Decentralized load balancing for highly irregular search problems

In this paper, we present a distributed computing framework for problems characterized by a highly irregular search tree, whereby no reliable workload prediction is available. The framework is based on a peer-to-peer computing environment and dynamic load balancing. The system allows for dynamic resource aggregation, does not depend on any specific meta-computing middleware and is suitable for large-scale, multi-domain, heterogeneous environments, such as computational Grids. Dynamic load balancing policies based on global statistics are known to provide optimal load balancing performance, while randomized techniques provide high scalability. The proposed method combines both advantages and adopts distributed job-pools and a randomized polling technique. The framework has been successfully adopted in a parallel search algorithm for subgraph mining and evaluated on a molecular compounds dataset. The parallel application has shown good calability and close-to linear speedup in a distributed network of workstations.

Metaheuristics for Search Problems in Genomics - New Algorithms and Applications

In this thesis we made the first steps towards the systematic application of a methodology for automatically building formal models of complex biological systems. Such a methodology could be useful also to design artificial systems possessing desirable properties such as robustness and evolvability. The approach we follow in this thesis is to manipulate formal models by means of adaptive search methods called metaheuristics. In the first part of the thesis we develop state-of-the-art hybrid metaheuristic algorithms to tackle two important problems in genomics, namely, the Haplotype Inference by parsimony and the Founder Sequence Reconstruction Problem. We compare our algorithms with other effective techniques in the literature, we show strength and limitations of our approaches to various problem formulations and, finally, we propose further enhancements that could possibly improve the performance of our algorithms and widen their applicability. In the second part, we concentrate on Boolean network (BN) models of gene regulatory networks (GRNs). We detail our automatic design methodology and apply it to four use cases which correspond to different design criteria and address some limitations of GRN modeling by BNs. Finally, we tackle the Density Classification Problem with the aim of showing the learning capabilities of BNs. Experimental evaluation of this methodology shows its efficacy in producing network that meet our design criteria. Our results, coherently to what has been found in other works, also suggest that networks manipulated by a search process exhibit a mixture of characteristics typical of different dynamical regimes.

Generating highly balanced sudoku problems as hard problems

Sudoku problems are some of the most known and enjoyed pastimes, with a never diminishing popularity, but, for the last few years those problems have gone from an entertainment to an interesting research area, a twofold interesting area, in fact. On the one side Sudoku problems, being a variant of Gerechte Designs and Latin Squares, are being actively used for experimental design, as in [8, 44, 39, 9]. On the other hand, Sudoku problems, as simple as they seem, are really hard structured combinatorial search problems, and thanks to their characteristics and behavior, they can be used as benchmark problems for refining and testing solving algorithms and approaches. Also, thanks to their high inner structure, their study can contribute more than studies of random problems to our goal of solving real-world problems and applications and understanding problem characteristics that make them hard to solve. In this work we use two techniques for solving and modeling Sudoku problems, namely, Constraint Satisfaction Problem (CSP) and Satisfiability Problem (SAT) approaches. To this effect we define the Generalized Sudoku Problem (GSP), where regions can be of rectangular shape, problems can be of any order, and solution existence is not guaranteed. With respect to the worst-case complexity, we prove that GSP with block regions of m rows and n columns with m = n is NP-complete. For studying the empirical hardness of GSP, we define a series of instance generators, that differ in the balancing level they guarantee between the constraints of the problem, by finely controlling how the holes are distributed in the cells of the GSP. Experimentally, we show that the more balanced are the constraints, the higher the complexity of solving the GSP instances, and that GSP is harder than the Quasigroup Completion Problem (QCP), a problem generalized by GSP. Finally, we provide a study of the correlation between backbone variables – variables with the same value in all the solutions of an instance– and hardness of GSP.

Information servers, present and future

Mainframes, corporate and central servers are becoming information servers. The requirement for more powerful information servers is the best opportunity to exploit the potential of parallelism. ICL recognized the opportunity of the 'knowledge spectrum' namely to convert raw data into information and then into high grade knowledge. Parallel Processing and Data Management Its response to this and to the underlying search problems was to introduce the CAFS retrieval engine. The CAFS product demonstrates that it is possible to move functionality within an established architecture, introduce a different technology mix and exploit parallelism to achieve radically new levels of performance. CAFS also demonstrates the benefit of achieving this transparently behind existing interfaces. ICL is now working with Bull and Siemens to develop the information servers of the future by exploiting new technologies as available. The objective of the joint Esprit II European Declarative System project is to develop a smoothly scalable, highly parallel computer system, EDS. EDS will in the main be an SQL server and an information server. It will support the many data-intensive applications which the companies foresee; it will also support application-intensive and logic-intensive systems.

Constructs and evaluation strategies for intelligent speculative parallelism - armageddon revisited

This report addresses speculative parallelism (the assignment of spare processing resources to tasks which are not known to be strictly required for the successful completion of a computation) at the user and application level. At this level, the execution of a program is seen as a (dynamic) tree —a graph, in general. A solution for a problem is a traversal of this graph from the initial state to a node known to be the answer. Speculative parallelism then represents the assignment of resources to múltiple branches of this graph even if they are not positively known to be on the path to a solution. In highly non-deterministic programs the branching factor can be very high and a naive assignment will very soon use up all the resources. This report presents work assignment strategies other than the usual depth-first and breadth-first. Instead, best-first strategies are used. Since their definition is application-dependent, the application language contains primitives that allow the user (or application programmer) to a) indícate when intelligent OR-parallelism should be used; b) provide the functions that define "best," and c) indícate when to use them. An abstract architecture enables those primitives to perform the search in a "speculative" way, using several processors, synchronizing them, killing the siblings of the path leading to the answer, etc. The user is freed from worrying about these interactions. Several search strategies are proposed and their implementation issues are addressed. "Armageddon," a global pruning method, is introduced, together with both a software and a hardware implementation for it. The concepts exposed are applicable to áreas of Artificial Intelligence such as extensive expert systems, planning, game playing, and in general to large search problems. The proposed strategies, although showing promise, have not been evaluated by simulation or experimentation.

Searching oligo sets of human chromosome 12 using evolutionary strategies

DNA microarray is a powerful tool to measure the level of a mixed population of nucleic acids at one time, which has great impact in many aspects of life sciences research. In order to distinguish nucleic acids with very similar composition by hybridization, it is necessary to design probes with high specificities, i.e. uniqueness, and also sensitivities, i.e., suitable melting temperature and no secondary structure. We make use of available biology tools to gain necessary sequence information of human chromosome 12, and combined with evolutionary strategy (ES) to find unique subsequences representing all predicted exons. The results are presented and discussed.

Instantiating deformable models with a neural net

Deformable models are an attractive approach to recognizing objects which have considerable within-class variability such as handwritten characters. However, there are severe search problems associated with fitting the models to data which could be reduced if a better starting point for the search were available. We show that by training a neural network to predict how a deformable model should be instantiated from an input image, such improved starting points can be obtained. This method has been implemented for a system that recognizes handwritten digits using deformable models, and the results show that the search time can be significantly reduced without compromising recognition performance. © 1997 Academic Press.

DNA Simulation of Genetic Algorithms: Fitness Computation

* This work has been partially supported by Spanish Project TIC2003-9319-c03-03 “Neural Networks and Networks of Evolutionary Processors”.

Two-B or not two-B? Design patterns for hybrid metaheuristics

Real world search problems, characterised by nonlinearity, noise and multidimensionality, are often best solved by hybrid algorithms. Techniques embodying different necessary features are triggered at specific iterations, in response to the current state of the problem space. In the existing literature, this alternation is managed either statically (through pre-programmed policies) or dynamically, at the cost of high coupling with algorithm inner representation. We extract two design patterns for hybrid metaheuristic search algorithms, the All-Seeing Eye and the Commentator patterns, which we argue should be replaced by the more flexible and loosely coupled Simple Black Box (Two-B) and Utility-based Black Box (Three-B) patterns that we propose here. We recommend the Two-B pattern for purely fitness based hybridisations and the Three-B pattern for more generic search quality evaluation based hybridisations.

A novel hybrid swarm based approach for curriculum based course timetabling problem

This work applies a hybrid approach in solving the university curriculum-based course timetabling problem as presented as part of the 2nd International Timetabling Competition 2007 (ITC2007). The core of the hybrid approach is based on an artificial bee colony algorithm. Past methods have applied artificial bee colony algorithms to university timetabling problems with high degrees of success. Nevertheless, there exist inefficiencies in the associated search abilities in term of exploration and exploitation. To improve the search abilities, this work introduces a hybrid approach entitled nelder-mead great deluge artificial bee colony algorithm (NMGD-ABC) where it combined additional positive elements of particle swarm optimization and great deluge algorithm. In addition, nelder-mead local search is incorporated into the great deluge algorithm to further enhance the performance of the resulting method. The proposed method is tested on curriculum-based course timetabling as presented in the ITC2007. Experimental results reveal that the proposed method is capable of producing competitive results as compared with the other approaches described in literature

Jeux de policiers et voleurs, Modèles et applications

Les jeux de policiers et voleurs sont étudiés depuis une trentaine d’années en informatique et en mathématiques. Comme dans les jeux de poursuite en général, des poursuivants (les policiers) cherchent à capturer des évadés (les voleurs), cependant ici les joueurs agissent tour à tour et sont contraints de se déplacer sur une structure discrète. On suppose toujours que les joueurs connaissent les positions exactes de leurs opposants, autrement dit le jeu se déroule à information parfaite. La première définition d’un jeu de policiers-voleurs remonte à celle de Nowakowski et Winkler [39] et, indépendamment, Quilliot [46]. Cette première définition présente un jeu opposant un seul policier et un seul voleur avec des contraintes sur leurs vitesses de déplacement. Des extensions furent graduellement proposées telles que l’ajout de policiers et l’augmentation des vitesses de mouvement. En 2014, Bonato et MacGillivray [6] proposèrent une généralisation des jeux de policiers-voleurs pour permettre l’étude de ceux-ci dans leur globalité. Cependant, leur modèle ne couvre aucunement les jeux possédant des composantes stochastiques tels que ceux dans lesquels les voleurs peuvent bouger de manière aléatoire. Dans ce mémoire est donc présenté un nouveau modèle incluant des aspects stochastiques. En second lieu, on présente dans ce mémoire une application concrète de l’utilisation de ces jeux sous la forme d’une méthode de résolution d’un problème provenant de la théorie de la recherche. Alors que les jeux de policiers et voleurs utilisent l’hypothèse de l’information parfaite, les problèmes de recherches ne peuvent faire cette supposition. Il appert cependant que le jeu de policiers et voleurs peut être analysé comme une relaxation de contraintes d’un problème de recherche. Ce nouvel angle de vue est exploité pour la conception d’une borne supérieure sur la fonction objectif d’un problème de recherche pouvant être mise à contribution dans une méthode dite de branch and bound.

Path relinking for the fixed spectrum frequency assignment problem

International audience

Problems and perspectives for Chagas disease control: in search of a realistic analysis

Chagas disease was an important medical and social problem in almost all of Latin America throughout the twentieth century. It has been combated over a broad swath of this continent over recent decades, with very satisfactory results in terms of vector and transfusional transmission. Today, a surveillance stage still remains to be consolidated, in parallel with appropriate care required for some millions of infected individuals who are today living in endemic and non-endemic areas. Contradictorily, the good results attained have generated excessive optimism and even disregard among health authorities, in relation to this disease and its control. The loss of visibility and priority may be a logical consequence, particularly in Latin American healthcare systems that are still disorganized and overburdened due to insufficiencies of financial and human resources. Consolidation of the victories against Chagas disease is attainable but depends on political will and continual attention from the most consequential protagonists in this struggle, especially the Latin American scientific community.