Papers by Christophe Ye
LLM as Entity Disambiguator for Biomedical Entity-Linking (2025.acl-short)
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| Challenge: | Entity linking involves normalizing a mention in medical text to a unique identifier in a knowledge base, such as UMLS or MeSH. |
| Approach: | They propose to use a large language model as an entity disambiguator to enhance the accuracy of alias-matching entity linking methods. |
| Outcome: | The proposed method surpasses existing methods on biomedical datasets by up to 16 points in accuracy. |
Where do LLMs currently stand on biomedical NER in both clean and noisy settings ? (2026.findings-eacl)
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| Challenge: | despite advances in medicine, many diseases remain without effective treatments . clinical meta-analysis is essential for drug discovery and clinical research . |
| Approach: | They investigate the performance of large language models (LLMs) on biomedical NER tasks . findings suggest LLMs exhibit a notable degree of robustness to noise . |
| Outcome: | The proposed models are closing the performance gap with BERT-based models and demonstrate particular strengths in low-data settings. |
BioEL: A Comprehensive Python Package for Biomedical Entity Linking (2025.findings-naacl)
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Prasanth Bathala, Christophe Ye, Batuhan Nursal, Shubham Lohiya, David Kartchner, Cassie S. Mitchell
| Challenge: | Entity Linking in biomedical literature is a critical task that enhances the extraction and integration of information from diverse scientific literature. |
| Approach: | They propose a Python package that allows for better Entity Linking in biomedical literature . the package includes four components: Ontology Object, Dataset Object and Evaluation Framework . |
| Outcome: | The proposed open-source package enables the implementation and comparison of biomedical entity linking tasks. |