From POS tagging to dependency parsing for biomedical event extraction

11 Aug 2018  ·  Dat Quoc Nguyen, Karin Verspoor ·

Background: Given the importance of relation or event extraction from biomedical research publications to support knowledge capture and synthesis, and the strong dependency of approaches to this information extraction task on syntactic information, it is valuable to understand which approaches to syntactic processing of biomedical text have the highest performance. Results: We perform an empirical study comparing state-of-the-art traditional feature-based and neural network-based models for two core natural language processing tasks of part-of-speech (POS) tagging and dependency parsing on two benchmark biomedical corpora, GENIA and CRAFT. To the best of our knowledge, there is no recent work making such comparisons in the biomedical context; specifically no detailed analysis of neural models on this data is available. Experimental results show that in general, the neural models outperform the feature-based models on two benchmark biomedical corpora GENIA and CRAFT. We also perform a task-oriented evaluation to investigate the influences of these models in a downstream application on biomedical event extraction, and show that better intrinsic parsing performance does not always imply better extrinsic event extraction performance. Conclusion: We have presented a detailed empirical study comparing traditional feature-based and neural network-based models for POS tagging and dependency parsing in the biomedical context, and also investigated the influence of parser selection for a biomedical event extraction downstream task. Availability of data and material: We make the retrained models available at

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Results from the Paper

Task Dataset Model Metric Name Metric Value Global Rank Result Benchmark
Dependency Parsing GENIA - LAS BiLSTM-CRF F1 91.92 # 1
Dependency Parsing GENIA - UAS BiLSTM-CRF F1 92.84 # 1


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