ArticleBioinformatics (Oxford, England)2026
DA-BioNER: data augmentation based on few-shot learning and distant supervision for biomedical named entity recognition.
Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
motivationNamed entity recognition (NER) is a fundamental component of structured knowledge extraction, yet its effectiveness in emerging domains remains by the scarcity of high-quality, domain-specific annotated corpora. Although data augmentation and distant supervision have been explored to alleviate this issue, existing methods often introduce limited entity diversity, noisy labels, or disrupt contextual integrity, thereby limiting their generalization ability in low-resource settings.
resultsIn this study, we propose DA-BioNER, a context-preserving data expansion framework for biomedical NER. DA-BioNER combines multiple base NER models trained on few-shot data to provide coarse annotations, followed by refinement using a large language model (LLM) guided by global biomedical knowledge. Unlike generation-based augmentation methods that synthesize new sentences, DA-BioNER performs annotation refinement within existing sentences, preserving both syntactic structure and semantic context. By constraining the role of LLM to refinement rather than open-ended generation, the framework effectively reduces hallucination while improving label precision and consistency. We evaluate DA-BioNER on three benchmark datasets (NCBI-Disease, BC5CDR, and BioRED), under low-resource conditions. In 40-shot settings, DA-BioNER achieves F1-scores of 0.750, 0.795, and 0.799, respectively, outperforming state-of-the-art methods, including LSMS, DAGA, and MELM, by up to 0.32. Under more extreme few-shot settings, DA-BioNER further improves F1-scores by up to 0.08, while generating an average of 1,391 additional unique entities, substantially enriching training diversity. These results demonstrate that DA-BioNER provides a scalable and adaptable solution for robust biomedical NER, particularly in domain adaptation and low-resource scenarios. AVAILABILITY: DA-BioNER is publicly available at https://github.com/DMnBI/DA-BioNER.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.