journal of biomedical informatics
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Assessment of contextualised representations in detecting outcome phrases in clinical trials.

Author(s): Micheal Abaho*, Danushka Bollegala, Paula Williamson and Susanna Dodd

Background: Automating the recognition of out- comes reported in clinical trials using machine learning has a huge potential of speeding up access to evidence necessary in healthcare decision making. Prior research has however acknowledged inadequate training corpora as a challenge for the Outcome detection (OD) task. Additionally, several contextualised representations (embeddings) like BERT and ELMO have achieved unparalleled success in detecting various diseases, genes, proteins and chemicals, however, the same cannot be emphatically stated for outcomes, because these representation models have been relatively undertested and studied for the OD task.

Methods: We introduce “EBM-COMET”, a dataset in which 300 Randomised Clinical Trial (RCT) PubMed abstracts are expertly annotated for clinical outcomes. Unlike prior related datasets that use arbitrary outcome classifications, we use labels from a taxonomy recently published to standardise outcome classifications. To extract outcomes, we fine-tune a variety of pretrained contextualised representations, additionally; we use frozen contextualised and context-independent representations in our custom neural model augmented with clinically informed Part-Of-Speech embeddings and a cost- sensitive loss function. We adopt strict evaluation for the trained models by rewarding them for correctly identifying full outcome phrases rather than words within the entities i.e. given an outcome phrase “systolic blood pressure”, the models are re- warded a classification score only when they predict all 3 words in sequence, otherwise they are not rewarded.

Results and Conclusion: We observe our best model (BioBERT) achieve 81.5% F1, 81.3% sensitivity and 98.0% specificity. We reach a consensus on which contextualised representations are best suited for detecting outcome phrases from clinical trial abstracts. Furthermore, our best model out performs scores published on the original EBM-NLP dataset leaderboard scores.

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