Chemical-protein Interaction Extraction via Gaussian Probability Distribution and External Biomedical Knowledge
This work addresses a domain-specific problem for biomedical researchers and drug discovery by improving automated extraction of chemical-protein interactions from literature, though it appears incremental as it builds on existing neural methods with specific enhancements.
The paper tackles chemical-protein interaction extraction from biomedical literature by proposing a neural network approach that incorporates Gaussian probability distribution to capture local sentence structure and external biomedical knowledge via attention mechanisms. The model achieves superior performance on the CHEMPROT corpus compared to state-of-the-art methods, showing that these components are complementary and improve extraction, particularly for sentences with overlapping relations.
Motivation: The biomedical literature contains a wealth of chemical-protein interactions (CPIs). Automatically extracting CPIs described in biomedical literature is essential for drug discovery, precision medicine, as well as basic biomedical research. Most existing methods focus only on the sentence sequence to identify these CPIs. However, the local structure of sentences and external biomedical knowledge also contain valuable information. Effective use of such information may improve the performance of CPI extraction. Results: In this paper, we propose a novel neural network-based approach to improve CPI extraction. Specifically, the approach first employs BERT to generate high-quality contextual representations of the title sequence, instance sequence, and knowledge sequence. Then, the Gaussian probability distribution is introduced to capture the local structure of the instance. Meanwhile, the attention mechanism is applied to fuse the title information and biomedical knowledge, respectively. Finally, the related representations are concatenated and fed into the softmax function to extract CPIs. We evaluate our proposed model on the CHEMPROT corpus. Our proposed model is superior in performance as compared with other state-of-the-art models. The experimental results show that the Gaussian probability distribution and external knowledge are complementary to each other. Integrating them can effectively improve the CPI extraction performance. Furthermore, the Gaussian probability distribution can effectively improve the extraction performance of sentences with overlapping relations in biomedical relation extraction tasks. Availability: Data and code are available at https://github.com/CongSun-dlut/CPI_extraction. Contact: yangzh@dlut.edu.cn, wangleibihami@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.