Language Specificity vs. Domain Diversity: Benchmarking Transformers for Bangla Medical NER

arXiv:2609.29101v1 Announce Type: new Abstract: Medical Named Entity Recognition (NER) for low-resource languages remains a challenging task due to high linguistic variability and a scarcity of domain-specific annotated corpora. This work presents a comprehensive empirical benchmark evaluating three fine-tuned transformer encoders-BanglaBERT, multilingual BERT (mBERT), and XLM-RoBERTa-against GPT-4o mini under zero-shot and few-shot prompting configurations for Bangla medical NER. In contrast to prior studies that evaluated large language models on limited subsets of only 50 samples, we conduct a large-scale evaluation across the full test set of 3,179 samples, providing statistically robust and reproducible baselines. Our fine-tuned XLM-RoBERTa model achieves an F1- score of 0.5959, establishing a new state-of-the-art and surpassing the previously reported best result of 0.5848. Crucially, we demonstrate that the language-specific BanglaBERT model consistently underperforms its multilingual counterparts with an F1-score of 0.4937, indicating that pretraining domain diversity can outweigh language specificity in highly specialized clinical settings. Furthermore, we present a detailed per-entity-type analysis for this task, revealing that Medicine and Specialist categories are recognized with high reliability, achieving F1- scores above 0.83, while the Symptom category remains the most challenging with an F1-score of 0.4367 despite being the most frequent training class. Finally, fine-tuned transformer models outperform the optimal prompting configuration by a factor of 3.76, confirming that prompt-only pipelines remain inadequate for structured clinical entity extraction in low-resource language environments.

Abstract:Medical Named Entity Recognition (NER) for low-resource languages remains a challenging task due to high linguistic variability and a scarcity of domain-specific annotated corpora. This work presents a comprehensive empirical benchmark evaluating three fine-tuned transformer encoders-BanglaBERT, multilingual BERT (mBERT), and XLM-RoBERTa-against GPT-4o mini under zero-shot and few-shot prompting configurations for Bangla medical NER. In contrast to prior studies that evaluated large language models on limited subsets of only 50 samples, we conduct a large-scale evaluation across the full test set of 3,179 samples, providing statistically robust and reproducible baselines. Our fine-tuned XLM-RoBERTa model achieves an F1- score of 0.5959, establishing a new state-of-the-art and surpassing the previously reported best result of 0.5848. Crucially, we demonstrate that the language-specific BanglaBERT model consistently underperforms its multilingual counterparts with an F1-score of 0.4937, indicating that pretraining domain diversity can outweigh language specificity in highly specialized clinical settings. Furthermore, we present a detailed per-entity-type analysis for this task, revealing that Medicine and Specialist categories are recognized with high reliability, achieving F1- scores above 0.83, while the Symptom category remains the most challenging with an F1-score of 0.4367 despite being the most frequent training class. Finally, fine-tuned transformer models outperform the optimal prompting configuration by a factor of 3.76, confirming that prompt-only pipelines remain inadequate for structured clinical entity extraction in low-resource language environments.

6 pages, 2 figures. Accepted at the 2026 IEEE International Conference on Biomedical Engineering, Computer and Information Technology for Health (BECITHCON), Dhaka, Bangladesh

Machine Learning (cs.LG)

arXiv:2609.29101 [cs.LG]

(or arXiv:2609.29101v1 [cs.LG] for this version)

https://doi.org/10.48550/arXiv.2609.29101 arXiv-issued DOI via DataCite (pending registration)

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Language Specificity vs. Domain Diversity: Benchmarking Transformers for Bangla Medical NER

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