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Zhenran Xu

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AAAI Conference 2023 Conference Paper

Improving Biomedical Entity Linking with Cross-Entity Interaction

Zhenran Xu
Yulin Chen
Baotian Hu

Biomedical entity linking (EL) is the task of linking mentions in a biomedical document to corresponding entities in a knowledge base (KB). The challenge in biomedical EL lies in leveraging mention context to select the most appropriate entity among possible candidates. Although some EL models achieve competitive results by retrieving candidate entities and then exploiting context to re-rank them, these re-ranking models concatenate mention context with one candidate at a time. They lack fine-grained interaction among candidates, and potentially cannot handle ambiguous mentions when facing candidates both with high lexical similarity. We cope with this issue using a re-ranking model based on prompt tuning, which represents mention context and all candidates at once, letting candidates in comparison attend to each other. We also propose a KB-enhanced self-supervised pretraining strategy. Instead of large-scale pretraining on biomedical EL data in previous work, we use masked language modeling with synonyms from KB. Our method achieves state-of-the-art results on 3 biomedical EL datasets: NCBI disease, BC5CDR and COMETA, showing the effectiveness of cross-entity interaction and KB-enhanced pretraining strategy. Code is available at https://github.com/HITsz-TMG/Prompt-BioEL.

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IJCAI Conference 2023 Conference Paper

PPAT: Progressive Graph Pairwise Attention Network for Event Causality Identification

Zhenyu Liu
Baotian Hu
Zhenran Xu
Min Zhang

Event Causality Identification (ECI) aims to identify the causality between a pair of event mentions in a document, which is composed of sentence-level ECI (SECI) and document-level ECI (DECI). Previous work applies various reasoning models to identify the implicit event causality. However, they indiscriminately reason all event causality in the same way, ignoring that most inter-sentence event causality depends on intra-sentence event causality to infer. In this paper, we propose a progressive graph pairwise attention network (PPAT) to consider the above dependence. PPAT applies a progressive reasoning strategy, as it first predicts the intra-sentence event causality, and then infers the more implicit inter-sentence event causality based on the SECI result. We construct a sentence boundary event relational graph, and PPAT leverages a simple pairwise attention mechanism, which attends to different reasoning chains on the graph. In addition, we propose a causality-guided training strategy for assisting PPAT in learning causality-related representations on every layer. Extensive experiments show that our model achieves state-of-the-art performance on three benchmark datasets (5. 5%, 2. 2% and 4. 5% F1 gains on EventStoryLine, MAVEN-ERE and Causal-TimeBank). Code is available at https: //github. com/HITsz-TMG/PPAT.

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