Matching Biomedical Ontologies via a Hybrid Graph Attention Network

Biomedical ontologies have been used extensively to formally define and organize biomedical terminologies, and these ontologies are typically manually created by biomedical experts. With more biomedical ontologies being built independently, matching them to address the problem of heterogeneity and interoperability has become a critical challenge in many biomedical applications. Existing matching methods have mostly focused on capturing features of terminological, structural, and contextual semantics in ontologies. However, these feature engineering-based techniques are not only labor-intensive but also ignore the hidden semantic relations in ontologies. In this study, we propose an alternative biomedical ontology-matching framework BioHAN via a hybrid graph attention network, and that consists of three techniques. First, we propose an effective ontology-enriching method that refines and enriches the ontologies through axioms and external resources. Subsequently, we use hyperbolic graph attention layers to encode hierarchical concepts in a unified hyperbolic space. Finally, we aggregate the features of both the direct and distant neighbors with a graph attention network. Experimental results on real-world biomedical ontologies demonstrate that BioHAN is competitive with the state-of-the-art ontology matching methods

Similarity Reasoning over Semantic Context-Graphs

Similarity is a central cognitive mechanism for humans which enables a broad range of perceptual and abstraction processes, including recognizing and categorizing objects, drawing parallelism, and predicting outcomes. It has been studied computationally through models designed to replicate human judgment. The work presented in this dissertation leverages general purpose semantic networks to derive similarity measures in a problem-independent manner. We model both general and relational similarity using connectivity between concepts within semantic networks. Our first contribution is to model general similarity using concept connectivity, which we use to partition vocabularies into topics without the need of document corpora. We apply this model to derive topics from unstructured dialog, specifically enabling an early literacy primer application to support parents in having better conversations with their young children, as they are using the primer together. Second, we model relational similarity in proportional analogies. To do so, we derive relational parallelism by searching in semantic networks for similar path pairs that connect either side of this analogy statement. We then derive human readable explanations from the resulting similar path pair. We show that our model can answer broad-vocabulary analogy questions designed for human test takers with high confidence. The third contribution is to enable symbolic plan repair in robot planning through object substitution. When a failure occurs due to unforeseen changes in the environment, such as missing objects, we enable the planning domain to be extended with a number of alternative objects such that the plan can be repaired and execution to continue. To evaluate this type of similarity, we use both general and relational similarity. We demonstrate that the task context is essential in establishing which objects are interchangeable

Exploiting general-purpose background knowledge for automated schema matching

The schema matching task is an integral part of the data integration process. It is usually the first step in integrating data. Schema matching is typically very complex and time-consuming. It is, therefore, to the largest part, carried out by humans. One reason for the low amount of automation is the fact that schemas are often defined with deep background knowledge that is not itself present within the schemas. Overcoming the problem of missing background knowledge is a core challenge in automating the data integration process. In this dissertation, the task of matching semantic models, so-called ontologies, with the help of external background knowledge is investigated in-depth in Part I. Throughout this thesis, the focus lies on large, general-purpose resources since domain-specific resources are rarely available for most domains. Besides new knowledge resources, this thesis also explores new strategies to exploit such resources. A technical base for the development and comparison of matching systems is presented in Part II. The framework introduced here allows for simple and modularized matcher development (with background knowledge sources) and for extensive evaluations of matching systems. One of the largest structured sources for general-purpose background knowledge are knowledge graphs which have grown significantly in size in recent years. However, exploiting such graphs is not trivial. In Part III, knowledge graph em- beddings are explored, analyzed, and compared. Multiple improvements to existing approaches are presented. In Part IV, numerous concrete matching systems which exploit general-purpose background knowledge are presented. Furthermore, exploitation strategies and resources are analyzed and compared. This dissertation closes with a perspective on real-world applications

Modélisation formelle des systèmes de détection d'intrusions

L’écosystème de la cybersécurité évolue en permanence en termes du nombre, de la diversité, et de la complexité des attaques. De ce fait, les outils de détection deviennent inefficaces face à certaines attaques. On distingue généralement trois types de systèmes de détection d’intrusions : détection par anomalies, détection par signatures et détection hybride. La détection par anomalies est fondée sur la caractérisation du comportement habituel du système, typiquement de manière statistique. Elle permet de détecter des attaques connues ou inconnues, mais génère aussi un très grand nombre de faux positifs. La détection par signatures permet de détecter des attaques connues en définissant des règles qui décrivent le comportement connu d’un attaquant. Cela demande une bonne connaissance du comportement de l’attaquant. La détection hybride repose sur plusieurs méthodes de détection incluant celles sus-citées. Elle présente l’avantage d’être plus précise pendant la détection. Des outils tels que Snort et Zeek offrent des langages de bas niveau pour l’expression de règles de reconnaissance d’attaques. Le nombre d’attaques potentielles étant très grand, ces bases de règles deviennent rapidement difficiles à gérer et à maintenir. De plus, l’expression de règles avec état dit stateful est particulièrement ardue pour reconnaître une séquence d’événements. Dans cette thèse, nous proposons une approche stateful basée sur les diagrammes d’état-transition algébriques (ASTDs) afin d’identifier des attaques complexes. Les ASTDs permettent de représenter de façon graphique et modulaire une spécification, ce qui facilite la maintenance et la compréhension des règles. Nous étendons la notation ASTD avec de nouvelles fonctionnalités pour représenter des attaques complexes. Ensuite, nous spécifions plusieurs attaques avec la notation étendue et exécutons les spécifications obtenues sur des flots d’événements à l’aide d’un interpréteur pour identifier des attaques. Nous évaluons aussi les performances de l’interpréteur avec des outils industriels tels que Snort et Zeek. Puis, nous réalisons un compilateur afin de générer du code exécutable à partir d’une spécification ASTD, capable d’identifier de façon efficiente les séquences d’événements.Abstract : The cybersecurity ecosystem continuously evolves with the number, the diversity, and the complexity of cyber attacks. Generally, we have three types of Intrusion Detection System (IDS) : anomaly-based detection, signature-based detection, and hybrid detection. Anomaly detection is based on the usual behavior description of the system, typically in a static manner. It enables detecting known or unknown attacks but also generating a large number of false positives. Signature based detection enables detecting known attacks by defining rules that describe known attacker’s behavior. It needs a good knowledge of attacker behavior. Hybrid detection relies on several detection methods including the previous ones. It has the advantage of being more precise during detection. Tools like Snort and Zeek offer low level languages to represent rules for detecting attacks. The number of potential attacks being large, these rule bases become quickly hard to manage and maintain. Moreover, the representation of stateful rules to recognize a sequence of events is particularly arduous. In this thesis, we propose a stateful approach based on algebraic state-transition diagrams (ASTDs) to identify complex attacks. ASTDs allow a graphical and modular representation of a specification, that facilitates maintenance and understanding of rules. We extend the ASTD notation with new features to represent complex attacks. Next, we specify several attacks with the extended notation and run the resulting specifications on event streams using an interpreter to identify attacks. We also evaluate the performance of the interpreter with industrial tools such as Snort and Zeek. Then, we build a compiler in order to generate executable code from an ASTD specification, able to efficiently identify sequences of events

EG-ICE 2021 Workshop on Intelligent Computing in Engineering

The 28th EG-ICE International Workshop 2021 brings together international experts working at the interface between advanced computing and modern engineering challenges. Many engineering tasks require open-world resolutions to support multi-actor collaboration, coping with approximate models, providing effective engineer-computer interaction, search in multi-dimensional solution spaces, accommodating uncertainty, including specialist domain knowledge, performing sensor-data interpretation and dealing with incomplete knowledge. While results from computer science provide much initial support for resolution, adaptation is unavoidable and most importantly, feedback from addressing engineering challenges drives fundamental computer-science research. Competence and knowledge transfer goes both ways

EG-ICE 2021 Workshop on Intelligent Computing in Engineering

The 28th EG-ICE International Workshop 2021 brings together international experts working at the interface between advanced computing and modern engineering challenges. Many engineering tasks require open-world resolutions to support multi-actor collaboration, coping with approximate models, providing effective engineer-computer interaction, search in multi-dimensional solution spaces, accommodating uncertainty, including specialist domain knowledge, performing sensor-data interpretation and dealing with incomplete knowledge. While results from computer science provide much initial support for resolution, adaptation is unavoidable and most importantly, feedback from addressing engineering challenges drives fundamental computer-science research. Competence and knowledge transfer goes both ways

Engineering Division

The objectives of the Engineering Division are to provide an association for those having an interest in library and information science as they apply to engineering and the physical sciences and to promote the use of materials and knowledge for the benefit of libraries and other educational organizations