Abstract
State-of-the-art methods for protein-protein interaction (PPI) extraction are primarily feature-based or kernel-based by leveraging lexical and syntactic information. But how to incorporate such knowledge in the recent deep learning methods remains an open question. In this paper, we propose a multichannel dependency-based convolutional neural network model (McDepCNN). It applies one channel to the embedding vector of each word in the sentence, and another channel to the embedding vector of the head of the corresponding word. Therefore, the model can use richer information obtained from different channels. Experiments on two public benchmarking datasets, AIMed and BioInfer, demonstrate that McDepCNN provides up to 6% F1-score improvement over rich feature-based methods and single-kernel methods. In addition, McDepCNN achieves 24.4% relative improvement in F1-score over the state-of-the-art methods on cross-corpus evaluation and 12% improvement in F1-score over kernel-based methods on “difficult” instances. These results suggest that McDepCNN generalizes more easily over different corpora, and is capable of capturing long distance features in the sentences.- Anthology ID:
- W17-2304
- Volume:
- BioNLP 2017
- Month:
- August
- Year:
- 2017
- Address:
- Vancouver, Canada,
- Editors:
- Kevin Bretonnel Cohen, Dina Demner-Fushman, Sophia Ananiadou, Junichi Tsujii
- Venue:
- BioNLP
- SIG:
- SIGBIOMED
- Publisher:
- Association for Computational Linguistics
- Note:
- Pages:
- 29–38
- Language:
- URL:
- https://aclanthology.org/W17-2304
- DOI:
- 10.18653/v1/W17-2304
- Cite (ACL):
- Yifan Peng and Zhiyong Lu. 2017. Deep learning for extracting protein-protein interactions from biomedical literature. In BioNLP 2017, pages 29–38, Vancouver, Canada,. Association for Computational Linguistics.
- Cite (Informal):
- Deep learning for extracting protein-protein interactions from biomedical literature (Peng & Lu, BioNLP 2017)
- PDF:
- https://preview.aclanthology.org/emnlp22-frontmatter/W17-2304.pdf