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Pattern matching approaches in reverse engineering aim to incorporate domain knowledge and system documentation in the software architecture extraction process, hence provide a user/tool collaborative environment for architectural design recovery. This thesis presents a model and an environment for recovering the high level design of legacy software systems based on user defined architectural patterns and graph matching techniques. In the proposed model, a high-level view of a software system in terms of the system components and their interactions is represented as a query, using a description language. A query is mapped onto a pattern-graph, where a module and its interactions with other modules are represented as a group of graph-nodes and a group of graph-edges, respectively. Interaction constraints can be modeled by the description language as a part of the query. Such a pattern-graph is applied against an entity-relation graph that represents the information extracted from the source code of the software system. An approximate graph matching process performs a series of graph edit operations (i. e. , node/edge insertion/deletion) on the pattern-graph and uses a ranking mechanism based on data mining association to obtain a sub-optimal solution. The obtained solution corresponds to an extracted architecture that complies with the given query. An interactive prototype toolkit implemented as part of this thesis provides an environment for architecture recovery in two levels. First the system is decomposed into a number of subsystems of files. Second each subsystem can be decomposed into a number of modules of functions, datatypes, and variables.

Pattern matching approaches in reverse engineering aim to incorporate domain knowledge and system documentation in the software architecture extraction process, hence provide a user/tool collaborative environment for architectural design recovery. This thesis presents a model and an environment for recovering the high level design of legacy software systems based on user defined architectural patterns and graph matching techniques. In the proposed model, a high-level view of a software system in terms of the system components and their interactions is represented as a query, using a description language. A query is mapped onto a pattern-graph, where a module and its interactions with other modules are represented as a group of graph-nodes and a group of graph-edges, respectively. Interaction constraints can be modeled by the description language as a part of the query. Such a pattern-graph is applied against an entity-relation graph that represents the information extracted from the source code of the software system. An approximate graph matching process performs a series of graph edit operations (i. e. , node/edge insertion/deletion) on the pattern-graph and uses a ranking mechanism based on data mining association to obtain a sub-optimal solution. The obtained solution corresponds to an extracted architecture that complies with the given query. An interactive prototype toolkit implemented as part of this thesis provides an environment for architecture recovery in two levels. First the system is decomposed into a number of subsystems of files. Second each subsystem can be decomposed into a number of modules of functions, datatypes, and variables.

Made available in DSpace on 2016-06-02T19:05:47Z (GMT). No. of bitstreams: 1 3340.pdf: 982188 bytes, checksum: 49ba39146aa7542a1670dd3d90507739 (MD5) Previous issue date: 2010-06-28 / Financiadora de Estudos e Projetos / In the context of automated manufacturing systems, combinatorial optimization problems, such as determining the production schedule, have been focused in many studies due to the high degree of complexity to their resolution. Several studies point to use of metaheuristics for the problem dealt, where different approaches perspectives have been proposed in order to find good solutions in a short time. In this paper, we propose an approach based on Ant Colony Optimization metaheuristic (ACO) for the reactive production scheduling problem in an FMS aiming the combination of problem characteristics with metaheuristic characteristics. For this, the problem is addressed from two perspectives, based on modeling and the search method. The problem representation is characterized by a description of the problem at the operations level, since the production schedule is included in this context. On the model is applied a constructive search method based on ACO that using the collaboration principle, establishing a relationship between operations so that it lead the search for promising regions of the solution space. The goal of this work is to obtain a reactive programming in acceptable response time in order to minimize the makespan values. Experimental results showed an improvement of the results obtained so far by other approaches. / No contexto de Sistemas Automatizados de Manufatura, problemas de otimização combinatória, como determinar a programação da produção, têm sido foco de estudo em muitas pesquisas devido ao alto grau de complexidade para sua resolução. Diversos trabalhos apontam para o uso de metaheurísticas para o tratamento do problema, onde diferentes perspectivas de abordagens têm sido propostas visando encontrar soluções de qualidade em um curto espaço de tempo. Neste trabalho, é proposta uma abordagem baseada na metaheurística Otimização por Colônia de Formigas (Ant Colony Optimization ACO) para o problema de programação reativa da produção em um FMS, com o objetivo de conciliar as características do problema com as características da metaheurística. Para isso, o problema é tratado em duas perspectivas, com base na modelagem e no método de busca. A modelagem do problema é caracterizada por uma descrição do problema em nível de operações, uma vez que a programação da produção está incluída neste contexto. Sobre o modelo é aplicado um método de busca construtiva baseado em ACO que usando o princípio de colaboração, estabelece uma relação entre as operações de forma que esta direcione a busca para regiões promissoras do espaço de soluções. O Objetivo deste trabalho é obter uma programação reativa em tempo de resposta aceitável, visando minimizar o valor de makespan. Resultados experimentais mostraram uma melhoria dos resultados até então obtidos por outras abordagens.

In recent biomedical research, graph representation learning and cell profiling techniques have emerged as transformative tools for analyzing high-dimensional biological data. The integration of these methods, as investigated in this study, has facilitated an enhanced understanding of complex biological systems, consequently improving drug discovery. The research aimed to decipher connections between chemical structures and cellular phenotypes while incorporating other biological information like proteins and pathways into the workflow. To achieve this, machine learning models' efficacy was examined for classification and regression tasks. The newly proposed graph-level and bio-graph integrative predictors were compared with traditional models. Results demonstrated their potential, particularly in classification tasks. Moreover, the topology of the COVID-19 BioGraph was analyzed, revealing the complex interconnections between chemicals, proteins, and biological pathways. By combining network analysis, graph representation learning, and statistical methods, the study was able to predict active chemical combinations within inactive compounds, thereby exhibiting significant potential for further investigations. Graph-based generative models were also used for molecule generation opening up further research avenues in finding lead compounds. In conclusion, this study underlines the potential of combining graph representation learning and cell profiling techniques in advancing biomedical research in drug repurposing and drug combination. This integration provides a better understanding of complex biological systems, assists in identifying therapeutic targets, and contributes to optimizing molecule generation for drug discovery. Future investigations should optimize these models and validate the drug combination discovery approach. As these techniques continue to evolve, they hold the potential to significantly impact the future of drug screening, drug repurposing, and drug combinations.

L’avènement de l'apprentissage profond a permis à l'apprentissage automatique d’exceller dans le traitement d'images et de texte. Donnant lieu à de nombreux succès dans les domaines d’applications tels que la vision par ordinateur ou le traitement du langage naturel. Cependant, il demeure un grand nombre de problèmes d’intérêt dont les données d’entrées ne peuvent être exprimées sous l’un de ces deux formats sans perte d'informations potentiellement cruciales pour leur résolution. C’est dans l’optique de répondre à ce besoin qu’a été développée la branche de l'apprentissage profond géométrique (GDL), qui s’intéresse aux espaces de représentations plus générales, mieux adaptées aux données dont la structure sous-jacente ne correspond pas au format de chaîne de caractères unidimensionnel (texte) ou bidimensionnel (images). Dans cette thèse, nous nous concentrerons plus particulièrement sur les graphes. Les graphes sont des structures de données omniprésentes, sous-jacentes à pratiquement toutes les tâches d'intérêt, y compris celles portant sur les données naturelles (par exemple les molécules), les relations entre entités (par exemple les réseaux de transport et les placements de puces), ou encore la liaison de concepts dans les processus de raisonnement (par exemple les algorithmes et autres constructions théoriques). Alors que les architectures modernes de réseaux de neurones de graphes (GNNs) dits expressifs peuvent obtenir des résultats impressionnants sur des benchmarks comme susmentionnés, leur application pratique est toujours en proie à de nombreux problèmes et lacunes, que cette thèse abordera. Les considérations issues de ces applications préparerons le terrain pour les chapitres suivants, qui se concentreront sur la résolution des limites des réseaux de neurones de graphes en proposant de nouveaux algorithmes d'apprentissage de graphes. Tout d'abord, nous porterons notre attention sur l'amélioration des réseaux de neurones de graphes pour les données qui nécessitent des interactions à longue portée, en construisant des modèles généraux pour compléter leur graphe de calcul. Viennent ensuite les réseaux de neurones de graphes pour les données hétérophiles, où les arêtes ont tendance à connecter des nœuds de différentes classes; dans ce cas, nous proposerons une modification particulière du graphe de calcul destinée à améliorer l'homophilie atténue le problème. Dans un troisième temps, nous tirerons parti d'une caractéristique avantageuse des réseaux de neurones de graphes - leur alignement avec la programmation dynamique. Elle permet aux réseaux de neurones de graphes d'exécuter des algorithmes, sur la base desquels nous proposons une nouvelle classe de planificateurs implicites pour la prise de décision. Enfin, nous capitalisons sur l'utilité de l'apprentissage profond géométrique dans l'apprentissage par renforcement et l'étendrons au-delà des GNNs, en tirant parti des réseaux de neurones à rotation équivariante dans les agents basés sur des modèles. / Since the deep learning revolution, machine learning has excelled at tasks based on images and text, many successes being possible under the umbrella of the computer vision and natural language processing fields. However, much remains that cannot be expressed in these forms without losing information. For these cases, the field of geometric deep learning was developed, covering the space of more general representations, for data whose underlying structure doesn't match the single-dimensional string of characters (text) or 2-D shape (images) format. In this thesis, I will particularly focus on graphs. Graphs are ubiquitous data structures underlying virtually all tasks of interest, including natural inputs such as molecules, entity relations for example transportation networks and chip placements, or concept linking in reasoning processes, including algorithms and other theoretical constructs. While modern expressive graph neural network architectures can achieve impressive results on benchmarks like these, their practical application is still plagued with many issues and shortcomings, which this thesis will address. The considerations from these applications will set the scene for the following chapters, which focus on tackling the limitations of graph neural networks by proposing new graph learning algorithms. Firstly, I focus on improving graph neural networks for data that requires long-range interactions by building general templates to complement their computation graph. This is followed by graph neural networks for heterophilic data, where the edges tend to connect nodes from different classes; in this case, a specialised modification of the computation graph meant to improve homophily alleviates the problem. In the third article, I leverage a strength of graph neural networks -- their alignment with dynamic programming. This enables graph neural networks to execute algorithms, based on which I propose a new class of implicit planners for decision making. Lastly, I capitalise on the utility of geometric deep learning in reinforcement learning and extend it beyond GNNs, leveraging rotation-equivariant neural networks in model-based agents.

<p dir="ltr">Semantic pairs, which consist of related entities or concepts, serve as the foundation for comprehending the meaning of language in both written and spoken forms. These pairs enable to grasp the nuances of relationships between words, phrases, or ideas, forming the basis for more advanced language tasks like entity recognition, sentiment analysis, machine translation, and question answering. They allow to infer causality, identify hierarchies, and connect ideas within a text, ultimately enhancing the depth and accuracy of automated language processing.</p><p dir="ltr">Nevertheless, the task of extracting semantic pairs from sentences poses a significant challenge, necessitating the relevance of syntactic dependency patterns (SDPs). Thankfully, semantic relationships exhibit adherence to distinct SDPs when connecting pairs of entities. Recognizing this fact underscores the critical importance of extracting these SDPs, particularly for specific semantic relationships like hyponym-hypernym, meronym-holonym, and cause-effect associations. The automated extraction of such SDPs carries substantial advantages for various downstream applications, including entity extraction, ontology development, and question answering. Unfortunately, this pivotal facet of pattern extraction has remained relatively overlooked by researchers in the domains of natural language processing (NLP) and information retrieval.</p><p dir="ltr">To address this gap, I introduce an attention-based supervised deep learning model, ASPER. ASPER is designed to extract SDPs that denote semantic relationships between entities within a given sentential context. I rigorously evaluate the performance of ASPER across three distinct semantic relations: hyponym-hypernym, cause-effect, and meronym-holonym, utilizing six datasets. My experimental findings demonstrate ASPER's ability to automatically identify an array of SDPs that mirror the presence of these semantic relationships within sentences, outperforming existing pattern extraction methods by a substantial margin.</p><p dir="ltr">Second, I want to use the SDPs to extract semantic pairs from sentences. I choose to extract cause-effect entities from medical literature. This task is instrumental in compiling various causality relationships, such as those between diseases and symptoms, medications and side effects, and genes and diseases. Existing solutions excel in sentences where cause and effect phrases are straightforward, such as named entities, single-word nouns, or short noun phrases. However, in the complex landscape of medical literature, cause and effect expressions often extend over several words, stumping existing methods, resulting in incomplete extractions that provide low-quality, non-informative, and at times, conflicting information. To overcome this challenge, I introduce an innovative unsupervised method for extracting cause and effect phrases, PatternCausality tailored explicitly for medical literature. PatternCausality employs a set of cause-effect dependency patterns as templates to identify the key terms within cause and effect phrases. It then utilizes a novel phrase extraction technique to produce comprehensive and meaningful cause and effect expressions from sentences. Experiments conducted on a dataset constructed from PubMed articles reveal that PatternCausality significantly outperforms existing methods, achieving a remarkable order of magnitude improvement in the F-score metric over the best-performing alternatives. I also develop various PatternCausality variants that utilize diverse phrase extraction methods, all of which surpass existing approaches. PatternCausality and its variants exhibit notable performance improvements in extracting cause and effect entities in a domain-neutral benchmark dataset, wherein cause and effect entities are confined to single-word nouns or noun phrases of one to two words.</p><p dir="ltr">Nevertheless, PatternCausality operates within an unsupervised framework and relies heavily on SDPs, motivating me to explore the development of a supervised approach. Although SDPs play a pivotal role in semantic relation extraction, pattern-based methodologies remain unsupervised, and the multitude of potential patterns within a language can be overwhelming. Furthermore, patterns do not consistently capture the broader context of a sentence, leading to the extraction of false-positive semantic pairs. As an illustration, consider the hyponym-hypernym pattern <i>the w of u</i> which can correctly extract semantic pairs for a sentence like <i>the village of Aasu</i> but fails to do so for the phrase <i>the moment of impact</i>. The root cause of this limitation lies in the pattern's inability to capture the nuanced meaning of words and phrases in a sentence and their contextual significance. These observations have spurred my exploration of a third model, DepBERT which constitutes a dependency-aware supervised transformer model. DepBERT's primary contribution lies in introducing the underlying dependency structure of sentences to a language model with the aim of enhancing token classification performance. To achieve this, I must first reframe the task of semantic pair extraction as a token classification problem. The DepBERT model can harness both the tree-like structure of dependency patterns and the masked language architecture of transformers, marking a significant milestone, as most large language models (LLMs) predominantly focus on semantics and word co-occurrence while neglecting the crucial role of dependency architecture.</p><p dir="ltr">In summary, my overarching contributions in this thesis are threefold. First, I validate the significance of the dependency architecture within various components of sentences and publish SDPs that incorporate these dependency relationships. Subsequently, I employ these SDPs in a practical medical domain to extract vital cause-effect pairs from sentences. Finally, my third contribution distinguishes this thesis by integrating dependency relations into a deep learning model, enhancing the understanding of language and the extraction of valuable semantic associations.</p>

<p>Research on graph representation learning (GRL) has made major strides over the past decade, with widespread applications in domains such as e-commerce, personalization, fraud & abuse, life sciences, and social network analysis. Despite its widespread success, fundamental questions on practices employed in modern day GRL have remained unanswered. Unraveling and advancing two such fundamental questions on the practices in modern day GRL forms the overarching theme of my thesis.</p> <p>The first part of my thesis deals with the mathematical foundations of GRL. GRL is used to solve tasks such as node classification, link prediction, clustering, graph classification, and so on, albeit with seemingly different frameworks (e.g. Graph neural networks for node/graph classification, (implicit) matrix factorization for link prediction/ clustering, etc.). The existence of very distinct frameworks for different graph tasks has puzzled researchers and practitioners alike. In my thesis, using group theory, I provide a theoretical blueprint that connects these seemingly different frameworks, bridging methods like matrix factorization and graph neural networks. With this renewed understanding, I then provide guidelines to better realize the full capabilities of these methods in a multitude of tasks.</p> <p>The second part of my thesis deals with cases where modeling real-world objects as a graph is an oversimplified description of the underlying data. Specifically, I look at two such objects (i) modeling hypergraphs (where edges encompass two or more vertices) and (ii) using GRL for predicting protein properties. Towards (i) hypergraphs, I develop a hypergraph neural network which takes advantage of the inherent sparsity of real world hypergraphs, without unduly sacrificing on its ability to distinguish non isomorphic hypergraphs. The designed hypergraph neural network is then leveraged to learn expressive representations of hyperedges for two tasks, namely hyperedge classification and hyperedge expansion. Experiments show that using our network results in improved performance over the current approach of converting the hypergraph into a dyadic graph and using (dyadic) GRL frameworks. Towards (ii) proteins, I introduce the concept of conditional invariances and leverage it to model the inherent flexibility present in proteins. Using conditional invariances, I provide a new framework for GRL which can capture protein-dependent conformations and ensures that all viable conformers of a protein obtain the same representation. Experiments show that endowing existing GRL models with my framework shows noticeable improvements on multiple different protein datasets and tasks.</p>

The core research of this thesis, mostly comprising chapter four, has been accepted to the Learning on Graphs (LoG) 2022 conference for a spotlight presentation as a standalone paper, under the title "Taxonomy of Benchmarks in Graph Representation Learning", and is to be published in the Proceedings of Machine Learning Research (PMLR) series. As a main author of the paper, my specific contributions to this paper cover problem formulation, design and implementation of our taxonomy framework and experimental pipeline, collation of our results and of course the writing of the article. / L'apprentissage profond sur les graphes a atteint des niveaux de succès sans précédent ces dernières années grâce aux réseaux de neurones de graphes (GNN), des architectures de réseaux de neurones spécialisées qui ont sans équivoque surpassé les approches antérieurs d'apprentissage définies sur des graphes. Les GNN étendent le succès des réseaux de neurones aux données structurées en graphes en tenant compte de leur géométrie intrinsèque. Bien que des recherches approfondies aient été effectuées sur le développement de GNN avec des performances supérieures à celles des modèles références d'apprentissage de représentation graphique, les procédures d'analyse comparative actuelles sont insuffisantes pour fournir des évaluations justes et efficaces des modèles GNN. Le problème peut-être le plus répandu et en même temps le moins compris en ce qui concerne l'analyse comparative des graphiques est la "couverture de domaine": malgré le nombre croissant d'ensembles de données graphiques disponibles, la plupart d'entre eux ne fournissent pas d'informations supplémentaires et au contraire renforcent les biais potentiellement nuisibles dans le développement d’un modèle GNN. Ce problème provient d'un manque de compréhension en ce qui concerne les aspects d'un modèle donné qui sont sondés par les ensembles de données de graphes. Par exemple, dans quelle mesure testent-ils la capacité d'un modèle à tirer parti de la structure du graphe par rapport aux fonctionnalités des nœuds? Ici, nous développons une approche fondée sur des principes pour taxonomiser les ensembles de données d'analyse comparative selon un "profil de sensibilité" qui est basé sur la quantité de changement de performance du GNN en raison d'une collection de perturbations graphiques. Notre analyse basée sur les données permet de mieux comprendre quelles caractéristiques des données de référence sont exploitées par les GNN. Par conséquent, notre taxonomie peut aider à la sélection et au développement de repères graphiques adéquats et à une évaluation mieux informée des futures méthodes GNN. Enfin, notre approche et notre implémentation dans le package GTaxoGym (https://github.com/G-Taxonomy-Workgroup/GTaxoGym) sont extensibles à plusieurs types de tâches de prédiction de graphes et à des futurs ensembles de données. / Deep learning on graphs has attained unprecedented levels of success in recent years thanks to Graph Neural Networks (GNNs), specialized neural network architectures that have unequivocally surpassed prior graph learning approaches. GNNs extend the success of neural networks to graph-structured data by accounting for their intrinsic geometry. While extensive research has been done on developing GNNs with superior performance according to a collection of graph representation learning benchmarks, current benchmarking procedures are insufficient to provide fair and effective evaluations of GNN models. Perhaps the most prevalent and at the same time least understood problem with respect to graph benchmarking is "domain coverage": Despite the growing number of available graph datasets, most of them do not provide additional insights and on the contrary reinforce potentially harmful biases in GNN model development. This problem stems from a lack of understanding with respect to what aspects of a given model are probed by graph datasets. For example, to what extent do they test the ability of a model to leverage graph structure vs. node features? Here, we develop a principled approach to taxonomize benchmarking datasets according to a "sensitivity profile" that is based on how much GNN performance changes due to a collection of graph perturbations. Our data-driven analysis provides a deeper understanding of which benchmarking data characteristics are leveraged by GNNs. Consequently, our taxonomy can aid in selection and development of adequate graph benchmarks, and better informed evaluation of future GNN methods. Finally, our approach and implementation in the GTaxoGym package (https://github.com/G-Taxonomy-Workgroup/GTaxoGym) are extendable to multiple graph prediction task types and future datasets.