Le Web sémantique propose un ensemble de standards et d'outils pour la formalisation et l'interopérabilité de connaissances partagées sur le Web, sous la forme d'ontologies. Les ontologies biomédicales et les données associées constituent de nos jours un ensemble de connaissances complexes, hétérogènes et interconnectées, dont l'analyse est porteuse de grands enjeux en santé, par exemple dans le cadre de la pharmacovigilance. On proposera dans cette thèse des méthodes permettant d'utiliser ces ontologies biomédicales pour étendre les possibilités d'un processus de fouille de données, en particulier, permettant de faire cohabiter et d'exploiter les connaissances de plusieurs ontologies biomédicales. Les travaux de cette thèse concernent dans un premier temps une méthode fondée sur les structures de patrons, une extension de l'analyse formelle de concepts pour la découverte de co-occurences de événements indésirables médicamenteux dans des données patients. Cette méthode utilise une ontologie de phénotypes et une ontologie de médicaments pour permettre la comparaison de ces événements complexes, et la découverte d'associations à différents niveaux de généralisation, par exemple, au niveau de médicaments ou de classes de médicaments. Dans un second temps, on utilisera une méthode numérique fondée sur des mesures de similarité sémantique pour la classification de déficiences intellectuelles génétiques. On étudiera deux mesures de similarité utilisant des méthodes de calcul différentes, que l'on utilisera avec différentes combinaisons d'ontologies phénotypiques et géniques. En particulier, on quantifiera l'influence que les différentes connaissances de domaine ont sur la capacité de classification de ces mesures, et comment ces connaissances peuvent coopérer au sein de telles méthodes numériques. Une troisième étude utilise les données ouvertes liées ou LOD du Web sémantique et les ontologies associées dans le but de caractériser des gènes responsables de déficiences intellectuelles. On utilise ici la programmation logique inductive, qui s'avère adaptée pour fouiller des données relationnelles comme les LOD, en prenant en compte leurs relations avec les ontologies, et en extraire un modèle prédictif et descriptif des gènes responsables de déficiences intellectuelles. L'ensemble des contributions de cette thèse montre qu'il est possible de faire coopérer avantageusement une ou plusieurs ontologies dans divers processus de fouille de données / The semantic Web proposes standards and tools to formalize and share knowledge on the Web, in the form of ontologies. Biomedical ontologies and associated data represents a vast collection of complex, heterogeneous and linked knowledge. The analysis of such knowledge presents great opportunities in healthcare, for instance in pharmacovigilance. This thesis explores several ways to make use of this biomedical knowledge in the data mining step of a knowledge discovery process. In particular, we propose three methods in which several ontologies cooperate to improve data mining results. A first contribution of this thesis describes a method based on pattern structures, an extension of formal concept analysis, to extract associations between adverse drug events from patient data. In this context, a phenotype ontology and a drug ontology cooperate to allow a semantic comparison of these complex adverse events, and leading to the discovery of associations between such events at varying degrees of generalization, for instance, at the drug or drug class level. A second contribution uses a numeric method based on semantic similarity measures to classify different types of genetic intellectual disabilities, characterized by both their phenotypes and the functions of their linked genes. We study two different similarity measures, applied with different combinations of phenotypic and gene function ontologies. In particular, we investigate the influence of each domain of knowledge represented in each ontology on the classification process, and how they can cooperate to improve that process. Finally, a third contribution uses the data component of the semantic Web, the Linked Open Data (LOD), together with linked ontologies, to characterize genes responsible for intellectual deficiencies. We use Inductive Logic Programming, a suitable method to mine relational data such as LOD while exploiting domain knowledge from ontologies by using reasoning mechanisms. Here, ILP allows to extract from LOD and ontologies a descriptive and predictive model of genes responsible for intellectual disabilities. These contributions illustrates the possibility of having several ontologies cooperate to improve various data mining processes

A comunicação multilíngue é uma tarefa cada vez mais imperativa no cenário atual de grande disseminação de informações em diversas línguas. Nesse contexto, são de grande relevância os sistemas de tradução automática, que auxiliam tal comunicação, automatizando-a. Apesar de ser uma área de pesquisa bastante antiga, a Tradução Automática ainda apresenta muitos problemas. Um dos principais problemas é a ambigüidade lexical, ou seja, a necessidade de escolha de uma palavra, na língua alvo, para traduzir uma palavra da língua fonte quando há várias opções de tradução. Esse problema se mostra ainda mais complexo quando são identificadas apenas variações de sentido nas opções de tradução. Ele é denominado, nesse caso, \"ambigüidade lexical de sentido\". Várias abordagens têm sido propostas para a desambiguação lexical de sentido, mas elas são, em geral, monolíngues (para o inglês) e independentes de aplicação. Além disso, apresentam limitações no que diz respeito às fontes de conhecimento que podem ser exploradas. Em se tratando da língua portuguesa, em especial, não há pesquisas significativas voltadas para a resolução desse problema. O objetivo deste trabalho é a proposta e desenvolvimento de uma nova abordagem de desambiguação lexical de sentido, voltada especificamente para a tradução automática, que segue uma metodologia híbrida (baseada em conhecimento e em córpus) e utiliza um formalismo relacional para a representação de vários tipos de conhecimentos e de exemplos de desambiguação, por meio da técnica de Programação Lógica Indutiva. Experimentos diversos mostraram que a abordagem proposta supera abordagens alternativas para a desambiguação multilíngue e apresenta desempenho superior ou comparável ao do estado da arte em desambiguação monolíngue. Adicionalmente, tal abordagem se mostrou efetiva como mecanismo auxiliar para a escolha lexical na tradução automática estatística / Crosslingual communication has become a very imperative task in the current scenario with the increasing amount of information dissemination in several languages. In this context, machine translation systems, which can facilitate such communication by providing automatic translations, are of great importance. Although research in Machine Translation dates back to the 1950\'s, the area still has many problems. One of the main problems is that of lexical ambiguity, that is, the need for lexical choice when translating a source language word that has several translation options in the target language. This problem is even more complex when only sense variations are found in the translation options, a problem named \"sense ambiguity\". Several approaches have been proposed for word sense disambiguation, but they are in general monolingual (for English) and application-independent. Moreover, they have limitations regarding the types of knowledge sources that can be exploited. Particularly, there is no significant research aiming to word sense disambiguation involving Portuguese. The goal of this PhD work is the proposal and development of a novel approach for word sense disambiguation which is specifically designed for machine translation, follows a hybrid methodology (knowledge and corpus-based), and employs a relational formalism to represent various kinds of knowledge sources and disambiguation examples, by using Inductive Logic Programming. Several experiments have shown that the proposed approach overcomes alternative approaches in multilingual disambiguation and achieves higher or comparable results to the state of the art in monolingual disambiguation. Additionally, the approach has shown to effectively assist lexical choice in a statistical machine translation system

La biologie des systèmes intègre données et connaissances par des méthodes bioinformatiques, afin de mieux appréhender la physiologie des organismes. Une problématique est l’applicabilité de ces techniques aux organismes non modèles, au centre de plus en plus d’études, grâce aux avancées de séquençage et à l’intérêt croissant de la recherche sur les microbiotes. Cette thèse s’intéresse à la modélisation du métabolisme par des réseaux, et de sa fonctionnalité par diverses sémantiques basées sur les graphes et les contraintes stoechiométriques. Une première partie présente des travaux sur la complétion de réseaux métaboliques pour les organismes non modèles. Une méthode basée sur les graphes est validée, et une seconde, hybride, est développée, en programmation par ensembles réponses (ASP). Ces complétions sont appliquées à des réseaux métaboliques d’algues en biologie marine, et étendues à la recherche de complémentarité métabolique entre Ectocarpus siliculosus et une bactérie symbiotique. En s’appuyant sur les méthodes de complétion, la seconde partie de la thèse vise à proposer et implémenter une sélection de communautés à l’échelle de grands microbiotes. Une approche en deux étapes permet de suggérer des symbiotes pour l’optimisation d’un objectif donné. Elle supporte la modélisation des échanges et couvre tout l’espace des solutions. Des applications sur le microbiote intestinal humain et la sélection de bactéries pour une algue brune sont présentées. Dans l’ensemble, cette thèse propose de modéliser, développer et appliquer des méthodes reposant sur des sémantiques de graphe pour élaborer des hypothèses sur le métabolisme des organismes. / Systems biology relies on computational biology to integrate knowledge and data, for a better understanding of organisms’ physiology. Challenges reside in the applicability of methods and tools to non-model organisms, for instance in marine biology. Sequencing advances and the growing importance of elucidating microbiotas’ roles, have led to an increased interest into these organisms. This thesis focuses on the modeling of the metabolism through networks, and of its functionality using graphs and constraints semantics. In particular, a first part presents work on gap-filling metabolic networks in the context of non-model organisms. A graph-based method is benchmarked and validated and a hybrid one is developed using Answer Set Programming (ASP) and linear programming. Such gap-filling is applied on algae and extended to decipher putative interactions between Ectocarpus siliculosus and a symbiotic bacterium. In this direction, the second part of the thesis aims at proposing formalisms and implementation of a tool for selecting and screening communities of interest within microbiotas. It enables to scale to large microbiotas and, with a two-step approach, to suggest symbionts that fit the desired objective. The modeling supports the computation of exchanges, and solving can cover the whole solution space. Applications are presented on the human gut microbiota and the selection of bacterial communities for a brown alga. Altogether, this thesis proposes modeling, software and biological applications using graph-based semantics to support the elaboration of hypotheses for elucidating the metabolism of organisms.

Application of neural networks in deep learning is rapidly growing due to their ability to outperform other machine learning algorithms in different kinds of problems. But one big disadvantage of deep neural networks is its internal logic to achieve the desired output or result that is un-understandable and unexplainable. This behavior of the deep neural network is known as “black box”. This leads to the following questions: how prevalent is the black box problem in the research literature during a specific period of time? The black box problems are usually addressed by socalled rule extraction. The second research question is: what rule extracting methods have been proposed to solve such kind of problems? To answer the research questions, a systematic literature review was conducted for data collection related to topics, the black box, and the rule extraction. The printed and online articles published in higher ranks journals and conference proceedings were selected to investigate and answer the research questions. The analysis unit was a set of journals and conference proceedings articles related to the topics, the black box, and the rule extraction. The results conclude that there has been gradually increasing interest in the black box problems with the passage of time mainly because of new technological development. The thesis also provides an overview of different methodological approaches used for rule extraction methods.

<p>This thesis presents the implementation of a knowledge base system for rough sets [Paw92]within the logic programming framework. The combination of rough set theory with logic programming is a novel approach. The presented implementation serves as a prototype system for the ideas presented in [VDM03a, VDM03b]. The system is available at "http://www.ida.liu.se/rkbs". </p><p>The presented language for describing knowledge in the rough knowledge base caters for implicit definition of rough sets by combining different regions (e.g. upper approximation, lower approximation, boundary) of other defined rough sets. The rough knowledge base system also provides methods for querying the knowledge base and methods for computing quantitative measures. </p><p>We test the implemented system on a medium sized application example to illustrate the usefulness of the system and the incorporated language. We also provide performance measurements of the system.</p>

In this dissertation we lay the groundwork of automated analysis of extended feature models with constraint programming. Among different proposals, feature modeling has proven to be very effective for modeling and managing variability in Software Product Lines. However, industrial experiences showed that feature models often grow too large with hundreds of features and complex cross-tree relationships, which necessitates automated analysis support. To address this issue we present a mapping from extended feature models, which may include complex feature-feature, feature-attribute and attribute-attribute cross-tree relationships as well as global constraints, to constraint logic programming over finite domains. Then, we discuss the effects of including complex feature attribute relationships on various analysis operations defined on the feature models. As new types of variability emerge due to the inclusion of feature attributes in cross-tree relationships, we discuss the necessity of reformulation of some of the analysis operations and suggest a revised understanding for some other. We also propose new analysis operations arising due to the nature of the new variability introduced. Then we propose a transformation from extended feature models to basic/cardinality-based feature models that may be applied under certain circumstances and enables using SAT or BDD solvers in automated analysis of extended feature models. Finally, we discuss the role of the context information in feature modeling, and propose to use context information in staged configuration of feature-models.

Αντικείμενο της εργασίας αυτής αποτελεί η χρήση της γλώσσας λογικού προγραμματισμού Prolog για τη συντακτική ανάλυση (parsing) παραδειγμάτων ρηματικής φράσης, ακολουθώντας τις τελευταίες εξελίξεις στο χώρο της γενετικής γραμματικής (Μινιμαλιστικό Πρόγραμμα). Στην προσπάθεια πλήρους περιγραφής του προβλήματος, όπως απαιτεί ο λογικός προγραμματισμός, στο επίκεντρο τοποθετείται η διεπαφή σύνταξης – σημασιολογίας. Γίνεται αναφορά σε θεωρητικά προβλήματα όπως η διάκριση μεταξύ ανεργαστικών και μεταβατικών ρημάτων και η φύση των ρημάτων καιρού (weather verbs), και προτείνονται τρόποι ερμηνείας και διαχείρισης των παραπάνω προβλημάτων στο περιβάλλον της Prolog. / The purpose of this study is to examine the use of the logic programming language Prolog as a parser for VPs within the generative grammar/Minimalist Program framework. We focus on the syntax- semantics interface and try to address issues such as the differences between unergative- transitive verbs and the structure of weather verbs within the Prolog environment.

This work presents business process analysis methodology which consists of presentation of the business processes created on the ground of the Resource Event Agent model by means of Piece–Linear Aggregate approach. The aggregate specification is analyzing using first order predicate logic while checking correctness by resolution method using logic programming based language Prolog. The work is concluded with concrete example of analysis of Resource Event Agent model based business process using the aggregate approach. The novelty of this work PLA (Piece-Linear Aggregate) model and the software tools, created on the ground of PLA (Piece-Linear Aggregate), are used the first time for business processes analysis that is defined using REA formalism. The use of such integrated models allows performing the automated analysis of general and individual properties (completeness, deadlock freeness, termination or cyclic behavior, boundedness) of defined business processes. The main results are achieved: • The methodology, that consists of presentation of the business processes created on the ground of the Resource Event Agent model by means of Piece–Linear Aggregate approach. • Verification and validation of general and individual properties by using PLA and PROLOG language approach designed system that executes the analysis of aggregate specification. • Implementing internal accounting controls as constraints in relational algebra, SQL and PROLOG language. • Concrete... [to full text]

Ο Επαγωγικός Λογικός Προγραμματισμός (Inductive Logic Programming ή, σε συντομογραφία ILP) είναι ο ερευνητικός τομέας της Τεχνητής Νοημοσύνης (Artificial Intelligence) που δραστηριοποιείται στη τομή των γνωστικών περιοχών της Μάθησης Μηχανής (Machine Learning) και του Λογικού Προγραμματισμού (Logic Programming).Ο όρος επαγωγικός εκφράζει την ιδέα του συλλογισμού από το επί μέρους στο γενικό. Μέσω της επαγωγικής μάθησης μηχανής ο Επαγωγικός Λογικός Προγραμματισμός επιτυγχάνει το στόχο του που είναι η δημιουργία εργαλείων και η ανάπτυξη τεχνικών για την εξαγωγή υποθέσεων από παρατηρήσεις (παραδείγματα) και η σύνθεση-απόκτηση νέας γνώσης από εμπειρικές παρατηρήσεις. Σε αντίθεση με της περισσότερες άλλες προσεγγίσεις της επαγωγικής μάθησης ο Επαγωγικός Λογικός Προγραμματισμός ενδιαφέρεται για της ιδιότητες του συμπερασμού με κανόνες για την σύγκλιση αλγορίθμων και για την υπολογιστική πολυπλοκότητα των διαδικασιών. Ο Επαγωγικός Λογικός Προγραμματισμός ασχολείται με την ανάπτυξη τεχνικών και εργαλείων για την σχεσιακή ανάλυση δεδομένων. Εφαρμόζεται απευθείας σε δεδομένα πολλαπλών συσχετισμών για την ανακάλυψη προτύπων. Τα πρότυπα που ανακαλύπτονται από τα συστήματα στον Επαγωγικό Λογικό Προγραμματισμό προκύπτουν από κάποιο γνωστό θεωρητικό υπόβαθρο και θετικά και αρνητικά παραδείγματα και εκφράζονται ως λογικά προγράμματα. Ο Επαγωγικός Λογικός Προγραμματισμός έχει χρησιμοποιηθεί εκτεταμένα σε προβλήματα που αφορούν τη μοριακή βιολογία, την βιοχημεία και την χημεία. Ο Επαγωγικός Λογικός Προγραμματισμός διαφοροποιείται από τις άλλες μορφές Μάθησης Μηχανής, αφ’ ενός μεν λόγω της χρήσης μιας εκφραστικής γλώσσας αναπαράστασης και αφ’ ετέρου από τη δυνατότητά του να χρησιμοποιεί τη γνώση υποβάθρου. Έχουν αναπτυχθεί διάφορες μηχανισμούς υλοποίησης του ILP, εκ των οποίων η πιο πρόσφατη είναι η Progol, που βασίζεται σε ένα διερμηνέα της Prolog ο οποίος συνοδεύεται από έναν αλγόριθμο Αντίστροφης Συνεπαγωγής (Inverse Entailment). Η Progol κατασκευάζει νέες προτάσεις με τη γενίκευση των παραδειγμάτων που περιέχονται στη βάση δεδομένων που της δίνεται. Η θεωρία του Επαγωγικού Λογικού Προγραμματισμού εγγυάται ότι η Progol θα διεξάγει μια αποδεκτή αναζήτηση στο διάστημα των γενικεύσεων, βρίσκοντας το ελάχιστο σύνολο προτάσεων, από το οποίο όλα τα παραδείγματα μπορούν να προκύψουν. Σε αυτή την εργασία θα αναπτυχθούν αναλυτικά η θεωρία και οι κανόνες του Επαγωγικού Λογικού Προγραμματισμού, τα είδη των προβλημάτων που επιλύονται μέσω του Επαγωγικού Λογικού Προγραμματισμού, οι μέθοδοι που ακολουθούνται καθώς και ο τρόπος με τον οποίο αναπτύσσονται οι εφαρμογές του Επαγωγικού Λογικού Προγραμματισμού. Θα δοθούν επίσης παραδείγματα κατάλληλα για την κατανόηση των γνώσεων αυτών από ένα ακροατήριο που διαθέτει βασικές γνώσεις Λογικής και Λογικού Προγραμματισμού. / Inductive Logic Programming is a research area of Artificial Intelligence that operates in the intersection of cognitive areas of Machine Learning and Logic Programming. Through inductive machine learning, Inductive Logic Programming‟s objective is creating tools and developing techniques to extract new knowledge composing a background one and empirical observations (examples). Some methods are employed, the best known of which is the reverse implication, the reverse resolution and the inverse implication. Based on Inductive Logic Programming, some systems have been developed for knowledge production. The most widely used system is Progol, which uses an input of examples and background knowledge, whichε is stated in a kind of grammar compatible to that the programming language Prolog, and generates procedures in the same language that illustrate these examples. Other systems are FOIL, MOBAL, GOLEM and LINUS. There is also Cigol which is a programming language based on the theory of Inductive Logic Programming. These systems are used in many applications. The most important is the area of pharmacology, such as predictive toxicology, the provision of rheumatic disease and the design of drugs for Alzheimer's. Applications can also be found in programming, linguistics and games like chess.

Ce travail de thèse, effectué dans la cadre du projet FUI Minalogic Bluesky, porte sur le test fonctionnel automatisé d'une classe particulière de contrôleurs logiques programmables (em4) produite par InnoVista Sensors. Ce sont des systèmes synchrones qui sont programmés au moyen d'un environnement de développement intégré (IDE). Les personnes qui utilisent et programment ces contrôleurs ne sont pas nécessairement des programmeurs experts. Le développement des applications logicielles doit être par conséquent simple et intuitif. Cela devrait également être le cas pour les tests. Même si les applications définies par ces utilisateurs ne sont pas nécessairement très critiques, il est important de les tester d'une manière adéquate et efficace. Un simulateur inclu dans l'IDE permet aux programmeurs de tester leurs programmes d'une façon qui reste à ce jour informelle et interactive en entrant manuellement des données de test. En se basant sur des recherches précédentes dans le domaine du test des programmes synchrones, nous proposons un nouveau langage de spécification de test, appelé SPTL (Synchronous Programs Testing Language) qui rend possible d'exprimer simplement des scénarios de test qui peuvent être exécutées à la volée pour générer automatiquement des séquences d'entrée de test. Il permet aussi de décrire l'environnement où évolue le système pour mettre des conditions sur les entrées afin d'arriver à des données de test réalistes et de limiter celles qui sont inutiles. SPTL facilite cette tâche de test en introduisant des notions comme les profils d'utilisation, les groupes et les catégories. Nous avons conçu et développé un prototype, nommé "Testium", qui traduit un programme SPTL en un ensemble de contraintes exploitées par un solveur Prolog qui choisit aléatoirement les entrées de test. La génération de données de test s'appuie ainsi sur des techniques de programmation logique par contraintes. Pour l'évaluer, nous avons expérimenté cette méthode sur des exemples d'applications EM4 typiques et réels. Bien que SPTL ait été évalué sur em4, son utilisation peut être envisagée pour la validation d'autres types de contrôleurs ou systèmes synchrones. / This thesis work done in the context of the FUI project Minalogic Bluesky, concerns the automated functional testing of a particular class of programmable logic controllers (em4) produced by InnoVista Sensors. These are synchronous systems that are programmed by means of an integrated development environment (IDE). People who use and program these controllers are not necessarily expert programmers. The development of software applications should be as result simple and intuitive. This should also be the case for testing. Although applications defined by these users need not be very critical, it is important to test them adequately and effectively. A simulator included in the IDE allows programmers to test their programs in a way that remains informal and interactive by manually entering test data.Based on previous research in the area of synchronous test programs, we propose a new test specification language, called SPTL (Synchronous Testing Programs Language) which makes possible to simply express test scenarios that can be executed on the fly to automatically generate test input sequences. It also allows describing the environment in which the system evolves to put conditions on inputs to arrive to realistic test data and limit unnecessary ones. SPTL facilitates this testing task by introducing concepts such as user profiles, groups and categories. We have designed and developed a prototype named "Testium", which translates a SPTL program to a set of constraints used by a Prolog solver that randomly selects the test inputs. So, generating test data is based on constraint logic programming techniques.To assess this, we experimented this method on realistic and typical examples of em4 applications. Although SPTL was evaluated on EM4, its use can be envisaged for the validation of other types of synchronous controllers or systems.