Optimization bounds from the branching dual

We present a general method for obtaining strong bounds for discrete optimization problems that is based on a concept of branching duality. It can be applied when no useful integer programming model is available, and we illustrate this with the minimum bandwidth problem. The method strengthens a known bound for a given problem by formulating a dual problem whose feasible solutions are partial branching trees. It solves the dual problem with a “worst-bound” local search heuristic that explores neighboring partial trees. After proving some optimality properties of the heuristic, we show that it substantially improves known combinatorial bounds for the minimum bandwidth problem with a modest amount of computation. It also obtains significantly tighter bounds than depth-first and breadth-first branching, demonstrating that the dual perspective can lead to better branching strategies when the object is to find valid bounds.Accepted manuscrip

Comparison of three vertical search spiders

The Web's dynamic,.unstructured nature makes locating resources difficult. Vertical search engines solve part of the problem by keeping indexes only in specific domains. They also offer more opportunity to apply domain knowledge in the spider applications that collect content for their databases. The authors used three approaches to investigate algorithms for improving the performance of vertical search engine spiders: a breadth-first graph-traversal algorithm with no heuristics to refine the search process, a best-first traversal algorithm that uses a hyperlink-analysis heuristic, and a spreading-activation algorithm based on modeling the Web as a neural network.published_or_final_versio

Finding minimum gene subsets with heuristic breadth-first search algorithm for robust tumor classification

Background: Previous studies on tumor classification based on gene expression profiles suggest that gene selection plays a key role in improving the classification performance. Moreover, finding important tumor-related genes with the highest accuracy is a very important task because these genes might serve as tumor biomarkers, which is of great benefit to not only tumor molecular diagnosis but also drug development. Results: This paper proposes a novel gene selection method with rich biomedical meaning based on Heuristic Breadth-first Search Algorithm (HBSA) to find as many optimal gene subsets as possible. Due to the curse of dimensionality, this type of method could suffer from over-fitting and selection bias problems. To address these potential problems, a HBSA-based ensemble classifier is constructed using majority voting strategy from individual classifiers constructed by the selected gene subsets, and a novel HBSA-based gene ranking method is designed to find important tumor-related genes by measuring the significance of genes using their occurrence frequencies in the selected gene subsets. The experimental results on nine tumor datasets including three pairs of cross-platform datasets indicate that the proposed method can not only obtain better generalization performance but also find many important tumor-related genes. Conclusions: It is found that the frequencies of the selected genes follow a power-law distribution, indicating that only a few top-ranked genes can be used as potential diagnosis biomarkers. Moreover, the top-ranked genes leading to very high prediction accuracy are closely related to specific tumor subtype and even hub genes. Compared with other related methods, the proposed method can achieve higher prediction accuracy with fewer genes. Moreover, they are further justified by analyzing the top-ranked genes in the context of individual gene function, biological pathway, and protein-protein interaction network. Keywords: Gene expression profiles; Gene selection; Tumor classification; Heuristic breadth-first search; Power-law distributio

Finding minimum gene subsets with heuristic breadth-first search algorithm for robust tumor classification

Background: Previous studies on tumor classification based on gene expression profiles suggest that gene selection plays a key role in improving the classification performance. Moreover, finding important tumor-related genes with the highest accuracy is a very important task because these genes might serve as tumor biomarkers, which is of great benefit to not only tumor molecular diagnosis but also drug development. Results: This paper proposes a novel gene selection method with rich biomedical meaning based on Heuristic Breadth-first Search Algorithm (HBSA) to find as many optimal gene subsets as possible. Due to the curse of dimensionality, this type of method could suffer from over-fitting and selection bias problems. To address these potential problems, a HBSA-based ensemble classifier is constructed using majority voting strategy from individual classifiers constructed by the selected gene subsets, and a novel HBSA-based gene ranking method is designed to find important tumor-related genes by measuring the significance of genes using their occurrence frequencies in the selected gene subsets. The experimental results on nine tumor datasets including three pairs of cross-platform datasets indicate that the proposed method can not only obtain better generalization performance but also find many important tumor-related genes. Conclusions: It is found that the frequencies of the selected genes follow a power-law distribution, indicating that only a few top-ranked genes can be used as potential diagnosis biomarkers. Moreover, the top-ranked genes leading to very high prediction accuracy are closely related to specific tumor subtype and even hub genes. Compared with other related methods, the proposed method can achieve higher prediction accuracy with fewer genes. Moreover, they are further justified by analyzing the top-ranked genes in the context of individual gene function, biological pathway, and protein-protein interaction network. Keywords: Gene expression profiles; Gene selection; Tumor classification; Heuristic breadth-first search; Power-law distributio

Random walk based heuristic algorithms for distributed memory model checking

technical reportModel checking techniques suffer from the state space explosion problem: as the size of the system being verified increases, the total state space of the system increases exponentially. Some of the methods that have been devised to tackle this problem are partial order reduction, symmetry reduction, hash compaction, selective state caching, etc. One approach to the problem that has gained interest in recent years is the parallelization of model checking algorithms. A random walk on the state space has some nice properties, the most important of which is the fact that it lends itself to being parallelized in a natural way. Random walk is a low overhead and a partial search method. Breadth first search, on the other hand, is a high overhead and a full search technique. In this article, we propose various heuristic algorithms that combine random walks on the state space with bounded breadth first search in a parallel context. These algorithms are in the process of being incorporated into a distributed memory model checker

Heuristic algorithms for the min-max edge 2-coloring problem

In multi-channel Wireless Mesh Networks (WMN), each node is able to use multiple non-overlapping frequency channels. Raniwala et al. (MC2R 2004, INFOCOM 2005) propose and study several such architectures in which a computer can have multiple network interface cards. These architectures are modeled as a graph problem named \emph{maximum edge $q$-coloring} and studied in several papers by Feng et. al (TAMC 2007), Adamaszek and Popa (ISAAC 2010, JDA 2016). Later on Larjomaa and Popa (IWOCA 2014, JGAA 2015) define and study an alternative variant, named the \emph{min-max edge $q$-coloring}. The above mentioned graph problems, namely the maximum edge $q$-coloring and the min-max edge $q$-coloring are studied mainly from the theoretical perspective. In this paper, we study the min-max edge 2-coloring problem from a practical perspective. More precisely, we introduce, implement and test four heuristic approximation algorithms for the min-max edge $2$-coloring problem. These algorithms are based on a \emph{Breadth First Search} (BFS)-based heuristic and on \emph{local search} methods like basic \emph{hill climbing}, \emph{simulated annealing} and \emph{tabu search} techniques, respectively. Although several algorithms for particular graph classes were proposed by Larjomaa and Popa (e.g., trees, planar graphs, cliques, bi-cliques, hypergraphs), we design the first algorithms for general graphs. We study and compare the running data for all algorithms on Unit Disk Graphs, as well as some graphs from the DIMACS vertex coloring benchmark dataset.Comment: This is a post-peer-review, pre-copyedit version of an article published in International Computing and Combinatorics Conference (COCOON'18). The final authenticated version is available online at: http://www.doi.org/10.1007/978-3-319-94776-1_5