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

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

A data mining approach to ontology learning for automatic content-related question-answering in MOOCs.

The advent of Massive Open Online Courses (MOOCs) allows massive volume of registrants to enrol in these MOOCs. This research aims to offer MOOCs registrants with automatic content related feedback to fulfil their cognitive needs. A framework is proposed which consists of three modules which are the subject ontology learning module, the short text classification module, and the question answering module. Unlike previous research, to identify relevant concepts for ontology learning a regular expression parser approach is used. Also, the relevant concepts are extracted from unstructured documents. To build the concept hierarchy, a frequent pattern mining approach is used which is guided by a heuristic function to ensure that sibling concepts are at the same level in the hierarchy. As this process does not require specific lexical or syntactic information, it can be applied to any subject. To validate the approach, the resulting ontology is used in a question-answering system which analyses students' content-related questions and generates answers for them. Textbook end of chapter questions/answers are used to validate the question-answering system. The resulting ontology is compared vs. the use of Text2Onto for the question-answering system, and it achieved favourable results. Finally, different indexing approaches based on a subject's ontology are investigated when classifying short text in MOOCs forum discussion data; the investigated indexing approaches are: unigram-based, concept-based and hierarchical concept indexing. The experimental results show that the ontology-based feature indexing approaches outperform the unigram-based indexing approach. Experiments are done in binary classification and multiple labels classification settings . The results are consistent and show that hierarchical concept indexing outperforms both concept-based and unigram-based indexing. The BAGGING and random forests classifiers achieved the best result among the tested classifiers