Knowledge extraction from unstructured data

Data availability is becoming more essential, considering the current growth of web-based data. The data available on the web are represented as unstructured, semi-structured, or structured data. In order to make the web-based data available for several Natural Language Processing or Data Mining tasks, the data needs to be presented as machine-readable data in a structured format. Thus, techniques for addressing the problem of capturing knowledge from unstructured data sources are needed. Knowledge extraction methods are used by the research communities to address this problem; methods that are able to capture knowledge in a natural language text and map the extracted knowledge to existing knowledge presented in knowledge graphs (KGs). These knowledge extraction methods include Named-entity recognition, Named-entity Disambiguation, Relation Recognition, and Relation Linking. This thesis addresses the problem of extracting knowledge over unstructured data and discovering patterns in the extracted knowledge. We devise a rule-based approach for entity and relation recognition and linking. The defined approach effectively maps entities and relations within a text to their resources in a target KG. Additionally, it overcomes the challenges of recognizing and linking entities and relations to a specific KG by employing devised catalogs of linguistic and domain-specific rules that state the criteria to recognize entities in a sentence of a particular language, and a deductive database that encodes knowledge in community-maintained KGs. Moreover, we define a Neuro-symbolic approach for the tasks of knowledge extraction in encyclopedic and domain-specific domains; it combines symbolic and sub-symbolic components to overcome the challenges of entity recognition and linking and the limitation of the availability of training data while maintaining the accuracy of recognizing and linking entities. Additionally, we present a context-aware framework for unveiling semantically related posts in a corpus; it is a knowledge-driven framework that retrieves associated posts effectively. We cast the problem of unveiling semantically related posts in a corpus into the Vertex Coloring Problem. We evaluate the performance of our techniques on several benchmarks related to various domains for knowledge extraction tasks. Furthermore, we apply these methods in real-world scenarios from national and international projects. The outcomes show that our techniques are able to effectively extract knowledge encoded in unstructured data and discover patterns over the extracted knowledge presented as machine-readable data. More importantly, the evaluation results provide evidence to the effectiveness of combining the reasoning capacity of the symbolic frameworks with the power of pattern recognition and classification of sub-symbolic models

Recommender system to support comprehensive exploration of large scale scientific datasets

Bases de dados de entidades científicas, como compostos químicos, doenças e objetos astronómicos, têm crescido em tamanho e complexidade, chegando a milhares de milhões de itens por base de dados. Os investigadores precisam de ferramentas novas e inovadoras para auxiliar na escolha desses itens. Este trabalho propõe o uso de Sistemas de Recomendação para auxiliar os investigadores a encontrar itens de interesse. Identificamos como um dos maiores desafios para a aplicação de sistemas de recomendação em áreas científicas a falta de conjuntos de dados padronizados e de acesso aberto com informações sobre as preferências dos utilizadores. Para superar esse desafio, desenvolvemos uma metodologia denominada LIBRETTI - Recomendação Baseada em Literatura de Itens Científicos, cujo objetivo é a criação de conjuntos de dados , relacionados com campos científicos. Estes conjuntos de dados são criados com base no principal recurso de conhecimento que a Ciência possui: a literatura científica. A metodologia LIBRETTI permitiu o desenvolvimento de novos algoritmos de recomendação específicos para vários campos científicos. Além do LIBRETTI, as principais contribuições desta tese são conjuntos de dados de recomendação padronizados nas áreas de Astronomia, Química e Saúde (relacionado com a doença COVID-19), um sistema de recomendação semântica híbrido para compostos químicos em conjuntos de dados de grande escala, uma abordagem híbrida baseada no enriquecimento sequencial (SeEn) para recomendações sequenciais, um pipeline baseado em semântica de vários campos para recomendar entidades biomédicas relacionadas com a doença COVID-19.Databases for scientific entities, such as chemical compounds, diseases and astronomical objects, are growing in size and complexity, reaching billions of items per database. Researchers need new and innovative tools for assisting the choice of these items. This work proposes the use of Recommender Systems approaches for helping researchers to find items of interest. We identified as one of the major challenges for applying RS in scientific fields the lack of standard and open-access datasets with information about the preferences of the users. To overcome this challenge, we developed a methodology called LIBRETTI - LIterature Based RecommEndaTion of scienTific Items, whose goal is to create datasets related to scientific fields. These datasets are created based on scientific literature, the major resource of knowledge that Science has. LIBRETTI methodology allowed the development and testing of new recommender algorithms specific for each field. Besides LIBRETTI, the main contributions of this thesis are standard and sequence-aware recommendation datasets in the fields of Astronomy, Chemistry, and Health (related to COVID-19 disease), a hybrid semantic recommender system for chemical compounds in large-scale datasets, a hybrid approach based on sequential enrichment (SeEn) for sequence-aware recommendations, a multi-field semantic-based pipeline for recommending biomedical entities related to COVID-19 disease

Network-driven strategies to integrate and exploit biomedical data

[eng] In the quest for understanding complex biological systems, the scientific community has been delving into protein, chemical and disease biology, populating biomedical databases with a wealth of data and knowledge. Currently, the field of biomedicine has entered a Big Data era, in which computational-driven research can largely benefit from existing knowledge to better understand and characterize biological and chemical entities. And yet, the heterogeneity and complexity of biomedical data trigger the need for a proper integration and representation of this knowledge, so that it can be effectively and efficiently exploited. In this thesis, we aim at developing new strategies to leverage the current biomedical knowledge, so that meaningful information can be extracted and fused into downstream applications. To this goal, we have capitalized on network analysis algorithms to integrate and exploit biomedical data in a wide variety of scenarios, providing a better understanding of pharmacoomics experiments while helping accelerate the drug discovery process. More specifically, we have (i) devised an approach to identify functional gene sets associated with drug response mechanisms of action, (ii) created a resource of biomedical descriptors able to anticipate cellular drug response and identify new drug repurposing opportunities, (iii) designed a tool to annotate biomedical support for a given set of experimental observations, and (iv) reviewed different chemical and biological descriptors relevant for drug discovery, illustrating how they can be used to provide solutions to current challenges in biomedicine.[cat] En la cerca d’una millor comprensió dels sistemes biològics complexos, la comunitat científica ha estat aprofundint en la biologia de les proteïnes, fàrmacs i malalties, poblant les bases de dades biomèdiques amb un gran volum de dades i coneixement. En l’actualitat, el camp de la biomedicina es troba en una era de “dades massives” (Big Data), on la investigació duta a terme per ordinadors se’n pot beneficiar per entendre i caracteritzar millor les entitats químiques i biològiques. No obstant, la heterogeneïtat i complexitat de les dades biomèdiques requereix que aquestes s’integrin i es representin d’una manera idònia, permetent així explotar aquesta informació d’una manera efectiva i eficient. L’objectiu d’aquesta tesis doctoral és desenvolupar noves estratègies que permetin explotar el coneixement biomèdic actual i així extreure informació rellevant per aplicacions biomèdiques futures. Per aquesta finalitat, em fet servir algoritmes de xarxes per tal d’integrar i explotar el coneixement biomèdic en diferents tasques, proporcionant un millor enteniment dels experiments farmacoòmics per tal d’ajudar accelerar el procés de descobriment de nous fàrmacs. Com a resultat, en aquesta tesi hem (i) dissenyat una estratègia per identificar grups funcionals de gens associats a la resposta de línies cel·lulars als fàrmacs, (ii) creat una col·lecció de descriptors biomèdics capaços, entre altres coses, d’anticipar com les cèl·lules responen als fàrmacs o trobar nous usos per fàrmacs existents, (iii) desenvolupat una eina per descobrir quins contextos biològics corresponen a una associació biològica observada experimentalment i, finalment, (iv) hem explorat diferents descriptors químics i biològics rellevants pel procés de descobriment de nous fàrmacs, mostrant com aquests poden ser utilitzats per trobar solucions a reptes actuals dins el camp de la biomedicina

Knowledge Modelling and Learning through Cognitive Networks

One of the most promising developments in modelling knowledge is cognitive network science, which aims to investigate cognitive phenomena driven by the networked, associative organization of knowledge. For example, investigating the structure of semantic memory via semantic networks has illuminated how memory recall patterns influence phenomena such as creativity, memory search, learning, and more generally, knowledge acquisition, exploration, and exploitation. In parallel, neural network models for artificial intelligence (AI) are also becoming more widespread as inferential models for understanding which features drive language-related phenomena such as meaning reconstruction, stance detection, and emotional profiling. Whereas cognitive networks map explicitly which entities engage in associative relationships, neural networks perform an implicit mapping of correlations in cognitive data as weights, obtained after training over labelled data and whose interpretation is not immediately evident to the experimenter. This book aims to bring together quantitative, innovative research that focuses on modelling knowledge through cognitive and neural networks to gain insight into mechanisms driving cognitive processes related to knowledge structuring, exploration, and learning. The book comprises a variety of publication types, including reviews and theoretical papers, empirical research, computational modelling, and big data analysis. All papers here share a commonality: they demonstrate how the application of network science and AI can extend and broaden cognitive science in ways that traditional approaches cannot

A multi-disciplinary co-design approach to social media sensemaking with text mining

This thesis presents the development of a bespoke social media analytics platform called Sentinel using an event driven co-design approach. The performance and outputs of this system, along with its integration into the routine research methodology of its users, were used to evaluate how the application of an event driven co-design approach to system design improves the degree to which Social Web data can be converted into actionable intelligence, with respect to robustness, agility, and usability. The thesis includes a systematic review into the state-of-the-art technology that can support real-time text analysis of social media data, used to position the text analysis elements of the Sentinel Pipeline. This is followed by research chapters that focus on combinations of robustness, agility, and usability as themes, covering the iterative developments of the system through the event driven co-design lifecycle. Robustness and agility are covered during initial infrastructure design and early prototyping of bottom-up and top-down semantic enrichment. Robustness and usability are then considered during the development of the Semantic Search component of the Sentinel Platform, which exploits the semantic enrichment developed in the prototype, alpha, and beta systems. Finally, agility and usability are used whilst building upon the Semantic Search functionality to produce a data download functionality for rapidly collecting corpora for further qualitative research. These iterations are evaluated using a number of case studies that were undertaken in conjunction with a wider research programme, within the field of crime and security, that the Sentinel platform was designed to support. The findings from these case studies are used in the co-design process to inform how developments should evolve. As part of this research programme the Sentinel platform has supported the production of a number of research papers authored by stakeholders, highlighting the impact the system has had in the field of crime and security researc

Geographic information extraction from texts

A large volume of unstructured texts, containing valuable geographic information, is available online. This information – provided implicitly or explicitly – is useful not only for scientific studies (e.g., spatial humanities) but also for many practical applications (e.g., geographic information retrieval). Although large progress has been achieved in geographic information extraction from texts, there are still unsolved challenges and issues, ranging from methods, systems, and data, to applications and privacy. Therefore, this workshop will provide a timely opportunity to discuss the recent advances, new ideas, and concepts but also identify research gaps in geographic information extraction