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

arXiv: https://arxiv.org/abs/2111.00611 · HTML: https://mlsanity.com/paper/2111.00611/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 6 of its 29 references that are in the map.
- First posted on arXiv 31 Oct 2021.

## Builds on (most cited first, 6 of 6)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [Don't Stop Pretraining: Adapt Language Models to Domains and Tasks](https://mlsanity.com/paper/2004.10964/) (2020)
- [KUISAIL at SemEval-2020 Task 12: BERT-CNN for Offensive Speech Identification in Social Media](https://mlsanity.com/paper/2007.13184/) (2020)
- [Enriching Pre-trained Language Model with Entity Information for Relation Classification](https://mlsanity.com/paper/1905.08284/) (2019)

## Built on by (most cited first, 2 of 2)

- [Review of Natural Language Processing in Pharmacology](https://mlsanity.com/paper/2208.10228/) (2022)
- [TERMinator: A system for scientific texts processing](https://mlsanity.com/paper/2209.14854/) (2022)

## Abstract (arXiv)

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% (and 63% on BioCreative VI ChemProt test corpus). The results show the potential of deep learning in extracting various types of DTIs.