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Theses

Argument Mining on Clinical Trials

Tobias Mayer 1
1 WIMMICS - Web-Instrumented Man-Machine Interactions, Communities and Semantics
CRISAM - Inria Sophia Antipolis - Méditerranée , Laboratoire I3S - SPARKS - Scalable and Pervasive softwARe and Knowledge Systems
Abstract : In the latest years, the healthcare domain has seen an increasing interest in the definition of intelligent systems to support clinicians in their everyday tasks and activities. Among others, this includes novel systems for the field of Evidence-based Medicine. The latter relies on the principle of critically appraising medical evidence and combining high quality evidence with the individual clinical experience of the practitioner with respect to the circumstances of a patient to achieve the best possible outcome. Hence, most of the proposed intelligent systems aim either at extracting information concerning the quality of evidence from clinical trials, clinical guidelines, or electronic health records, or assist in the decision making processes, based on reasoning frameworks. The work in this thesis goes beyond the state-of-the-art of currently proposed information extraction systems. It employs Argument Mining methods to extract and classify argumentative components (i.e., evidence and claims of a clinical trial) and their relations (i.e., support, attack). An Argument Mining pipeline is proposed and further enhanced to integrate additional information inspired by prevalent biomedical frameworks for the analysis of clinical trials. These extensions comprise the detection of PICO elements and an outcome analysis module to identify and classify the effects (i.e., improved, increased, decreased, no difference, no occurrence) of an intervention on the outcome of the trial. In this context, a dataset, composed of 660 Randomized Controlled Trial abstracts from the MEDLINE database, was annotated, leading to a labeled dataset with 4198 argument components, 2601 argument relations, and 3351 outcomes on five different diseases (i.e., neoplasm, glaucoma, hepatitis, diabetes, hypertension). Various Machine Learning approaches ranging from feature-based SVMs to recent neural architectures have been experimented with, where deep bidirectional transformers obtain a macro F1-score of .87 for argument component detection and .68 for argument relation prediction, outperforming current state-of-the-art Argument Mining systems. Additionally, a Proof-of-Concept system, called ACTA, was developed to demonstrate the practical use of the developed argument-based approach to analyse clinical trials. This demo system was further integrated in the context of the Covid-on-the-Web project to create rich and actionable Linked Data about the Covid-19.
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https://hal.archives-ouvertes.fr/tel-03209489
Contributor : Tobias Mayer <>
Submitted on : Wednesday, February 10, 2021 - 4:22:20 PM
Last modification on : Friday, May 7, 2021 - 11:50:28 AM
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  • HAL Id : tel-03209489, version 1

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Tobias Mayer. Argument Mining on Clinical Trials. Document and Text Processing. Université Côte d’Azur, 2020. English. ⟨tel-03209489v1⟩

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