Visual exploration of semantic-web-based knowledge structures

Humans have a curious nature and seek a better understanding of the world. Data, in- formation, and knowledge became assets of our modern society through the information technology revolution in the form of the internet. However, with the growing size of accumulated data, new challenges emerge, such as searching and navigating in these large collections of data, information, and knowledge. The current developments in academic and industrial contexts target the corresponding challenges using Semantic Web techno- logies. The Semantic Web is an extension of the Web and provides machine-readable representations of knowledge for various domains. These machine-readable representations allow intelligent machine agents to understand the meaning of the data and information; and enable additional inference of new knowledge. Generally, the Semantic Web is designed for information exchange and its processing and does not focus on presenting such semantically enriched data to humans. Visualizations support exploration, navigation, and understanding of data by exploiting humans’ ability to comprehend complex data through visual representations. In the context of Semantic- Web-Based knowledge structures, various visualization methods and tools are available, and new ones are being developed every year. However, suitable visualizations are highly dependent on individual use cases and targeted user groups. In this thesis, we investigate visual exploration techniques for Semantic-Web-Based knowledge structures by addressing the following challenges: i) how to engage various user groups in modeling such semantic representations; ii) how to facilitate understanding using customizable visual representations; and iii) how to ease the creation of visualizations for various data sources and different use cases. The achieved results indicate that visual modeling techniques facilitate the engagement of various user groups in ontology modeling. Customizable visualizations enable users to adjust visualizations to the current needs and provide different views on the data. Additionally, customizable visualization pipelines enable rapid visualization generation for various use cases, data sources, and user group

Thinking outside the graph: scholarly knowledge graph construction leveraging natural language processing

Despite improved digital access to scholarly knowledge in recent decades, scholarly communication remains exclusively document-based. The document-oriented workflows in science publication have reached the limits of adequacy as highlighted by recent discussions on the increasing proliferation of scientific literature, the deficiency of peer-review and the reproducibility crisis. In this form, scientific knowledge remains locked in representations that are inadequate for machine processing. As long as scholarly communication remains in this form, we cannot take advantage of all the advancements taking place in machine learning and natural language processing techniques. Such techniques would facilitate the transformation from pure text based into (semi-)structured semantic descriptions that are interlinked in a collection of big federated graphs. We are in dire need for a new age of semantically enabled infrastructure adept at storing, manipulating, and querying scholarly knowledge. Equally important is a suite of machine assistance tools designed to populate, curate, and explore the resulting scholarly knowledge graph. In this thesis, we address the issue of constructing a scholarly knowledge graph using natural language processing techniques. First, we tackle the issue of developing a scholarly knowledge graph for structured scholarly communication, that can be populated and constructed automatically. We co-design and co-implement the Open Research Knowledge Graph (ORKG), an infrastructure capable of modeling, storing, and automatically curating scholarly communications. Then, we propose a method to automatically extract information into knowledge graphs. With Plumber, we create a framework to dynamically compose open information extraction pipelines based on the input text. Such pipelines are composed from community-created information extraction components in an effort to consolidate individual research contributions under one umbrella. We further present MORTY as a more targeted approach that leverages automatic text summarization to create from the scholarly article's text structured summaries containing all required information. In contrast to the pipeline approach, MORTY only extracts the information it is instructed to, making it a more valuable tool for various curation and contribution use cases. Moreover, we study the problem of knowledge graph completion. exBERT is able to perform knowledge graph completion tasks such as relation and entity prediction tasks on scholarly knowledge graphs by means of textual triple classification. Lastly, we use the structured descriptions collected from manual and automated sources alike with a question answering approach that builds on the machine-actionable descriptions in the ORKG. We propose JarvisQA, a question answering interface operating on tabular views of scholarly knowledge graphs i.e., ORKG comparisons. JarvisQA is able to answer a variety of natural language questions, and retrieve complex answers on pre-selected sub-graphs. These contributions are key in the broader agenda of studying the feasibility of natural language processing methods on scholarly knowledge graphs, and lays the foundation of which methods can be used on which cases. Our work indicates what are the challenges and issues with automatically constructing scholarly knowledge graphs, and opens up future research directions

Transformers and the representation of biomedical background knowledge

BioBERT and BioMegatron are Transformers models adapted for the biomedical domain based on publicly available biomedical corpora. As such, they have the potential to encode large-scale biological knowledge. We investigate the encoding and representation of biological knowledge in these models, and its potential utility to support inference in cancer precision medicine - namely, the interpretation of the clinical significance of genomic alterations. We compare the performance of different transformer baselines; we use probing to determine the consistency of encodings for distinct entities; and we use clustering methods to compare and contrast the internal properties of the embeddings for genes, variants, drugs and diseases. We show that these models do indeed encode biological knowledge, although some of this is lost in fine-tuning for specific tasks. Finally, we analyse how the models behave with regard to biases and imbalances in the dataset.Comment: 22 pages, 12 figures, supplementary methods, tables and figures at the end of the manuscrip

Expressing high-level scientific claims with formal semantics

The use of semantic technologies is gaining significant traction in science communication with a wide array of applications in disciplines including the life sciences, computer science, and the social sciences. Languages like RDF, OWL, and other formalisms based on formal logic are applied to make scientific knowledge accessible not only to human readers but also to automated systems. These approaches have mostly focused on the structure of scientific publications themselves, on the used scientific methods and equipment, or on the structure of the used datasets. The core claims or hypotheses of scientific work have only been covered in a shallow manner, such as by linking mentioned entities to established identifiers. In this research, we therefore want to find out whether we can use existing semantic formalisms to fully express the content of high-level scientific claims using formal semantics in a systematic way. Analyzing the main claims from a sample of scientific articles from all disciplines, we find that their semantics are more complex than what a straight-forward application of formalisms like RDF or OWL account for, but we managed to elicit a clear semantic pattern which we call the "super-pattern''. We show here how the instantiation of the five slots of this super-pattern leads to a strictly defined statement in higher-order logic. We successfully applied this super-pattern to an enlarged sample of scientific claims. We show that knowledge representation experts, when instructed to independently instantiate the super-pattern with given scientific claims, show a high degree of consistency and convergence given the complexity of the task and the subject. These results therefore open the door on the longer run for allowing researchers to express their high-level scientific findings in a manner they can be automatically interpreted. This in turn will allow for automated consistency checking, question answering, aggregation, and much more

Knowledge Graph Building Blocks: An easy-to-use Framework for developing FAIREr Knowledge Graphs

Knowledge graphs and ontologies provide promising technical solutions for implementing the FAIR Principles for Findable, Accessible, Interoperable, and Reusable data and metadata. However, they also come with their own challenges. Nine such challenges are discussed and associated with the criterion of cognitive interoperability and specific FAIREr principles (FAIR + Explorability raised) that they fail to meet. We introduce an easy-to-use, open source knowledge graph framework that is based on knowledge graph building blocks (KGBBs). KGBBs are small information modules for knowledge-processing, each based on a specific type of semantic unit. By interrelating several KGBBs, one can specify a KGBB-driven FAIREr knowledge graph. Besides implementing semantic units, the KGBB Framework clearly distinguishes and decouples an internal in-memory data model from data storage, data display, and data access/export models. We argue that this decoupling is essential for solving many problems of knowledge management systems. We discuss the architecture of the KGBB Framework as we envision it, comprising (i) an openly accessible KGBB-Repository for different types of KGBBs, (ii) a KGBB-Engine for managing and operating FAIREr knowledge graphs (including automatic provenance tracking, editing changelog, and versioning of semantic units); (iii) a repository for KGBB-Functions; (iv) a low-code KGBB-Editor with which domain experts can create new KGBBs and specify their own FAIREr knowledge graph without having to think about semantic modelling. We conclude with discussing the nine challenges and how the KGBB Framework provides solutions for the issues they raise. While most of what we discuss here is entirely conceptual, we can point to two prototypes that demonstrate the principle feasibility of using semantic units and KGBBs to manage and structure knowledge graphs

CrossData: Leveraging Text-Data Connections for Authoring Data Documents

Data documents play a central role in recording, presenting, and disseminating data. Despite the proliferation of applications and systems designed to support the analysis, visualization, and communication of data, writing data documents remains a laborious process, requiring a constant back-and-forth between data processing and writing tools. Interviews with eight professionals revealed that their workflows contained numerous tedious, repetitive, and error-prone operations. The key issue that we identified is the lack of persistent connection between text and data. Thus, we developed CrossData, a prototype that treats text-data connections as persistent, interactive, first-class objects. By automatically identifying, establishing, and leveraging text-data connections, CrossData enables rich interactions to assist in the authoring of data documents. An expert evaluation with eight users demonstrated the usefulness of CrossData, showing that it not only reduced the manual effort in writing data documents but also opened new possibilities to bridge the gap between data exploration and writing

Representation learning for dialogue systems

Cette thèse présente une série de mesures prises pour étudier l’apprentissage de représentations (par exemple, l’apprentissage profond) afin de mettre en place des systèmes de dialogue et des agents de conversation virtuels. La thèse est divisée en deux parties générales. La première partie de la thèse examine l’apprentissage des représentations pour les modèles de dialogue génératifs. Conditionnés sur une séquence de tours à partir d’un dialogue textuel, ces modèles ont la tâche de générer la prochaine réponse appropriée dans le dialogue. Cette partie de la thèse porte sur les modèles séquence-à-séquence, qui est une classe de réseaux de neurones profonds génératifs. Premièrement, nous proposons un modèle d’encodeur-décodeur récurrent hiérarchique ("Hierarchical Recurrent Encoder-Decoder"), qui est une extension du modèle séquence-à-séquence traditionnel incorporant la structure des tours de dialogue. Deuxièmement, nous proposons un modèle de réseau de neurones récurrents multi-résolution ("Multiresolution Recurrent Neural Network"), qui est un modèle empilé séquence-à-séquence avec une représentation stochastique intermédiaire (une "représentation grossière") capturant le contenu sémantique abstrait communiqué entre les locuteurs. Troisièmement, nous proposons le modèle d’encodeur-décodeur récurrent avec variables latentes ("Latent Variable Recurrent Encoder-Decoder"), qui suivent une distribution normale. Les variables latentes sont destinées à la modélisation de l’ambiguïté et l’incertitude qui apparaissent naturellement dans la communication humaine. Les trois modèles sont évalués et comparés sur deux tâches de génération de réponse de dialogue: une tâche de génération de réponses sur la plateforme Twitter et une tâche de génération de réponses de l’assistance technique ("Ubuntu technical response generation task"). La deuxième partie de la thèse étudie l’apprentissage de représentations pour un système de dialogue utilisant l’apprentissage par renforcement dans un contexte réel. Cette partie porte plus particulièrement sur le système "Milabot" construit par l’Institut québécois d’intelligence artificielle (Mila) pour le concours "Amazon Alexa Prize 2017". Le Milabot est un système capable de bavarder avec des humains sur des sujets populaires à la fois par la parole et par le texte. Le système consiste d’un ensemble de modèles de récupération et de génération en langage naturel, comprenant des modèles basés sur des références, des modèles de sac de mots et des variantes des modèles décrits ci-dessus. Cette partie de la thèse se concentre sur la tâche de sélection de réponse. À partir d’une séquence de tours de dialogues et d’un ensemble des réponses possibles, le système doit sélectionner une réponse appropriée à fournir à l’utilisateur. Une approche d’apprentissage par renforcement basée sur un modèle appelée "Bottleneck Simulator" est proposée pour sélectionner le candidat approprié pour la réponse. Le "Bottleneck Simulator" apprend un modèle approximatif de l’environnement en se basant sur les trajectoires de dialogue observées et le "crowdsourcing", tout en utilisant un état abstrait représentant la sémantique du discours. Le modèle d’environnement est ensuite utilisé pour apprendre une stratégie d’apprentissage du renforcement par le biais de simulations. La stratégie apprise a été évaluée et comparée à des approches concurrentes via des tests A / B avec des utilisateurs réel, où elle démontre d’excellente performance.This thesis presents a series of steps taken towards investigating representation learning (e.g. deep learning) for building dialogue systems and conversational agents. The thesis is split into two general parts. The first part of the thesis investigates representation learning for generative dialogue models. Conditioned on a sequence of turns from a text-based dialogue, these models are tasked with generating the next, appropriate response in the dialogue. This part of the thesis focuses on sequence-to-sequence models, a class of generative deep neural networks. First, we propose the Hierarchical Recurrent Encoder-Decoder model, which is an extension of the vanilla sequence-to sequence model incorporating the turn-taking structure of dialogues. Second, we propose the Multiresolution Recurrent Neural Network model, which is a stacked sequence-to-sequence model with an intermediate, stochastic representation (a "coarse representation") capturing the abstract semantic content communicated between the dialogue speakers. Third, we propose the Latent Variable Recurrent Encoder-Decoder model, which is a variant of the Hierarchical Recurrent Encoder-Decoder model with latent, stochastic normally-distributed variables. The latent, stochastic variables are intended for modelling the ambiguity and uncertainty occurring naturally in human language communication. The three models are evaluated and compared on two dialogue response generation tasks: a Twitter response generation task and the Ubuntu technical response generation task. The second part of the thesis investigates representation learning for a real-world reinforcement learning dialogue system. Specifically, this part focuses on the Milabot system built by the Quebec Artificial Intelligence Institute (Mila) for the Amazon Alexa Prize 2017 competition. Milabot is a system capable of conversing with humans on popular small talk topics through both speech and text. The system consists of an ensemble of natural language retrieval and generation models, including template-based models, bag-of-words models, and variants of the models discussed in the first part of the thesis. This part of the thesis focuses on the response selection task. Given a sequence of turns from a dialogue and a set of candidate responses, the system must select an appropriate response to give the user. A model-based reinforcement learning approach, called the Bottleneck Simulator, is proposed for selecting the appropriate candidate response. The Bottleneck Simulator learns an approximate model of the environment based on observed dialogue trajectories and human crowdsourcing, while utilizing an abstract (bottleneck) state representing high-level discourse semantics. The learned environment model is then employed to learn a reinforcement learning policy through rollout simulations. The learned policy has been evaluated and compared to competing approaches through A/B testing with real-world users, where it was found to yield excellent performance

Mapping and the Citizen Sensor

Maps are a fundamental resource in a diverse array of applications ranging from everyday activities, such as route planning through the legal demarcation of space to scientific studies, such as those seeking to understand biodiversity and inform the design of nature reserves for species conservation. For a map to have value, it should provide an accurate and timely representation of the phenomenon depicted and this can be a challenge in a dynamic world. Fortunately, mapping activities have benefitted greatly from recent advances in geoinformation technologies. Satellite remote sensing, for example, now offers unparalleled data acquisition and authoritative mapping agencies have developed systems for the routine production of maps in accordance with strict standards. Until recently, much mapping activity was in the exclusive realm of authoritative agencies but technological development has also allowed the rise of the amateur mapping community. The proliferation of inexpensive and highly mobile and location aware devices together with Web 2.0 technology have fostered the emergence of the citizen as a source of data. Mapping presently benefits from vast amounts of spatial data as well as people able to provide observations of geographic phenomena, which can inform map production, revision and evaluation. The great potential of these developments is, however, often limited by concerns. The latter span issues from the nature of the citizens through the way data are collected and shared to the quality and trustworthiness of the data. This book reports on some of the key issues connected with the use of citizen sensors in mapping. It arises from a European Co-operation in Science and Technology (COST) Action, which explored issues linked to topics ranging from citizen motivation, data acquisition, data quality and the use of citizen derived data in the production of maps that rival, and sometimes surpass, maps arising from authoritative agencies