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Deep learning for extracting protein-protein interactions from biomedical literature - ACL Anthology
Correct Metadata for
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:
- Proceedings of the 16th BioNLP Workshop
- 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
- Bibkey:
- Cite (ACL):
- Yifan Peng and Zhiyong Lu. 2017. Deep learning for extracting protein-protein interactions from biomedical literature. In Proceedings of the 16th BioNLP Workshop, 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)
- Copy Citation:
- PDF:
- https://aclanthology.org/W17-2304.pdf
Export citation
@inproceedings{peng-lu-2017-deep,
title = "Deep learning for extracting protein-protein interactions from biomedical literature",
author = "Peng, Yifan and
Lu, Zhiyong",
editor = "Cohen, Kevin Bretonnel and
Demner-Fushman, Dina and
Ananiadou, Sophia and
Tsujii, Junichi",
booktitle = "Proceedings of the 16th {B}io{NLP} Workshop",
month = aug,
year = "2017",
address = "Vancouver, Canada,",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/W17-2304/",
doi = "10.18653/v1/W17-2304",
pages = "29--38",
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."
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<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.</abstract>
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%0 Conference Proceedings %T Deep learning for extracting protein-protein interactions from biomedical literature %A Peng, Yifan %A Lu, Zhiyong %Y Cohen, Kevin Bretonnel %Y Demner-Fushman, Dina %Y Ananiadou, Sophia %Y Tsujii, Junichi %S Proceedings of the 16th BioNLP Workshop %D 2017 %8 August %I Association for Computational Linguistics %C Vancouver, Canada, %F peng-lu-2017-deep %X 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. %R 10.18653/v1/W17-2304 %U https://aclanthology.org/W17-2304/ %U https://doi.org/10.18653/v1/W17-2304 %P 29-38
Markdown (Informal)
[Deep learning for extracting protein-protein interactions from biomedical literature](https://aclanthology.org/W17-2304/) (Peng & Lu, BioNLP 2017)
- Deep learning for extracting protein-protein interactions from biomedical literature (Peng & Lu, BioNLP 2017)
ACL
- Yifan Peng and Zhiyong Lu. 2017. Deep learning for extracting protein-protein interactions from biomedical literature. In Proceedings of the 16th BioNLP Workshop, pages 29–38, Vancouver, Canada,. Association for Computational Linguistics.