R-BERT-CNN: Drug-target interactions extraction from biomedical literature

10/31/2021
by   Jehad Aldahdooh, et al.
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In this research, we present our work participation for the DrugProt task of BioCreative VII challenge. Drug-target interactions (DTIs) are critical for drug discovery and repurposing, which are often manually extracted from the experimental articles. There are >32M biomedical articles on PubMed and manually extracting DTIs from such a huge knowledge base is challenging. To solve this issue, we provide a solution for Track 1, which aims to extract 10 types of interactions between drug and protein entities. We applied an Ensemble Classifier model that combines BioMed-RoBERTa, a state of art language model, with Convolutional Neural Networks (CNN) to extract these relations. Despite the class imbalances in the BioCreative VII DrugProt test corpus, our model achieves a good performance compared to the average of other submissions in the challenge, with the micro F1 score of 55.67 ChemProt test corpus). The results show the potential of deep learning in extracting various types of DTIs.

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