用自然语言标签实现生物医学实体零样本识别,效果超越现有方法。
GLiNER-BioMed: A Suite of Efficient Models for Open Biomedical Named Entity Recognition
- 用大模型生成合成数据,让小模型学会识别任意生物医学实体
- 在多个数据集上零样本和少样本测试中F1提升5.96%(显著优于基线)
- 适合需要快速适应新实体类型的生物医学研究者使用
生物医学命名实体识别因专业词汇多、实体数量庞大且不断涌现新实体而面临挑战。传统模型受限于固定类别和人工标注,难以泛化到未定义类型。为此,我们提出针对生物医学领域的GLiNER-BioMed,一种基于通用轻量级命名实体识别模型(GLiNER)的适配系列。与传统方法不同,GLiNER采用自然语言标签推断任意实体类型,支持零样本识别。首先将大语言模型(LLM)的标注能力蒸馏至小型高效模型,生成高覆盖的合成生物医学NER数据;随后在多尺度下训练单向和双向编码器架构,平衡效率与性能。在多个生物医学数据集上的实验表明,GLiNER-BioMed在零样本与少样本场景均优于当前最优模型,F1得分相比最强基线提升5.96%(p<0.001)。消融实验验证了合成数据生成策略的有效性,并强调了合成生物医学预训练与通用领域标注微调的互补优势。所有数据集、模型及训练流程已公开于https://github.com/ds4dh/GLiNER-biomed。
原文摘要 · Abstract (English)
Biomedical named entity recognition (NER) presents unique challenges due to specialized vocabularies, the sheer volume of entities, and the continuous emergence of novel entities. Traditional NER models, constrained by fixed taxonomies and human annotations, struggle to generalize beyond predefined entity types. To address these issues, we introduce GLiNER-BioMed, a domain-adapted suite of Generalist and Lightweight Model for NER (GLiNER) models specifically tailored for biomedicine. In contrast to conventional approaches, GLiNER uses natural language labels to infer arbitrary entity types, enabling zero-shot recognition. Our approach first distills the annotation capabilities of large language models (LLMs) into a smaller, more efficient model, enabling the generation of high-coverage synthetic biomedical NER data. We subsequently train two GLiNER architectures, uni- and bi-encoder, at multiple scales to balance computational efficiency and recognition performance. Experiments on several biomedical datasets demonstrate that GLiNER-BioMed outperforms the state-of-the-art in both zero- and few-shot scenarios, achieving 5.96% improvement in F1-score over the strongest baseline (p-value < 0.001). Ablation studies highlight the effectiveness of our synthetic data generation strategy and emphasize the complementary benefits of synthetic biomedical pre-training combined with fine-tuning on general-domain annotations. All datasets, models, and training pipelines are publicly available at https://github.com/ds4dh/GLiNER-biomed.
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