PEMRC: A Positive Enhanced Machine Reading Comprehension Method for Few-Shot Named Entity Recognition in Biomedical Domain

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Health Information Processing (CHIP 2023)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 1993))

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Abstract

In this paper, we propose a simple and effective few-shot named entity recognition (NER) method for biomedical domain, called PEMRC (Positive Enhanced Machine Reading Comprehension). PEMRC is based on the idea of using machine reading comprehension reading comprehension (MRC) framework to perfome few-shot NER and fully exploit the prior knowledge implied in the label information. On one hand, we design three different query templates to better induce knowledge from pre-trained language models (PLMs). On the other hand, we design a positive enhanced loss function to improve the model’s accuracy in identifying the start and end positions of entities under low-resources scenarios. Extensive experimental results on eight benchmark datasets in biomedical domain show that PEMRC significantly improves the performance of few-shot NER.

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References

  1. Brown, T.B., et al.: Language models are few-shot learners. In: Proceedings of the 34th International Conference on Neural Information Processing Systems. NIPS’20, Curran Associates Inc., Red Hook, NY, USA (2020)

    Google Scholar 

  2. Chen, X., et al.: LightNER: A lightweight tuning paradigm for low-resource NER via pluggable prompting. In: Proceedings of the 29th International Conference on Computational Linguistics, pp. 2374–2387. Gyeongju, Republic of Korea (2022)

    Google Scholar 

  3. Chiu, J.P., Nichols, E.: Named entity recognition with bidirectional LSTM-CNNs. Trans. Assoc. Comput. linguist. 4, 357–370 (2016)

    Article  Google Scholar 

  4. Cui, L., Wu, Y., Liu, J., Yang, S., Zhang, Y.: Template-based named entity recognition using BART. In: Findings of the Association for Computational Linguistics: ACL-IJCNLP 2021, pp. 1835–1845. Association for Computational Linguistics (2021)

    Google Scholar 

  5. Das, S.S.S., Katiyar, A., Passonneau, R., Zhang, R.: CONTaiNER: few-shot named entity recognition via contrastive learning. In: Proceedings of the 60th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers), pp. 6338–6353. Association for Computational Linguistics, Dublin, Ireland (2022)

    Google Scholar 

  6. Ding, N., et al.: Few-NERD: a few-shot named entity recognition dataset. In: Proceedings of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing (Volume 1: Long Papers), pp. 3198–3213. Association for Computational Linguistics (2021)

    Google Scholar 

  7. Fritzler, A., Logacheva, V., Kretov, M.: Few-shot classification in named entity recognition task. In: Proceedings of the 34th ACM/SIGAPP Symposium on Applied Computing, pp. 993–1000 (2019)

    Google Scholar 

  8. Gao, T., Fisch, A., Chen, D.: Making pre-trained language models better few-shot learners. In: Proceedings of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing (Volume 1: Long Papers), pp. 3816–3830. Association for Computational Linguistics (2021). https://doi.org/10.18653/v1/2021.acl-long.295. https://aclanthology.org/2021.acl-long.295

  9. Han, X., Zhao, W., Ding, N., Liu, Z., Sun, M.: PTR: prompt tuning with rules for text classification. Ar**v abs/2105.11259 (2021). https://api.semanticscholar.org/CorpusID:235166723

  10. Hou, Y., et al.: Few-shot slot tagging with collapsed dependency transfer and label-enhanced task-adaptive projection network. In: Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics, pp. 1381–1393. Association for Computational Linguistics (2020)

    Google Scholar 

  11. Huang, Y., et al.: COPNER: contrastive learning with prompt guiding for few-shot named entity recognition. In: Proceedings of the 29th International Conference on Computational Linguistics, pp. 2515–2527. International Committee on Computational Linguistics, Gyeongju, Republic of Korea (2022)

    Google Scholar 

  12. Lee, J., et al: BioBERT: a pre-trained biomedical language representation model for biomedical text mining. Bioinformatics 36(4), 1234–1240 (2019)

    Google Scholar 

  13. Li, J., Shang, S., Shao, L.: MetaNER: named entity recognition with meta-learning. In: Proceedings of The Web Conference 2020, pp. 429–440. WWW ’20, Association for Computing Machinery, New York, NY, USA (2020)

    Google Scholar 

  14. Li, J., Sun, A., Han, J., Li, C.: A survey on deep learning for named entity recognition. IEEE Trans. Knowl. Data Eng. 34(1), 50–70 (2020)

    Article  Google Scholar 

  15. Li, X.L., Liang, P.: Prefix-tuning: optimizing continuous prompts for generation. In: Proceedings of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing (Volume 1: Long Papers), pp. 4582–4597. Association for Computational Linguistics (2021)

    Google Scholar 

  16. Liu, S., Zhang, X., Zhang, S., Wang, H., Zhang, W.: Neural machine reading comprehension: methods and trends. Ar**v abs/1907.01118 (2019)

    Google Scholar 

  17. Ma, R., et al.: Template-free prompt tuning for few-shot NER. In: Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, pp. 5721–5732. Association for Computational Linguistics, Seattle, United States (2022)

    Google Scholar 

  18. Nguyen, N.D., Du, L., Buntine, W., Chen, C., Beare, R.: Hardness-guided domain adaptation to recognise biomedical named entities under low-resource scenarios. In: Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing, pp. 4063–4071. Abu Dhabi, United Arab Emirates (2022)

    Google Scholar 

  19. Radford, A., Wu, J., Child, R., Luan, D., Amodei, D., Sutskever, I.: Language models are unsupervised multitask learners (2019)

    Google Scholar 

  20. Schick, T., Schütze, H.: Exploiting cloze-questions for few-shot text classification and natural language inference. In: Proceedings of the 16th Conference of the European Chapter of the Association for Computational Linguistics: Main Volume, pp. 255–269. Association for Computational Linguistics (2021)

    Google Scholar 

  21. Schick, T., Schütze, H.: It’s not just size that matters: small language models are also few-shot learners. In: Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, pp. 2339–2352. Association for Computational Linguistics (2021). https://doi.org/10.18653/v1/2021.naacl-main.185. https://aclanthology.org/2021.naacl-main.185

  22. Shin, T., Razeghi, Y., Logan IV, R.L., Wallace, E., Singh, S.: AutoPrompt: eliciting knowledge from language models with automatically generated prompts. In: Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP), pp. 4222–4235. Association for Computational Linguistics (2020). https://doi.org/10.18653/v1/2020.emnlp-main.346. https://aclanthology.org/2020.emnlp-main.346

  23. Snell, J., Swersky, K., Zemel, R.: Prototypical networks for few-shot learning, pp. 4080–4090. NIPS’17, Curran Associates Inc., Red Hook, NY, USA (2017)

    Google Scholar 

  24. Wiseman, S., Stratos, K.: Label-agnostic sequence labeling by copying nearest neighbors. In: Proceedings of the 57th Annual Meeting of the Association for Computational Linguistics, pp. 5363–5369. Association for Computational Linguistics, Florence, Italy (2019)

    Google Scholar 

  25. Yadav, V., Bethard, S.: A survey on recent advances in named entity recognition from deep learning models. In: Proceedings of the 27th International Conference on Computational Linguistics, pp. 2145–2158. Association for Computational Linguistics, Santa Fe, New Mexico, USA (2018)

    Google Scholar 

  26. Yang, Y., Katiyar, A.: Simple and effective few-shot named entity recognition with structured nearest neighbor learning. In: Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP), pp. 6365–6375. Association for Computational Linguistics (2020)

    Google Scholar 

  27. Zhang, Y., Fei, H., Li, D., Li, P.: PromptGen: automatically generate prompts using generative models. In: Findings of the Association for Computational Linguistics: NAACL 2022, pp. 30–37. Association for Computational Linguistics, Seattle, United States (2022). https://doi.org/10.18653/v1/2022.findings-naacl.3. https://aclanthology.org/2022.findings-naacl.3

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Funding

This research is supported by the National Natural Science Foundation of China [61976147] and the research grant of The Hong Kong Polytechnical University Projects [# 1-W182].

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Correspondence to Longhua Qian .

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Dong, Y., Li, D., Gu, J., Qian, L., Zhou, G. (2024). PEMRC: A Positive Enhanced Machine Reading Comprehension Method for Few-Shot Named Entity Recognition in Biomedical Domain. In: Xu, H., et al. Health Information Processing. CHIP 2023. Communications in Computer and Information Science, vol 1993. Springer, Singapore. https://doi.org/10.1007/978-981-99-9864-7_2

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  • DOI: https://doi.org/10.1007/978-981-99-9864-7_2

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  • Online ISBN: 978-981-99-9864-7

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