Searle, T; Kraljevic, Z; Bendayan, R; Bean, D; Dobson, R; (2020) MedCATTrainer: A biomedical free text annotation interface with active learning and research use case specific customisation. In: Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP): System Demonstrations. (pp. pp. 139-144). Association for Computational Linguistics: Hong Kong, China.

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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.

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