Fuzzy-Granular Based Data Mining for Effective Decision Support in Biomedical Applications

Due to complexity of biomedical problems, adaptive and intelligent knowledge discovery and data mining systems are highly needed to help humans to understand the inherent mechanism of diseases. For biomedical classification problems, typically it is impossible to build a perfect classifier with 100% prediction accuracy. Hence a more realistic target is to build an effective Decision Support System (DSS). In this dissertation, a novel adaptive Fuzzy Association Rules (FARs) mining algorithm, named FARM-DS, is proposed to build such a DSS for binary classification problems in the biomedical domain. Empirical studies show that FARM-DS is competitive to state-of-the-art classifiers in terms of prediction accuracy. More importantly, FARs can provide strong decision support on disease diagnoses due to their easy interpretability. This dissertation also proposes a fuzzy-granular method to select informative and discriminative genes from huge microarray gene expression data. With fuzzy granulation, information loss in the process of gene selection is decreased. As a result, more informative genes for cancer classification are selected and more accurate classifiers can be modeled. Empirical studies show that the proposed method is more accurate than traditional algorithms for cancer classification. And hence we expect that genes being selected can be more helpful for further biological studies

Curvature-based sparse rule base generation for fuzzy rule interpolation

Fuzzy logic has been successfully widely utilised in many real-world applications. The most common application of fuzzy logic is the rule-based fuzzy inference system, which is composed of mainly two parts including an inference engine and a fuzzy rule base. Conventional fuzzy inference systems always require a rule base that fully covers the entire problem domain (i.e., a dense rule base). Fuzzy rule interpolation (FRI) makes inference possible with sparse rule bases which may not cover some parts of the problem domain (i.e., a sparse rule base). In addition to extending the applicability of fuzzy inference systems, fuzzy interpolation can also be used to reduce system complexity for over-complex fuzzy inference systems. There are typically two methods to generate fuzzy rule bases, i.e., the knowledge driven and data-driven approaches. Almost all of these approaches only target dense rule bases for conventional fuzzy inference systems. The knowledge-driven methods may be negatively affected by the limited availability of expert knowledge and expert knowledge may be subjective, whilst redundancy often exists in fuzzy rule-based models that are acquired from numerical data. Note that various rule base reduction approaches have been proposed, but they are all based on certain similarity measures and are likely to cause performance deterioration along with the size reduction. This project, for the first time, innovatively applies curvature values to distinguish important features and instances in a dataset, to support the construction of a neat and concise sparse rule base for fuzzy rule interpolation. In addition to working in a three-dimensional problem space, the work also extends the natural three-dimensional curvature calculation to problems with high dimensions, which greatly broadens the applicability of the proposed approach. As a result, the proposed approach alleviates the ‘curse of dimensionality’ and helps to reduce the computational cost for fuzzy inference systems. The proposed approach has been validated and evaluated by three real-world applications. The experimental results demonstrate that the proposed approach is able to generate sparse rule bases with less rules but resulting in better performance, which confirms the power of the proposed system. In addition to fuzzy rule interpolation, the proposed curvature-based approach can also be readily used as a general feature selection tool to work with other machine learning approaches, such as classifiers

Fuzzy set covering as a new paradigm for the induction of fuzzy classification rules

In 1965 Lofti A. Zadeh proposed fuzzy sets as a generalization of crisp (or classic) sets to address the incapability of crisp sets to model uncertainty and vagueness inherent in the real world. Initially, fuzzy sets did not receive a very warm welcome as many academics stood skeptical towards a theory of imprecise'' mathematics. In the middle to late 1980's the success of fuzzy controllers brought fuzzy sets into the limelight, and many applications using fuzzy sets started appearing. In the early 1970's the first machine learning algorithms started appearing. The AQ family of algorithms pioneered by Ryszard S. Michalski is a good example of the family of set covering algorithms. This class of learning algorithm induces concept descriptions by a greedy construction of rules that describe (or cover) positive training examples but not negative training examples. The learning process is iterative, and in each iteration one rule is induced and the positive examples covered by the rule removed from the set of positive training examples. Because positive instances are separated from negative instances, the term separate-and-conquer has been used to contrast the learning strategy against decision tree induction that use a divide-and-conquer learning strategy. This dissertation proposes fuzzy set covering as a powerful rule induction strategy. We survey existing fuzzy learning algorithms, and conclude that very few fuzzy learning algorithms follow a greedy rule construction strategy and no publications to date made the link between fuzzy sets and set covering explicit. We first develop the theoretical aspects of fuzzy set covering, and then apply these in proposing the first fuzzy learning algorithm that apply set covering and make explicit use of a partial order for fuzzy classification rule induction. We also investigate several strategies to improve upon the basic algorithm, such as better search heuristics and different rule evaluation metrics. We then continue by proposing a general unifying framework for fuzzy set covering algorithms. We demonstrate the benefits of the framework and propose several further fuzzy set covering algorithms that fit within the framework. We compare fuzzy and crisp rule induction, and provide arguments in favour of fuzzy set covering as a rule induction strategy. We also show that our learning algorithms outperform other fuzzy rule learners on real world data. We further explore the idea of simultaneous concept learning in the fuzzy case, and continue to propose the first fuzzy decision list induction algorithm. Finally, we propose a first strategy for encoding the rule sets generated by our fuzzy set covering algorithms inside an equivalent neural network

Proceedings of the ECCS 2005 satellite workshop: embracing complexity in design - Paris 17 November 2005

Embracing complexity in design is one of the critical issues and challenges of the 21st century. As the realization grows that design activities and artefacts display properties associated with complex adaptive systems, so grows the need to use complexity concepts and methods to understand these properties and inform the design of better artifacts. It is a great challenge because complexity science represents an epistemological and methodological swift that promises a holistic approach in the understanding and operational support of design. But design is also a major contributor in complexity research. Design science is concerned with problems that are fundamental in the sciences in general and complexity sciences in particular. For instance, design has been perceived and studied as a ubiquitous activity inherent in every human activity, as the art of generating hypotheses, as a type of experiment, or as a creative co-evolutionary process. Design science and its established approaches and practices can be a great source for advancement and innovation in complexity science. These proceedings are the result of a workshop organized as part of the activities of a UK government AHRB/EPSRC funded research cluster called Embracing Complexity in Design (www.complexityanddesign.net) and the European Conference in Complex Systems (complexsystems.lri.fr). Embracing complexity in design is one of the critical issues and challenges of the 21st century. As the realization grows that design activities and artefacts display properties associated with complex adaptive systems, so grows the need to use complexity concepts and methods to understand these properties and inform the design of better artifacts. It is a great challenge because complexity science represents an epistemological and methodological swift that promises a holistic approach in the understanding and operational support of design. But design is also a major contributor in complexity research. Design science is concerned with problems that are fundamental in the sciences in general and complexity sciences in particular. For instance, design has been perceived and studied as a ubiquitous activity inherent in every human activity, as the art of generating hypotheses, as a type of experiment, or as a creative co-evolutionary process. Design science and its established approaches and practices can be a great source for advancement and innovation in complexity science. These proceedings are the result of a workshop organized as part of the activities of a UK government AHRB/EPSRC funded research cluster called Embracing Complexity in Design (www.complexityanddesign.net) and the European Conference in Complex Systems (complexsystems.lri.fr)

Fuzzy set covering as a new paradigm for the induction of fuzzy classification rules

In 1965 Lofti A. Zadeh proposed fuzzy sets as a generalization of crisp (or classic) sets to address the incapability of crisp sets to model uncertainty and vagueness inherent in the real world. Initially, fuzzy sets did not receive a very warm welcome as many academics stood skeptical towards a theory of imprecise'' mathematics. In the middle to late 1980's the success of fuzzy controllers brought fuzzy sets into the limelight, and many applications using fuzzy sets started appearing. In the early 1970's the first machine learning algorithms started appearing. The AQ family of algorithms pioneered by Ryszard S. Michalski is a good example of the family of set covering algorithms. This class of learning algorithm induces concept descriptions by a greedy construction of rules that describe (or cover) positive training examples but not negative training examples. The learning process is iterative, and in each iteration one rule is induced and the positive examples covered by the rule removed from the set of positive training examples. Because positive instances are separated from negative instances, the term separate-and-conquer has been used to contrast the learning strategy against decision tree induction that use a divide-and-conquer learning strategy. This dissertation proposes fuzzy set covering as a powerful rule induction strategy. We survey existing fuzzy learning algorithms, and conclude that very few fuzzy learning algorithms follow a greedy rule construction strategy and no publications to date made the link between fuzzy sets and set covering explicit. We first develop the theoretical aspects of fuzzy set covering, and then apply these in proposing the first fuzzy learning algorithm that apply set covering and make explicit use of a partial order for fuzzy classification rule induction. We also investigate several strategies to improve upon the basic algorithm, such as better search heuristics and different rule evaluation metrics. We then continue by proposing a general unifying framework for fuzzy set covering algorithms. We demonstrate the benefits of the framework and propose several further fuzzy set covering algorithms that fit within the framework. We compare fuzzy and crisp rule induction, and provide arguments in favour of fuzzy set covering as a rule induction strategy. We also show that our learning algorithms outperform other fuzzy rule learners on real world data. We further explore the idea of simultaneous concept learning in the fuzzy case, and continue to propose the first fuzzy decision list induction algorithm. Finally, we propose a first strategy for encoding the rule sets generated by our fuzzy set covering algorithms inside an equivalent neural network

Context dependent fuzzy modelling and its applications

Fuzzy rule-based systems (FRBS) use the principle of fuzzy sets and fuzzy logic to describe vague and imprecise statements and provide a facility to express the behaviours of the system with a human-understandable language. Fuzzy information, once defined by a fuzzy system, is fixed regardless of the circumstances and therefore makes it very difficult to capture the effect of context on the meaning of the fuzzy terms. While efforts have been made to integrate contextual information into the representation of fuzzy sets, it remains the case that often the context model is very restrictive and/or problem specific. The work reported in this thesis is our attempt to create a practical frame work to integrate contextual information into the representation of fuzzy sets so as to improve the interpretability as well as the accuracy of the fuzzy system. Throughout this thesis, we have looked at the capability of the proposed context dependent fuzzy sets as a stand alone as well as in combination with other methods in various application scenarios ranging from time series forecasting to complicated car racing control systems. In all of the applications, the highly competitive performance nature of our approach has proven its effectiveness and efficiency compared with existing techniques in the literature

Vers une description évolutive et une exploration efficace des concepts et des artefacts d'architecture microservices

RÉSUMÉ : L'adoption de l'architecture Microservices (MSA) pour la conception de systèmes logiciels est une tendance en industrie et en recherche. De nature compositionnelle et distribuée, les systèmes basés sur l'architecture Microservices sont composés de services ayant une responsabilité restreinte et bien définie, visant un isolement complet dans une perspective de non-partage de ressources. Les systèmes basés sur des microservices sont souvent classés comme de systèmes « Cloud-Native ». L'adoption de l'architecture Microservices représente un changement de paradigme technologique et managérial comportant des défis, notamment : la taille, la portée et le nombre de services, et leurs interopérabilité et réutilisation. Outre ces défis, la compréhension, l'adoption et l'implémentation des principes fondamentaux de ce style architectural sont des challenges qui impactent la conception d'architectures microservices efficaces et cohérentes. En effet, l'absence d'un large consensus sur certains principes et termes clés de cette architecture mènent à sa mauvaise compréhension et par conséquent à des implémentations incorrectes. Cette absence de consensus est une manifestation concrète de l'immaturité de cette architecture qui mène à des défis lors de la formalisation des connaissances. Également, il manque une méthode uniforme capable de supporter les concepteurs lors de la modélisation des microservices, notamment dans l'agencement des différentes composantes. À cela s'ajoute l'absence de modèles conceptuels pouvant guider les ingénieurs dans les premières phases de conception de ces systèmes. Plusieurs approches ont été utilisées pour la modélisation d'architectures microservices, tels que : formelle et informelle, manuelle et automatique et toutes les combinaisons de ces quatre, mais ces approches ne répondent pas à tous les défis rencontrés par les concepteurs. Pour faciliter la modélisation des microservices et rendre le processus plus efficace, il est nécessaire de développer des approches de conception et de représentation alternatives. Dans cette perspective, nous proposons une approche ontologique capable de répondre autant aux défis de conception que de représentation des architectures microservices. Dans ce mémoire, nous vous présentons nos résultats de recherche dont la principale contribution est une ontologie du domaine des architectures Microservices définie en suivant les principes de logique de description et formalisée en utilisant le langage « Web Ontology Language » (OWL), une technologie clé du Web sémantique. À cette ontologie nous avons donné le nom d'« Ontology of Microservices Architecture Concepts » (OMSAC). OMSAC contient suffisamment de vocabulaire pour décrire les concepts qui définissent l'architecture Microservices et pour représenter les différents artefacts composant ces architectures. Sa structure permet une évolution rapide et est capable de prendre en charge les enjeux liés à l'immaturité actuelle de ces architectures. En tant que technologie d'intelligence artificielle (IA), les ontologies possèdent des capacités de raisonnement avancées auxquelles il est possible d'ajouter d'autres technologies pour les étendre et ainsi répondre à différents besoins. Avec cet objectif, nous avons utilisé OMSAC conjointement avec des techniques d'apprentissage machine pour modéliser et analyser des architectures microservices afin de calculer le degré de similitude entre différents microservices appartenant à différents systèmes. Ce cas d'utilisation d'OMSAC constitue une contribution supplémentaire de notre recherche et renforce les perspectives de recherche dans l'assistance, l'outillage et l'automatisation de la modélisation des architectures microservices. Cette contribution montre également la pertinence de la recherche de mécanismes permettant de faire de l'analytique avancée sur les modèles d'architectures. Dans des travaux de recherche futurs, nous nous intéresserons au développent de ces mécanismes, et planifions la conception d'un assistant intelligent capable de projeter des architectures microservices basées sur les meilleures pratiques et favorisant la réutilisation de microservices existants. Également, nous souhaitons développer un langage dédié afin d'abstraire les syntaxes d'OWL et du langage de requête SPARQL pour faciliter l'utilisation d'OMSAC par les concepteurs, ingénieurs et programmeurs qui ne sont pas familiers avec ces technologies du Web sémantique. -- Mot(s) clé(s) en français : Architectures microservices, ontologies, modélisation de systèmes logiciels, apprentissage automatique. -- ABSTRACT : The use of Microservices Architecture (MSA) for designing software systems has become a trend in industry and research. Adopting MSA represents a technological and managerial shift with challenges including the size, scope, number, interoperability and reuse of microservices, modelling using multi-viewpoints, as well as the adequate understanding, adoption, and implementation of fundamental principles of the Microservices Architecture. Adequately undertaking these challenges is mandatory for designing effective MSA-based systems. In this thesis, we explored an ontological representation of the knowledge concerning the Microservices Architecture domain. This representation is capable of addressing MSA understanding and modelling challenges. As a result of this research, we propose the Ontology of Microservices Architecture Concepts (OMSAC), which is a domain ontology containing enough vocabulary to describe MSA concepts and artifacts and in a form to allow fast evolution and advanced analytical capabilities. -- Mot(s) clé(s) en anglais : Microservices Architecture, Ontologies, Conceptual modelling, machine learning