MedCATTrainer: A biomedical free text annotation interface with active learning and research use case specific customisation

Research output: Chapter in Book/Report/Conference proceedingConference paperpeer-review

9 Citations (Scopus)

Abstract

We present MedCATTrainer1 an interface for building, improving and customising a given Named Entity Recognition and Linking (NER+L) model for biomedical domain text. NER+L is often used as a first step in deriving value from clinical text. Collecting labelled data for training models is difficult due to the need for specialist domain knowledge. MedCATTrainer offers an interactive web-interface to inspect and improve recognised entities from an underlying NER+L model via active learning. Secondary use of data for clinical research often has task and context specific criteria. MedCATTrainer provides a further interface to define and collect supervised learning training data for researcher specific use cases. Initial results suggest our approach allows for efficient and accurate collection of research use case specific training data.

Original languageEnglish
Title of host publicationEMNLP-IJCNLP 2019 - 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing, Proceedings of System Demonstrations
PublisherAssociation for Computational Linguistics (ACL)
Pages139-144
Number of pages6
ISBN (Electronic)9781950737925
Publication statusPublished - 1 Jan 2020
Event2019 Conference on Empirical Methods in Natural Language Processing and 9th International Joint Conference on Natural Language Processing, EMNLP-IJCNLP 2019 - Hong Kong, China
Duration: 3 Nov 20197 Nov 2019

Publication series

NameEMNLP-IJCNLP 2019 - 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing, Proceedings of System Demonstrations

Conference

Conference2019 Conference on Empirical Methods in Natural Language Processing and 9th International Joint Conference on Natural Language Processing, EMNLP-IJCNLP 2019
Country/TerritoryChina
CityHong Kong
Period3/11/20197/11/2019

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