A Comprehensive Evaluation of Biomedical Entity-centric Search (2022.emnlp-industry)
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| Challenge: | a novel algorithm for information retrieval from biomedical abstracts is used to identify entities. |
| Approach: | They perform a fine-grained evaluation of a BERT-based biomedical search engine . they use manually annotated PubMed abstracts and off-she-shelf Elasticsearch . |
| Outcome: | The proposed system performs better for disease and gene search queries than other systems. |
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Marco Martinelli, Stefano Marchesin, Vanessa Bonato, Giorgio Di Nunzio, Nicola Ferro, Ornella Irrera, Laura Menotti, Federica Vezzani, Gianmaria Silvello
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BERT might be Overkill: A Tiny but Effective Biomedical Entity Linker based on Residual Convolutional Neural Networks (2021.findings-emnlp)
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| Challenge: | Biomedical entity linking is a task of linking entities in biomedical documents to referent entities in a knowledge base. |
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Entity Decomposition with Filtering: A Zero-Shot Clinical Named Entity Recognition Framework (2025.naacl-long)
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| Challenge: | Recent studies have demonstrated that large language models (LLMs) can perform in named entity recognition tasks. |
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Zero-shot Medical Entity Retrieval without Annotation: Learning From Rich Knowledge Graph Semantics (2021.findings-acl)
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| Challenge: | Current approaches to medical entity retrieval generalize poorly to unseen sub-specialties . zero-shot retrieval is challenging due to the high degree of ambiguity and variability in medical corpora . |
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A Comprehensive Evaluation of Biomedical Entity Linking Models (2023.emnlp-main)
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David Kartchner, Jennifer Deng, Shubham Lohiya, Tejasri Kopparthi, Prasanth Bathala, Daniel Domingo-Fernández, Cassie Mitchell
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Named Entity Recognition for Chinese biomedical patents (2020.coling-main)
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| Challenge: | Existing attempts to address NER for Chinese biomedical texts have been limited due to the amount of Chinese biomedicine discoveries being patented. |
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OpenBioNER: Lightweight Open-Domain Biomedical Named Entity Recognition Through Entity Type Description (2025.findings-naacl)
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Alessio Cocchieri, Giacomo Frisoni, Marcos Martínez Galindo, Gianluca Moro, Giuseppe Tagliavini, Francesco Candoli
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Fine-grained Information Extraction from Biomedical Literature based on Knowledge-enriched Abstract Meaning Representation (2021.acl-long)
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| Challenge: | Compared with general natural language texts, sentences from scientific papers usually possess wider contexts between knowledge elements. |
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Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning (2022.naacl-main)
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| Challenge: | Generative methods for biomedical entity linking (EL) use synonyms knowledge from knowledge bases (KB) this is not trivial to inject into a generative method, but it is cost-effective. |
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Named Entity Recognition for Entity Linking: What Works and What’s Next (2021.findings-emnlp)
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| Challenge: | Entity Linking (EL) systems have achieved impressive results on standard benchmarks thanks to the contextualized representations provided by recent pretrained language models. |
| Approach: | They propose to exploit Named Entity Recognition (NER) to narrow the gap between EL systems trained on high and low amounts of labeled data. |
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