MIMICause : Defining, identifying and predicting types of causal relationships between biomedical concepts from clinical notes

• URL: http://arxiv.org/abs/2110.07090v1
• Date: Thu, 14 Oct 2021 00:15:36 GMT
• Title: MIMICause : Defining, identifying and predicting types of causal relationships between biomedical concepts from clinical notes
• Authors: Vivek Khetan, Md Imbesat Hassan Rizvi, Jessica Huber, Paige Bartusiak, Bogdan Sacaleanu, Andrew Fano
• Abstract summary: We propose annotation guidelines, develop an annotated corpus and provide baseline scores to identify types and direction of causal relations between a pair of biomedical concepts in clinical notes. We annotate a total of 2714 de-identified examples sampled from the 2018 n2c2 shared task dataset and train four different language model based architectures. The high inter-annotator agreement for clinical text shows the quality of our annotation guidelines while the provided baseline F1 score sets the direction for future research towards understanding narratives in clinical texts.
• Score: 0.0
• License: http://creativecommons.org/licenses/by-nc-nd/4.0/
• Abstract: Understanding of causal narratives communicated in clinical notes can help make strides towards personalized healthcare. In this work, MIMICause, we propose annotation guidelines, develop an annotated corpus and provide baseline scores to identify types and direction of causal relations between a pair of biomedical concepts in clinical notes; communicated implicitly or explicitly, identified either in a single sentence or across multiple sentences. We annotate a total of 2714 de-identified examples sampled from the 2018 n2c2 shared task dataset and train four different language model based architectures. Annotation based on our guidelines achieved a high inter-annotator agreement i.e. Fleiss' kappa score of 0.72 and our model for identification of causal relation achieved a macro F1 score of 0.56 on test data. The high inter-annotator agreement for clinical text shows the quality of our annotation guidelines while the provided baseline F1 score sets the direction for future research towards understanding narratives in clinical texts.

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