Stronger ILPs for the Graph Genus Problem

The minimum genus of a graph is an important question in graph theory and a key ingredient in several graph algorithms. However, its computation is NP-hard and turns out to be hard even in practice. Only recently, the first non-trivial approach - based on SAT and ILP (integer linear programming) models - has been presented, but it is unable to successfully tackle graphs of genus larger than 1 in practice. Herein, we show how to improve the ILP formulation. The crucial ingredients are two-fold. First, we show that instead of modeling rotation schemes explicitly, it suffices to optimize over partitions of the (bidirected) arc set A of the graph. Second, we exploit the cycle structure of the graph, explicitly mapping short closed walks on A to faces in the embedding. Besides the theoretical advantages of our models, we show their practical strength by a thorough experimental evaluation. Contrary to the previous approach, we are able to quickly solve many instances of genus > 1

Towards Structural Classification of Proteins based on Contact Map Overlap

A multitude of measures have been proposed to quantify the similarity between protein 3-D structure. Among these measures, contact map overlap (CMO) maximization deserved sustained attention during past decade because it offers a fine estimation of the natural homology relation between proteins. Despite this large involvement of the bioinformatics and computer science community, the performance of known algorithms remains modest. Due to the complexity of the problem, they got stuck on relatively small instances and are not applicable for large scale comparison. This paper offers a clear improvement over past methods in this respect. We present a new integer programming model for CMO and propose an exact B &B algorithm with bounds computed by solving Lagrangian relaxation. The efficiency of the approach is demonstrated on a popular small benchmark (Skolnick set, 40 domains). On this set our algorithm significantly outperforms the best existing exact algorithms, and yet provides lower and upper bounds of better quality. Some hard CMO instances have been solved for the first time and within reasonable time limits. From the values of the running time and the relative gap (relative difference between upper and lower bounds), we obtained the right classification for this test. These encouraging result led us to design a harder benchmark to better assess the classification capability of our approach. We constructed a large scale set of 300 protein domains (a subset of ASTRAL database) that we have called Proteus 300. Using the relative gap of any of the 44850 couples as a similarity measure, we obtained a classification in very good agreement with SCOP. Our algorithm provides thus a powerful classification tool for large structure databases

Logic learning and optimized drawing: two hard combinatorial problems

Nowadays, information extraction from large datasets is a recurring operation in countless fields of applications. The purpose leading this thesis is to ideally follow the data flow along its journey, describing some hard combinatorial problems that arise from two key processes, one consecutive to the other: information extraction and representation. The approaches here considered will focus mainly on metaheuristic algorithms, to address the need for fast and effective optimization methods. The problems studied include data extraction instances, as Supervised Learning in Logic Domains and the Max Cut-Clique Problem, as well as two different Graph Drawing Problems. Moreover, stemming from these main topics, other additional themes will be discussed, namely two different approaches to handle Information Variability in Combinatorial Optimization Problems (COPs), and Topology Optimization of lightweight concrete structures

On the one-sided crossing minimization in a bipartite graph with large degrees

AbstractGiven a bipartite graph G=(V,W,E), a 2-layered drawing consists of placing nodes in the first node set V on a straight line L1 and placing nodes in the second node set W on a parallel line L2. For a given ordering of nodes in W on L2, the one-sided crossing minimization problem asks to find an ordering of nodes in V on L1 so that the number of arc crossings is minimized. A well-known lower bound LB on the minimum number of crossings is obtained by summing up min{cuv,cvu} over all node pairs u,v∈V, where cuv denotes the number of crossings generated by arcs incident to u and v when u precedes v in an ordering. In this paper, we prove that there always exists a solution whose crossing number is at most (1.2964+12/(δ-4))LB if the minimum degree δ of a node in V is at least 5

Algorithms for network expansion

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Flood lamination strategy based on a three-flood-diversion-area system management

The flood lamination has for principal objective to maintain a downstream flow at a fixed lamination level. For this goal, it is necessary to proceed to the dimensioning of the river system capacity and to make sure of its management by taking into account socio-economic and environmental constraints. The use of flood diversion areas on a river has for main interest to protect inhabited downstream areas. In this paper, a flood lamination strategy aiming at deforming the wave of flood at the entrance of the zone to be protected is presented. A transportation network modeling and a flow optimization method are proposed. The flow optimization method, is based on the modeling of a Min-Cost-Max-flow problem with a linear programming formulation. The optimization algorithm used in this method is the interior-point algorithm which allows a relaxation of the solution of the problem and avoids some non feasibility cases due to the use of constraints based on real data. For a forecast horizon corresponding to the flood episode, the management method of the flood volumes is evaluated on a 2D simulator of a river equipped with a three-flood-diversion- area system. Performances show the effectiveness of the method and its ability to manage flood lamination with efficient water storage

Polynomial fixed-parameter algorithms : a case study for longest path on interval graphs.

We study the design of fixed-parameter algorithms for problems already known to be solvable in polynomial time. The main motivation is to get more efficient algorithms for problems with unattractive polynomial running times. Here, we focus on a fundamental graph problem: Longest Path; it is NP-hard in general but known to be solvable in O(n^4) time on n-vertex interval graphs. We show how to solve Longest Path on Interval Graphs, parameterized by vertex deletion number k to proper interval graphs, in O(k^9n) time. Notably, Longest Path is trivially solvable in linear time on proper interval graphs, and the parameter value k can be approximated up to a factor of 4 in linear time. From a more general perspective, we believe that using parameterized complexity analysis for polynomial-time solvable problems offers a very fertile ground for future studies for all sorts of algorithmic problems. It may enable a refined understanding of efficiency aspects for polynomial-time solvable problems, similarly to what classical parameterized complexity analysis does for NP-hard problems

A Unified Framework for Integer Programming Formulation of Graph Matching Problems

Graph theory has been a powerful tool in solving difficult and complex problems arising in all disciplines. In particular, graph matching is a classical problem in pattern analysis with enormous applications. Many graph problems have been formulated as a mathematical program then solved using exact, heuristic and/or approximated-guaranteed procedures. On the other hand, graph theory has been a powerful tool in visualizing and understanding of complex mathematical programming problems, especially integer programs. Formulating a graph problem as a natural integer program (IP) is often a challenging task. However, an IP formulation of the problem has many advantages. Several researchers have noted the need for natural IP formulation of graph theoretic problems. The aim of the present study is to provide a unified framework for IP formulation of graph matching problems. Although there are many surveys on graph matching problems, however, none is concerned with IP formulation. This paper is the first to provide a comprehensive IP formulation for such problems. The framework includes variety of graph optimization problems in the literature. While these problems have been studied by different research communities, however, the framework presented here helps to bring efforts from different disciplines to tackle such diverse and complex problems. We hope the present study can significantly help to simplify some of difficult problems arising in practice, especially in pattern analysis