Knowledge-based Biomedical Data Science 2019

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages with 3 table

Large-Scale Pattern-Based Information Extraction from the World Wide Web

Extracting information from text is the task of obtaining structured, machine-processable facts from information that is mentioned in an unstructured manner. It thus allows systems to automatically aggregate information for further analysis, efficient retrieval, automatic validation, or appropriate visualization. This work explores the potential of using textual patterns for Information Extraction from the World Wide Web

Mining Meaning from Wikipedia

Wikipedia is a goldmine of information; not just for its many readers, but also for the growing community of researchers who recognize it as a resource of exceptional scale and utility. It represents a vast investment of manual effort and judgment: a huge, constantly evolving tapestry of concepts and relations that is being applied to a host of tasks. This article provides a comprehensive description of this work. It focuses on research that extracts and makes use of the concepts, relations, facts and descriptions found in Wikipedia, and organizes the work into four broad categories: applying Wikipedia to natural language processing; using it to facilitate information retrieval and information extraction; and as a resource for ontology building. The article addresses how Wikipedia is being used as is, how it is being improved and adapted, and how it is being combined with other structures to create entirely new resources. We identify the research groups and individuals involved, and how their work has developed in the last few years. We provide a comprehensive list of the open-source software they have produced.Comment: An extensive survey of re-using information in Wikipedia in natural language processing, information retrieval and extraction and ontology building. Accepted for publication in International Journal of Human-Computer Studie

Automatic taxonomy evaluation

This thesis would not be made possible without the generous support of IATA.Les taxonomies sont une représentation essentielle des connaissances, jouant un rôle central dans de nombreuses applications riches en connaissances. Malgré cela, leur construction est laborieuse que ce soit manuellement ou automatiquement, et l'évaluation quantitative de taxonomies est un sujet négligé. Lorsque les chercheurs se concentrent sur la construction d'une taxonomie à partir de grands corpus non structurés, l'évaluation est faite souvent manuellement, ce qui implique des biais et se traduit souvent par une reproductibilité limitée. Les entreprises qui souhaitent améliorer leur taxonomie manquent souvent d'étalon ou de référence, une sorte de taxonomie bien optimisée pouvant service de référence. Par conséquent, des connaissances et des efforts spécialisés sont nécessaires pour évaluer une taxonomie. Dans ce travail, nous soutenons que l'évaluation d'une taxonomie effectuée automatiquement et de manière reproductible est aussi importante que la génération automatique de telles taxonomies. Nous proposons deux nouvelles méthodes d'évaluation qui produisent des scores moins biaisés: un modèle de classification de la taxonomie extraite d'un corpus étiqueté, et un modèle de langue non supervisé qui sert de source de connaissances pour évaluer les relations hyperonymiques. Nous constatons que nos substituts d'évaluation corrèlent avec les jugements humains et que les modèles de langue pourraient imiter les experts humains dans les tâches riches en connaissances.Taxonomies are an essential knowledge representation and play an important role in classification and numerous knowledge-rich applications, yet quantitative taxonomy evaluation remains to be overlooked and left much to be desired. While studies focus on automatic taxonomy construction (ATC) for extracting meaningful structures and semantics from large corpora, their evaluation is usually manual and subject to bias and low reproducibility. Companies wishing to improve their domain-focused taxonomies also suffer from lacking ground-truths. In fact, manual taxonomy evaluation requires substantial labour and expert knowledge. As a result, we argue in this thesis that automatic taxonomy evaluation (ATE) is just as important as taxonomy construction. We propose two novel taxonomy evaluation methods for automatic taxonomy scoring, leveraging supervised classification for labelled corpora and unsupervised language modelling as a knowledge source for unlabelled data. We show that our evaluation proxies can exert similar effects and correlate well with human judgments and that language models can imitate human experts on knowledge-rich tasks

Ontology learning for Semantic Web Services

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University, 18/10/2010.The expansion of Semantic Web Services is restricted by traditional ontology engineering methods. Manual ontology development is time consuming, expensive and a resource exhaustive task. Consequently, it is important to support ontology engineers by automating the ontology acquisition process to help deliver the Semantic Web vision. Existing Web Services offer an affluent source of domain knowledge for ontology engineers. Ontology learning can be seen as a plug-in in the Web Service ontology development process, which can be used by ontology engineers to develop and maintain an ontology that evolves with current Web Services. Supporting the domain engineer with an automated tool whilst building an ontological domain model, serves the purpose of reducing time and effort in acquiring the domain concepts and relations from Web Service artefacts, whilst effectively speeding up the adoption of Semantic Web Services, thereby allowing current Web Services to accomplish their full potential. With that in mind, a Service Ontology Learning Framework (SOLF) is developed and applied to a real set of Web Services. The research contributes a rigorous method that effectively extracts domain concepts, and relations between these concepts, from Web Services and automatically builds the domain ontology. The method applies pattern-based information extraction techniques to automatically learn domain concepts and relations between those concepts. The framework is automated via building a tool that implements the techniques. Applying the SOLF and the tool on different sets of services results in an automatically built domain ontology model that represents semantic knowledge in the underlying domain. The framework effectiveness, in extracting domain concepts and relations, is evaluated by its appliance on varying sets of commercial Web Services including the financial domain. The standard evaluation metrics, precision and recall, are employed to determine both the accuracy and coverage of the learned ontology models. Both the lexical and structural dimensions of the models are evaluated thoroughly. The evaluation results are encouraging, providing concrete outcomes in an area that is little researched

Exploiting Wikipedia Semantics for Computing Word Associations

Semantic association computation is the process of automatically quantifying the strength of a semantic connection between two textual units based on various lexical and semantic relations such as hyponymy (car and vehicle) and functional associations (bank and manager). Humans have can infer implicit relationships between two textual units based on their knowledge about the world and their ability to reason about that knowledge. Automatically imitating this behavior is limited by restricted knowledge and poor ability to infer hidden relations. Various factors affect the performance of automated approaches to computing semantic association strength. One critical factor is the selection of a suitable knowledge source for extracting knowledge about the implicit semantic relations. In the past few years, semantic association computation approaches have started to exploit web-originated resources as substitutes for conventional lexical semantic resources such as thesauri, machine readable dictionaries and lexical databases. These conventional knowledge sources suffer from limitations such as coverage issues, high construction and maintenance costs and limited availability. To overcome these issues one solution is to use the wisdom of crowds in the form of collaboratively constructed knowledge sources. An excellent example of such knowledge sources is Wikipedia which stores detailed information not only about the concepts themselves but also about various aspects of the relations among concepts. The overall goal of this thesis is to demonstrate that using Wikipedia for computing word association strength yields better estimates of humans' associations than the approaches based on other structured and unstructured knowledge sources. There are two key challenges to achieve this goal: first, to exploit various semantic association models based on different aspects of Wikipedia in developing new measures of semantic associations; and second, to evaluate these measures compared to human performance in a range of tasks. The focus of the thesis is on exploring two aspects of Wikipedia: as a formal knowledge source, and as an informal text corpus. The first contribution of the work included in the thesis is that it effectively exploited the knowledge source aspect of Wikipedia by developing new measures of semantic associations based on Wikipedia hyperlink structure, informative-content of articles and combinations of both elements. It was found that Wikipedia can be effectively used for computing noun-noun similarity. It was also found that a model based on hybrid combinations of Wikipedia structure and informative-content based features performs better than those based on individual features. It was also found that the structure based measures outperformed the informative content based measures on both semantic similarity and semantic relatedness computation tasks. The second contribution of the research work in the thesis is that it effectively exploited the corpus aspect of Wikipedia by developing a new measure of semantic association based on asymmetric word associations. The thesis introduced the concept of asymmetric associations based measure using the idea of directional context inspired by the free word association task. The underlying assumption was that the association strength can change with the changing context. It was found that the asymmetric association based measure performed better than the symmetric measures on semantic association computation, relatedness based word choice and causality detection tasks. However, asymmetric-associations based measures have no advantage for synonymy-based word choice tasks. It was also found that Wikipedia is not a good knowledge source for capturing verb-relations due to its focus on encyclopedic concepts specially nouns. It is hoped that future research will build on the experiments and discussions presented in this thesis to explore new avenues using Wikipedia for finding deeper and semantically more meaningful associations in a wide range of application areas based on humans' estimates of word associations