Towards Incorporating Entity-specific Knowledge Graph Information in Predicting Drug-Drug Interactions

• URL: http://arxiv.org/abs/2012.11142v1
• Date: Mon, 21 Dec 2020 06:44:32 GMT
• Title: Towards Incorporating Entity-specific Knowledge Graph Information in Predicting Drug-Drug Interactions
• Authors: Ishani Mondal
• Abstract summary: We propose a new method, BERTKG-DDI, to combine drug embeddings obtained from its interaction with other biomedical entities along with domain-specific BioBERT embedding-based RC architecture. Experiments conducted on the DDIExtraction 2013 corpus clearly indicate that this strategy improves other baselines architectures by 4.1% macro F1-score.
• Score: 1.14219428942199
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Off-the-shelf biomedical embeddings obtained from the recently released various pre-trained language models (such as BERT, XLNET) have demonstrated state-of-the-art results (in terms of accuracy) for the various natural language understanding tasks (NLU) in the biomedical domain. Relation Classification (RC) falls into one of the most critical tasks. In this paper, we explore how to incorporate domain knowledge of the biomedical entities (such as drug, disease, genes), obtained from Knowledge Graph (KG) Embeddings, for predicting Drug-Drug Interaction from textual corpus. We propose a new method, BERTKG-DDI, to combine drug embeddings obtained from its interaction with other biomedical entities along with domain-specific BioBERT embedding-based RC architecture. Experiments conducted on the DDIExtraction 2013 corpus clearly indicate that this strategy improves other baselines architectures by 4.1% macro F1-score.

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