 2$, $(k,c)$-Decomposition is NP-complete in bipartite graphs. Also, when both $k$ and $c$ are part of the input, $(k,c)$-Decomposition is NP-complete even in trees. Moreover, $(k,c)$-Decomposition in trees is W[1]-hard with parameter $k$, and is FPT with paramete…
Inductive $k$-independent graphs generalize chordal graphs and have recently been advocated in the context of interference-avoiding wireless communication scheduling. The NP-hard problem of finding maximum-weight induced $c$-colorable subgraphs, which is a generalization of finding maximum independent sets, naturally occurs when selecting $c$ sets of pairwise non-conflicting jobs (modeled as graph vertices). We investigate the parameterized complexity of this problem on inductive $k$-independent graphs. We show that the Independent Set problem is W[1]-hard even on 2-simplicial 3-minoes---a sub…
We consider graphs without loops or parallel edges in which every edge is assigned + or -. Such a signed graph is balanced if its vertex set can be partitioned into parts $V_1$ and $V_2$ such that all edges between vertices in the same part have sign + and all edges between vertices of different parts have sign $-$ (one of the parts may be empty). It is well-known that every connected signed graph with $n$ vertices and $m$ edges has a balanced subgraph with at least $\frac{m}{2} + \frac{n-1}{4}$ edges and this bound is tight. We consider the following parameterized problem: given a connected s…
