Using genetic algorithms for the single allocation hub location problem

Hub location problem is an NP-hard problem that frequently arises in the design of transportation and distribution systems, postal delivery networks, and airline passenger flow. This work focuses on the Single Allocation Hub Location Problem (SAHLP). Genetic Algorithms (GAs) for the capacitated and uncapacitated variants of the SAHLP based on new chromosome representations and crossover operators are explored. The GAs is tested on two well-known sets of real-world problems with up to 200 nodes. The obtained results are very promising. For most of the test problems the GA obtains improved or best-known solutions and the computational time remains low. The proposed GAs can easily be extended to other variants of location problems arising in network design planning in transportation systems.

Automatic evolution of conceptual building architectures

This thesis describes research in which genetic programming is used to automatically evolve shape grammars that construct three dimensional models of possible external building architectures. A completely automated fitness function is used, which evaluates the three dimensional building models according to different geometric properties such as surface normals, height, building footprint, and more. In order to evaluate the buildings on the different criteria, a multi-objective fitness function is used. The results obtained from the automated system were successful in satisfying the multiple objective criteria as well as creating interesting and unique designs that a human-aided system might not discover. In this study of evolutionary design, the architectures created are not meant to be fully functional and structurally sound blueprints for constructing a building, but are meant to be inspirational ideas for possible architectural designs. The evolved models are applicable for today's architectural industries as well as in the video game and movie industries. Many new avenues for future work have also been discovered and highlighted.

A Multi-Objective Genetic Algorithm with Side Effect Machines for Motif Discovery

Understanding the machinery of gene regulation to control gene expression has been one of the main focuses of bioinformaticians for years. We use a multi-objective genetic algorithm to evolve a specialized version of side effect machines for degenerate motif discovery. We compare some suggested objectives for the motifs they find, test different multi-objective scoring schemes and probabilistic models for the background sequence models and report our results on a synthetic dataset and some biological benchmarking suites. We conclude with a comparison of our algorithm with some widely used motif discovery algorithms in the literature and suggest future directions for research in this area.

Enabling and Measuring Complexity in Evolving Designs using Generative Representations for Artificial Architecture

As the complexity of evolutionary design problems grow, so too must the quality of solutions scale to that complexity. In this research, we develop a genetic programming system with individuals encoded as tree-based generative representations to address scalability. This system is capable of multi-objective evaluation using a ranked sum scoring strategy. We examine Hornby's features and measures of modularity, reuse and hierarchy in evolutionary design problems. Experiments are carried out, using the system to generate three-dimensional forms, and analyses of feature characteristics such as modularity, reuse and hierarchy were performed. This work expands on that of Hornby's, by examining a new and more difficult problem domain. The results from these experiments show that individuals encoded with those three features performed best overall. It is also seen, that the measures of complexity conform to the results of Hornby. Moving forward with only this best performing encoding, the system was applied to the generation of three-dimensional external building architecture. One objective considered was passive solar performance, in which the system was challenged with generating forms that optimize exposure to the Sun. The results from these and other experiments satisfied the requirements. The system was shown to scale well to the architectural problems studied.

A Study of Ordered Gene Problems Featuring DNA Error Correction and DNA Fragment Assembly with a Variety of Heuristics, Genetic Algorithm Variations, and Dynamic Representations

Ordered gene problems are a very common classification of optimization problems. Because of their popularity countless algorithms have been developed in an attempt to find high quality solutions to the problems. It is also common to see many different types of problems reduced to ordered gene style problems as there are many popular heuristics and metaheuristics for them due to their popularity. Multiple ordered gene problems are studied, namely, the travelling salesman problem, bin packing problem, and graph colouring problem. In addition, two bioinformatics problems not traditionally seen as ordered gene problems are studied: DNA error correction and DNA fragment assembly. These problems are studied with multiple variations and combinations of heuristics and metaheuristics with two distinct types or representations. The majority of the algorithms are built around the Recentering- Restarting Genetic Algorithm. The algorithm variations were successful on all problems studied, and particularly for the two bioinformatics problems. For DNA Error Correction multiple cases were found with 100% of the codes being corrected. The algorithm variations were also able to beat all other state-of-the-art DNA Fragment Assemblers on 13 out of 16 benchmark problem instances.

Disease-Gene Association Using a Genetic Algorithm

Understanding the relationship between genetic diseases and the genes associated with them is an important problem regarding human health. The vast amount of data created from a large number of high-throughput experiments performed in the last few years has resulted in an unprecedented growth in computational methods to tackle the disease gene association problem. Nowadays, it is clear that a genetic disease is not a consequence of a defect in a single gene. Instead, the disease phenotype is a reflection of various genetic components interacting in a complex network. In fact, genetic diseases, like any other phenotype, occur as a result of various genes working in sync with each other in a single or several biological module(s). Using a genetic algorithm, our method tries to evolve communities containing the set of potential disease genes likely to be involved in a given genetic disease. Having a set of known disease genes, we first obtain a protein-protein interaction (PPI) network containing all the known disease genes. All the other genes inside the procured PPI network are then considered as candidate disease genes as they lie in the vicinity of the known disease genes in the network. Our method attempts to find communities of potential disease genes strongly working with one another and with the set of known disease genes. As a proof of concept, we tested our approach on 16 breast cancer genes and 15 Parkinson's Disease genes. We obtained comparable or better results than CIPHER, ENDEAVOUR and GPEC, three of the most reliable and frequently used disease-gene ranking frameworks.

Improving automation in model-driven engineering using examples

Cette thèse a pour but d’améliorer l’automatisation dans l’ingénierie dirigée par les modèles (MDE pour Model Driven Engineering). MDE est un paradigme qui promet de réduire la complexité du logiciel par l’utilisation intensive de modèles et des transformations automatiques entre modèles (TM). D’une façon simplifiée, dans la vision du MDE, les spécialistes utilisent plusieurs modèles pour représenter un logiciel, et ils produisent le code source en transformant automatiquement ces modèles. Conséquemment, l’automatisation est un facteur clé et un principe fondateur de MDE. En plus des TM, d’autres activités ont besoin d’automatisation, e.g. la définition des langages de modélisation et la migration de logiciels. Dans ce contexte, la contribution principale de cette thèse est de proposer une approche générale pour améliorer l’automatisation du MDE. Notre approche est basée sur la recherche méta-heuristique guidée par les exemples. Nous appliquons cette approche sur deux problèmes importants de MDE, (1) la transformation des modèles et (2) la définition précise de langages de modélisation. Pour le premier problème, nous distinguons entre la transformation dans le contexte de la migration et les transformations générales entre modèles. Dans le cas de la migration, nous proposons une méthode de regroupement logiciel (Software Clustering) basée sur une méta-heuristique guidée par des exemples de regroupement. De la même façon, pour les transformations générales, nous apprenons des transformations entre modèles en utilisant un algorithme de programmation génétique qui s’inspire des exemples des transformations passées. Pour la définition précise de langages de modélisation, nous proposons une méthode basée sur une recherche méta-heuristique, qui dérive des règles de bonne formation pour les méta-modèles, avec l’objectif de bien discriminer entre modèles valides et invalides. Les études empiriques que nous avons menées, montrent que les approches proposées obtiennent des bons résultats tant quantitatifs que qualitatifs. Ceux-ci nous permettent de conclure que l’amélioration de l’automatisation du MDE en utilisant des méthodes de recherche méta-heuristique et des exemples peut contribuer à l’adoption plus large de MDE dans l’industrie à là venir.

A Mono- and Multi-objective Approach for Recommending Software Refactoring

Les systèmes logiciels sont devenus de plus en plus répondus et importants dans notre société. Ainsi, il y a un besoin constant de logiciels de haute qualité. Pour améliorer la qualité de logiciels, l’une des techniques les plus utilisées est le refactoring qui sert à améliorer la structure d'un programme tout en préservant son comportement externe. Le refactoring promet, s'il est appliqué convenablement, à améliorer la compréhensibilité, la maintenabilité et l'extensibilité du logiciel tout en améliorant la productivité des programmeurs. En général, le refactoring pourra s’appliquer au niveau de spécification, conception ou code. Cette thèse porte sur l'automatisation de processus de recommandation de refactoring, au niveau code, s’appliquant en deux étapes principales: 1) la détection des fragments de code qui devraient être améliorés (e.g., les défauts de conception), et 2) l'identification des solutions de refactoring à appliquer. Pour la première étape, nous traduisons des régularités qui peuvent être trouvés dans des exemples de défauts de conception. Nous utilisons un algorithme génétique pour générer automatiquement des règles de détection à partir des exemples de défauts. Pour la deuxième étape, nous introduisons une approche se basant sur une recherche heuristique. Le processus consiste à trouver la séquence optimale d'opérations de refactoring permettant d'améliorer la qualité du logiciel en minimisant le nombre de défauts tout en priorisant les instances les plus critiques. De plus, nous explorons d'autres objectifs à optimiser: le nombre de changements requis pour appliquer la solution de refactoring, la préservation de la sémantique, et la consistance avec l’historique de changements. Ainsi, réduire le nombre de changements permets de garder autant que possible avec la conception initiale. La préservation de la sémantique assure que le programme restructuré est sémantiquement cohérent. De plus, nous utilisons l'historique de changement pour suggérer de nouveaux refactorings dans des contextes similaires. En outre, nous introduisons une approche multi-objective pour améliorer les attributs de qualité du logiciel (la flexibilité, la maintenabilité, etc.), fixer les « mauvaises » pratiques de conception (défauts de conception), tout en introduisant les « bonnes » pratiques de conception (patrons de conception).

Evaluating the state of the art of parallel programming systems

This paper describes our plans to evaluate the present state of affairs concerning parallel programming and its systems. Three subprojects are proposed: a survey among programmers and scientists, a comparison of parallel programming systems using a standard set of test programs, and a wiki resource for the parallel programming community - the Parawiki. We would like to invite you to participate and turn these subprojects into true community efforts.

Observations on the Publicity and Usage of Parallel Programming Systems and Languages: A Survey Approach

In this publication, we report on an online survey that was carried out among parallel programmers. More than 250 people worldwide have submitted answers to our questions, and their responses are analyzed here. Although not statistically sound, the data we provide give useful insights about which parallel programming systems and languages are known and in actual use. For instance, the collected data indicate that for our survey group MPI and (to a lesser extent) C are the most widely used parallel programming system and language, respectively.

Offline Emergence Engineering For Agent Societies

Many examples for emergent behaviors may be observed in self-organizing physical and biological systems which prove to be robust, stable, and adaptable. Such behaviors are often based on very simple mechanisms and rules, but artificially creating them is a challenging task which does not comply with traditional software engineering. In this article, we propose a hybrid approach by combining strategies from Genetic Programming and agent software engineering, and demonstrate that this approach effectively yields an emergent design for given problems.

A User-Centric Perspective on Parallel Programming with Focus on OpenMP

The process of developing software that takes advantage of multiple processors is commonly referred to as parallel programming. For various reasons, this process is much harder than the sequential case. For decades, parallel programming has been a problem for a small niche only: engineers working on parallelizing mostly numerical applications in High Performance Computing. This has changed with the advent of multi-core processors in mainstream computer architectures. Parallel programming in our days becomes a problem for a much larger group of developers. The main objective of this thesis was to find ways to make parallel programming easier for them. Different aims were identified in order to reach the objective: research the state of the art of parallel programming today, improve the education of software developers about the topic, and provide programmers with powerful abstractions to make their work easier. To reach these aims, several key steps were taken. To start with, a survey was conducted among parallel programmers to find out about the state of the art. More than 250 people participated, yielding results about the parallel programming systems and languages in use, as well as about common problems with these systems. Furthermore, a study was conducted in university classes on parallel programming. It resulted in a list of frequently made mistakes that were analyzed and used to create a programmers' checklist to avoid them in the future. For programmers' education, an online resource was setup to collect experiences and knowledge in the field of parallel programming - called the Parawiki. Another key step in this direction was the creation of the Thinking Parallel weblog, where more than 50.000 readers to date have read essays on the topic. For the third aim (powerful abstractions), it was decided to concentrate on one parallel programming system: OpenMP. Its ease of use and high level of abstraction were the most important reasons for this decision. Two different research directions were pursued. The first one resulted in a parallel library called AthenaMP. It contains so-called generic components, derived from design patterns for parallel programming. These include functionality to enhance the locks provided by OpenMP, to perform operations on large amounts of data (data-parallel programming), and to enable the implementation of irregular algorithms using task pools. AthenaMP itself serves a triple role: the components are well-documented and can be used directly in programs, it enables developers to study the source code and learn from it, and it is possible for compiler writers to use it as a testing ground for their OpenMP compilers. The second research direction was targeted at changing the OpenMP specification to make the system more powerful. The main contributions here were a proposal to enable thread-cancellation and a proposal to avoid busy waiting. Both were implemented in a research compiler, shown to be useful in example applications, and proposed to the OpenMP Language Committee.

Global Optimization Algorithms and their Application to Distributed Systems

In this report, we discuss the application of global optimization and Evolutionary Computation to distributed systems. We therefore selected and classified many publications, giving an insight into the wide variety of optimization problems which arise in distributed systems. Some interesting approaches from different areas will be discussed in greater detail with the use of illustrative examples.

Applicability of Emergence Engineering to Distributed Systems Scenarios

Genetic Programming can be effectively used to create emergent behavior for a group of autonomous agents. In the process we call Offline Emergence Engineering, the behavior is at first bred in a Genetic Programming environment and then deployed to the agents in the real environment. In this article we shortly describe our approach, introduce an extended behavioral rule syntax, and discuss the impact of the expressiveness of the behavioral description to the generation success, using two scenarios in comparison: the election problem and the distributed critical section problem. We evaluate the results, formulating criteria for the applicability of our approach.

Reasoning about Temporal Context using Ontology and Abductive Constraint Logic Programming

The underlying assumptions for interpreting the meaning of data often change over time, which further complicates the problem of semantic heterogeneities among autonomous data sources. As an extension to the COntext INterchange (COIN) framework, this paper introduces the notion of temporal context as a formalization of the problem. We represent temporal context as a multi-valued method in F-Logic; however, only one value is valid at any point in time, the determination of which is constrained by temporal relations. This representation is then mapped to an abductive constraint logic programming framework with temporal relations being treated as constraints. A mediation engine that implements the framework automatically detects and reconciles semantic differences at different times. We articulate that this extended COIN framework is suitable for reasoning on the Semantic Web.