Polyhedral study of the maximum common induced subgraph problem

O problema do Máximo Subgrafo Induzido Comum (MSIC) pertence a classe NP-difícil e possui aplicações em diversas áreas. Apesar de sua complexidade, ainda é importante conhecer soluções exatas para instâncias deste problema. Os algoritmos exatos encontrados na literatura buscam resolvê-lo através de técnicas de backtracking ou através de sua redução para o problema da Clique Máxima. Neste trabalho procuramos dar uma solução exata para o MSIC, tratando-o diretamente através da utilização de modelos de Programação Linear Inteira (PLI) e técnicas de combinatória poliédrica. Assim, realizamos um estudo teórico do poliedro do MSIC e fomos capazes de encontrar algumas desigualdades válidas fortes, inclusive com provas de que algumas delas representam facetas daquele poliedro. Adicionalmente, provamos que existe uma equivalâencia entre o modelo PLI aqui apresentado para o MSIC e uma formulação bem conhecida para o problema da Clique Máxima. Posteriormente, foram implementados algoritmos de Branch-and-Bound (B&B) e Branch-and-Cut (B&C) utilizando as desigualdades encontradas e algumas técnicas para tentar tornar os algoritmos mais eficientes. Experimentos foram executados com os algoritmos implementados neste trabalho e, também, com um algoritmo já existente para resolver o problema da Clique, chamado Cliquer. Os resultados foram comparados e, dentre os algoritmos de PLI, constatamos que o mais eficiente foi aquele que utilizou uma formulação para o MSIC que chamamos de Clique-IS, utilizando B&B e técnicas mais básicas que outros algoritmos. Este algoritmo mostrou-se mais eficiente, inclusive, que um algoritmo PLI com um modelo baseado no problema da Clique Máaxima. Este fato sugere que para uma abordagem baseada em PLI, vale a pena utilizar uma formulação do MSIC diretamente, ao invés de uma que se apóie na redução deste para o problema da Clique Máxima. Ja a comparaçao do melhor algoritmo desenvolvido neste trabalho com o Cliquer, mostrou que este último é mais eficiente. Para que um algoritmo baseado em PLI (utilizando uma formulação com as mesmas variáveis usadas por nós) tivesse alguma chance de vencer um algoritmo combinatório como o Cliquer, seria necessário conhecer mais desigualdades que estivessem ativas na solução ótima do problema._________________________________________________________________________________________ ABSTRACT: The Maximum Common Subgraph problem (MSIC) is in MV-hard and has applications in several fields. Despite its complexity, it is still important to know exact solutions for instances of this problem. The exact algorithms found in literature try to solve it through backtracking techniques or through its reduction to the Maximum Clique problem. In this work we try to give an exact solution to MSIC by addressing it directly, using Linear Integer Programming (PLI) and polyhedral combinatorics techniques. So, we performed a study of the MSIC polyhedron and we were able to find some strong valid inequalities, including some that were proven to define facets of that polyhedron. Additionally, we proved that an equivalence between the PLI model presented here for MSIC and a well known formulation for the Maximum Clique problem exists. Later, Branch-and-Bound (B&B) and Branch-and-Cut (B&C) algorithms were implemented using the inequalities found and some techniques to try to render the algorithms more efficient. Experiments were performed with the algorithms implemented in this work and, also, with an already existing algorithm to solve the Maximum Clique problem, called Cliquer. The results were compared and, among the PLI algorithms, we found that the most efficient was the one that used the formulation which we called Clique-IS, using B&B and more basic techniques than other algorithms. This algorithm was even more efficient than a PLI algorithm with a Clique-based model. This fact suggests that for a PLI approach it is worth to use a formulation based on the MSIC polyhedron instead of one based on its reduction to the Maximum Clique problem. The comparison of the best algorithm developed in this work with Cliquer, though, showed that the latest is more efficient. In order to some PLI-based algorithm (using a formulation with the same variables used by us) to have any chance of outperforming a combinatorial algorithm like Cliquer, it would be necessary to know more inequalities that are active in the problem's optimal solution

Polyhedral study of the maximum common induced subgraph problem

Orientador: Cid Carvalho de SouzaDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: O problema do Máximo Subgrafo Induzido Comum (MSIC) pertence a classe NP-difícil e possui aplicações em diversas áreas. Apesar de sua complexidade, ainda é importante conhecer soluções exatas para instâncias deste problema. Os algoritmos exatos encontrados na literatura buscam resolvê-lo através de técnicas de backtracking ou através de sua redução para o problema da Clique Máxima. Neste trabalho procuramos dar uma solução exata para o MSIC, tratando-o diretamente através da utilização de modelos de Programação Linear Inteira (PLI) e técnicas de combinatória poliédrica. Assim, realizamos um estudo teórico do poliedro do MSIC e fomos capazes de encontrar algumas desigualdades válidas fortes, inclusive com provas de que algumas delas representam facetas daquele poliedro. Adicionalmente, provamos que existe uma equivalâencia entre o modelo PLI aqui apresentado para o MSIC e uma formulação bem conhecida para o problema da Clique Máxima. Posteriormente, foram implementados algoritmos de Branch-and-Bound (B&B) e Branch-and-Cut (B&C) utilizando as desigualdades encontradas e algumas técnicas para tentar tornar os algoritmos mais eficientes. Experimentos foram executados com os algoritmos implementados neste trabalho e, também, com um algoritmo já existente para resolver o problema da Clique, chamado Cliquer. Os resultados foram comparados e, dentre os algoritmos de PLI, constatamos que o mais eficiente foi aquele que utilizou uma formulação para o MSIC que chamamos de Clique-IS, utilizando B&B e técnicas mais básicas que outros algoritmos. Este algoritmo mostrou-se mais eficiente, inclusive, que um algoritmo PLI com um modelo baseado no problema da Clique Máaxima. Este fato sugere que para uma abordagem baseada em PLI, vale a pena utilizar uma formulação do MSIC diretamente, ao invés de uma que se apóie na redução deste para o problema da Clique Máxima. Ja a comparaçao do melhor algoritmo desenvolvido neste trabalho com o Cliquer, mostrou que este último é mais eficiente. Para que um algoritmo baseado em PLI (utilizando uma formulação com as mesmas variáveis usadas por nós) tivesse alguma chance de vencer um algoritmo combinatório como o Cliquer, seria necessário conhecer mais desigualdades que estivessem ativas na solução ótima do problemaAbstract: The Maximum Common Subgraph problem (MSIC) is in MV-hard and has applications in several fields. Despite its complexity, it is still important to know exact solutions for instances of this problem. The exact algorithms found in literature try to solve it through backtracking techniques or through its reduction to the Maximum Clique problem. In this work we try to give an exact solution to MSIC by addressing it directly, using Linear Integer Programming (PLI) and polyhedral combinatorics techniques. So, we performed a study of the MSIC polyhedron and we were able to find some strong valid inequalities, including some that were proven to define facets of that polyhedron. Additionally, we proved that an equivalence between the PLI model presented here for MSIC and a well known formulation for the Maximum Clique problem exists. Later, Branch-and-Bound (B&B) and Branch-and-Cut (B&C) algorithms were implemented using the inequalities found and some techniques to try to render the algorithms more efficient. Experiments were performed with the algorithms implemented in this work and, also, with an already existing algorithm to solve the Maximum Clique problem, called Cliquer. The results were compared and, among the PLI algorithms, we found that the most efficient was the one that used the formulation which we called Clique-IS, using B&B and more basic techniques than other algorithms. This algorithm was even more efficient than a PLI algorithm with a Clique-based model. This fact suggests that for a PLI approach it is worth to use a formulation based on the MSIC polyhedron instead of one based on its reduction to the Maximum Clique problem. The comparison of the best algorithm developed in this work with Cliquer, though, showed that the latest is more efficient. In order to some PLI-based algorithm (using a formulation with the same variables used by us) to have any chance of outperforming a combinatorial algorithm like Cliquer, it would be necessary to know more inequalities that are active in the problem's optimal solutionMestradoOtimização CombinatoriaMestre em Ciência da Computaçã

Polyhedral study of the maximum common induced subgraph problem

O problema do Máximo Subgrafo Induzido Comum (MSIC) pertence a classe NP-difícil e possui aplicações em diversas áreas. Apesar de sua complexidade, ainda é importante conhecer soluções exatas para instâncias deste problema. Os algoritmos exatos encontrados na literatura buscam resolvê-lo através de técnicas de backtracking ou através de sua redução para o problema da Clique Máxima. Neste trabalho procuramos dar uma solução exata para o MSIC, tratando-o diretamente através da utilização de modelos de Programação Linear Inteira (PLI) e técnicas de combinatória poliédrica. Assim, realizamos um estudo teórico do poliedro do MSIC e fomos capazes de encontrar algumas desigualdades válidas fortes, inclusive com provas de que algumas delas representam facetas daquele poliedro. Adicionalmente, provamos que existe uma equivalâencia entre o modelo PLI aqui apresentado para o MSIC e uma formulação bem conhecida para o problema da Clique Máxima. Posteriormente, foram implementados algoritmos de Branch-and-Bound (B&B) e Branch-and-Cut (B&C) utilizando as desigualdades encontradas e algumas técnicas para tentar tornar os algoritmos mais eficientes. Experimentos foram executados com os algoritmos implementados neste trabalho e, também, com um algoritmo já existente para resolver o problema da Clique, chamado Cliquer. Os resultados foram comparados e, dentre os algoritmos de PLI, constatamos que o mais eficiente foi aquele que utilizou uma formulação para o MSIC que chamamos de Clique-IS, utilizando B&B e técnicas mais básicas que outros algoritmos. Este algoritmo mostrou-se mais eficiente, inclusive, que um algoritmo PLI com um modelo baseado no problema da Clique Máaxima. Este fato sugere que para uma abordagem baseada em PLI, vale a pena utilizar uma formulação do MSIC diretamente, ao invés de uma que se apóie na redução deste para o problema da Clique Máxima. Ja a comparaçao do melhor algoritmo desenvolvido neste trabalho com o Cliquer, mostrou que este último é mais eficiente. Para que um algoritmo baseado em PLI (utilizando uma formulação com as mesmas variáveis usadas por nós) tivesse alguma chance de vencer um algoritmo combinatório como o Cliquer, seria necessário conhecer mais desigualdades que estivessem ativas na solução ótima do problema._________________________________________________________________________________________ ABSTRACT: The Maximum Common Subgraph problem (MSIC) is in MV-hard and has applications in several fields. Despite its complexity, it is still important to know exact solutions for instances of this problem. The exact algorithms found in literature try to solve it through backtracking techniques or through its reduction to the Maximum Clique problem. In this work we try to give an exact solution to MSIC by addressing it directly, using Linear Integer Programming (PLI) and polyhedral combinatorics techniques. So, we performed a study of the MSIC polyhedron and we were able to find some strong valid inequalities, including some that were proven to define facets of that polyhedron. Additionally, we proved that an equivalence between the PLI model presented here for MSIC and a well known formulation for the Maximum Clique problem exists. Later, Branch-and-Bound (B&B) and Branch-and-Cut (B&C) algorithms were implemented using the inequalities found and some techniques to try to render the algorithms more efficient. Experiments were performed with the algorithms implemented in this work and, also, with an already existing algorithm to solve the Maximum Clique problem, called Cliquer. The results were compared and, among the PLI algorithms, we found that the most efficient was the one that used the formulation which we called Clique-IS, using B&B and more basic techniques than other algorithms. This algorithm was even more efficient than a PLI algorithm with a Clique-based model. This fact suggests that for a PLI approach it is worth to use a formulation based on the MSIC polyhedron instead of one based on its reduction to the Maximum Clique problem. The comparison of the best algorithm developed in this work with Cliquer, though, showed that the latest is more efficient. In order to some PLI-based algorithm (using a formulation with the same variables used by us) to have any chance of outperforming a combinatorial algorithm like Cliquer, it would be necessary to know more inequalities that are active in the problem's optimal solution

The Multi-Maximum and Quasi-Maximum Common Subgraph Problem

The Maximum Common Subgraph problem has been long proven NP-hard. Nevertheless, it has countless practical applications, and researchers are still searching for exact solutions and scalable heuristic approaches. Driven by applications in molecular science and cyber-security, we concentrate on the Maximum Common Subgraph among an indefinite number of graphs. We first extend a state-of-the-art branch-and-bound procedure working on two graphs to N graphs. Then, given the high computational cost of this approach, we trade off complexity for accuracy, and we propose a set of heuristics to approximate the exact solution for N graphs. We analyze sequential, parallel multi-core, and parallel-many core (GPU-based) approaches, exploiting several leveraging techniques to decrease the contention among threads, improve the workload balance of the different tasks, reduce the computation time, and increase the final result size. We also present several sorting heuristics to order the vertices of the graphs and the graphs themselves. We compare our algorithms with a state-of-the-art method on publicly available benchmark sets. On graph pairs, we are able to speed up the exact computation by a 2× factor, pruning the search space by more than 60%. On sets of more than two graphs, all exact solutions are extremely time-consuming and of a complex application in many real cases. On the contrary, our heuristics are far less expensive (as they show a lower-bound for the speed up of 10×), have a far better asymptotic complexity (with speed ups up to several orders of magnitude in our experiments), and obtain excellent approximations of the maximal solution with 98.5% of the nodes on average

The Maximum Common Subgraph Problem: A Parallel and Multi-Engine Approach

The maximum common subgraph of two graphs is the largest possible common subgraph, i.e., the common subgraph with as many vertices as possible. Even if this problem is very challenging, as it has been long proven NP-hard, its countless practical applications still motivates searching for exact solutions. This work discusses 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 minimizes data structure repetitions. We also extend the original 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 to reorder the adjacency matrix, to deal with “dead-ends”, and to randomize the search with automatic restarts. These heuristics can achieve significant speed-ups on specific instances, even if they may not be competitive with the original strategy on average. 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 fragility 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

Comparing graphs

Graphs are a well-studied mathematical concept, which has become ubiquitous to represent structured data in many application domains like computer vision, social network analysis or chem- and bioinformatics. The ever-increasing amount of data in these domains requires to efficiently organize and extract information from large graph data sets. In this context techniques for comparing graphs are fundamental, e.g., in order to obtain meaningful similarity measures between graphs. These are a prerequisite for the application of a variety of data mining algorithms to the domain of graphs. Hence, various approaches to graph comparison evolved and are wide-spread in practice. This thesis is dedicated to two different strategies for comparing graphs: maximum common subgraph problems and graph kernels. We study maximum common subgraph problems, which are based on classical graph-theoretical concepts for graph comparison and are NP-hard in the general case. We consider variants of the maximum common subgraph problem in restricted graph classes, which are highly relevant for applications in cheminformatics. We develop a polynomial-time algorithm, which allows to compute a maximum common subgraph under block and bridge preserving isomorphism in series-parallel graphs. This generalizes the problem of computing maximum common biconnected subgraphs in series-parallel graphs. We show that previous approaches to this problem, which are based on the separators represented by standard graph decompositions, fail. We introduce the concept of potential separators to overcome this issue and use them algorithmically to solve the problem in series-parallel graphs. We present algorithms with improved bounds on running time for the subclass of outerplanar graphs. Finally, we establish a sufficient condition for maximum common subgraph variants to allow derivation of graph distance metrics. This leads to polynomial-time computable graph distance metrics in restricted graph classes. This progress constitutes a step towards solving practically relevant maximum common subgraph problems in polynomial time. The second contribution of this thesis is to graph kernels, which have their origin in specific data mining algorithms. A key property of graph kernels is that they allow to consider a large (possibly infinite) number of features and can support graphs with arbitrary annotation, while being efficiently computable. The main contributions of this part of the thesis are (i) the development of novel graph kernels, which are especially designed for attributed graphs with arbitrary annotations and (ii) the systematic study of implicit and explicit mapping into a feature space for computation of graph kernels w.r.t. its impact on the running time and the ability to consider arbitrary annotations. We propose graph kernels based on bijections between subgraphs and walks of fixed length. In an experimental study we show that these approaches provide a viable alternative to known techniques, in particular for graphs with complex annotations