Fabian Eckert


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Semantic role labeling tools for biomedical question answering: a study of selected tools on the BioASQ datasets
Fabian Eckert | Mariana Neves
Proceedings of the 6th BioASQ Workshop A challenge on large-scale biomedical semantic indexing and question answering

Question answering (QA) systems usually rely on advanced natural language processing components to precisely understand the questions and extract the answers. Semantic role labeling (SRL) is known to boost performance for QA, but its use for biomedical texts has not yet been fully studied. We analyzed the performance of three SRL tools (BioKIT, BIOSMILE and PathLSTM) on 1776 questions from the BioASQ challenge. We compared the systems regarding the coverage of the questions and snippets, as well as based on pre-defined criteria, such as easiness of installation, supported formats and usability. Finally, we integrated two of the tools in a simple QA system to further evaluate their performance over the official BioASQ test sets.


Assessing the performance of Olelo, a real-time biomedical question answering application
Mariana Neves | Fabian Eckert | Hendrik Folkerts | Matthias Uflacker
BioNLP 2017

Question answering (QA) can support physicians and biomedical researchers to find answers to their questions in the scientific literature. Such systems process large collections of documents in real time and include many natural language processing (NLP) procedures. We recently developed Olelo, a QA system for biomedicine which includes various NLP components, such as question processing, document and passage retrieval, answer processing and multi-document summarization. In this work, we present an evaluation of our system on the the fifth BioASQ challenge. We participated with the current state of the application and with an extension based on semantic role labeling that we are currently investigating. In addition to the BioASQ evaluation, we compared our system to other on-line biomedical QA systems in terms of the response time and the quality of the answers.