# Enhancing Biomedical Named Entity Recognition via Multiple Programming Languages Instruction Tuning and Ensemble Method

arXiv: https://arxiv.org/abs/2610.02949 · HTML: https://mlsanity.com/paper/2610.02949/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 15 of its 33 references that are in the map.
- First posted on arXiv 2 Oct 2026.

## Builds on (most cited first, 15 of 15)

- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [Qwen2.5 Technical Report](https://mlsanity.com/paper/2412.15115/) (2024)
- [Code Llama: Open Foundation Models for Code](https://mlsanity.com/paper/2308.12950/) (2023)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Qwen2.5-Coder Technical Report](https://mlsanity.com/paper/2409.12186/) (2024)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [InstructUIE: Multi-task Instruction Tuning for Unified Information Extraction](https://mlsanity.com/paper/2304.08085/) (2023)
- [GoLLIE: Annotation Guidelines improve Zero-Shot Information-Extraction](https://mlsanity.com/paper/2310.03668/) (2023)
- [UniversalNER: Targeted Distillation from Large Language Models for Open Named Entity Recognition](https://mlsanity.com/paper/2308.03279/) (2023)
- [KnowCoder: Coding Structured Knowledge into LLMs for Universal Information Extraction](https://mlsanity.com/paper/2403.07969/) (2024)
- [MT-BioNER: Multi-task Learning for Biomedical Named Entity Recognition using Deep Bidirectional Transformers](https://mlsanity.com/paper/2001.08904/) (2020)
- [AIONER: All-in-one scheme-based biomedical named entity recognition using deep learning](https://mlsanity.com/paper/2211.16944/) (2022)
- [UniM: A Unified Any-to-Any Interleaved Multimodal Benchmark](https://mlsanity.com/paper/2603.05075/) (2026)
- [Entity Decomposition with Filtering: A Zero-Shot Clinical Named Entity Recognition Framework](https://mlsanity.com/paper/2407.04629/) (2024)
- [VANER: Leveraging Large Language Model for Versatile and Adaptive Biomedical Named Entity Recognition](https://mlsanity.com/paper/2404.17835/) (2024)

## Built on by (most cited first, 1 of 1)

- [Conditional Rank Allocation for Taxonomy-Aware Medical Language Model Adaptation](https://mlsanity.com/paper/2610.06765/) (2026)

## Abstract (arXiv)

Instruction tuning has become a common paradigm for applying large language models (LLMs) to biomedical named entity recognition (BioNER). However, existing instruction-tuning approaches still face two key challenges. First, conventional natural-language instructions typically serialize BioNER annotations as flat textual outputs, providing limited structural constraints for typed entity extraction. Second, high-quality biomedical annotations are limited, and learning from a single serialized output form may restrict structural diversity and reduce model robustness. Although external biomedical knowledge can be introduced to alleviate data scarcity, it often requires costly resource construction. To address these challenges, we propose MITE, a Multiple Programming Languages Instruction Tuning and Ensemble method for BioNER. MITE reformulates BioNER as a structure-to-structure generation task by representing both instructions and entity outputs in code-formatted representations. Specifically, each training instance is transformed into multiple programming-language formats, including Python, C++, and Java, while preserving the same underlying entity semantics. These language-specific representations provide structurally diverse supervision without requiring external biomedical knowledge or additional annotations. During inference, MITE aggregates predictions from different code formats through an entity-level voting strategy, reducing language-specific prediction variance and improving robustness. Experiments on six widely used BioNER datasets demonstrate that MITE consistently outperforms representative BERT-based and LLM-based baselines and exhibits strong cross-dataset generalization. Ablation and parameter analyses further verify the effectiveness and robustness of the proposed components.