Papers with BioNER
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
| Challenge: | Biomedical Named Entity Recognition (BioNER) is a computationally expensive and limited tool . specialized 7B NER LLMs and GPT-4o can't match textual spans with entity types . |
| Approach: | They propose a lightweight BERT-based cross-encoder architecture that can identify any biomedical entity using only its description. |
| Outcome: | The proposed system outperforms existing models that match textual spans with entity types rather than descriptions on biomedical benchmarks. |
A Multi-Task Approach for Improving Biomedical Named Entity Recognition by Incorporating Multi-Granularity information (2021.findings-acl)
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| Challenge: | Neural named entity recognition (BioNER) methods require large amount of annotated data, while the annotating BioNER datasets are often difficult to obtain and small in scale due to the limitations of privacy, ethics and high degree of specialization. |
| Approach: | They propose a method that utilizes latent multi-granularity information in annotated bioNER datasets to alleviate the lack of training samples. |
| Outcome: | The proposed model improves over the BioBERT baseline and can get more than 3% improvement of F1score in low-resource scenarios. |