# BioMamba: Domain-Adaptive Biomedical Language Models

arXiv: https://arxiv.org/abs/2408.02600 · HTML: https://mlsanity.com/paper/2408.02600/

## Key facts

- Cited by 8 papers in the map (data through 14 Oct 2026).
- Builds on 46 of its 74 references that are in the map.
- First posted on arXiv 5 Aug 2024.

## Builds on (most cited first, 30 of 46)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [Pointer Sentinel Mixture Models](https://mlsanity.com/paper/1609.07843/) (2016)
- [Efficiently Modeling Long Sequences with Structured State Spaces](https://mlsanity.com/paper/2111.00396/) (2021)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [Don't Stop Pretraining: Adapt Language Models to Domains and Tasks](https://mlsanity.com/paper/2004.10964/) (2020)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [Transformers are SSMs: Generalized Models and Efficient Algorithms Through Structured State Space Duality](https://mlsanity.com/paper/2405.21060/) (2024)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [GPT-NeoX-20B: An Open-Source Autoregressive Language Model](https://mlsanity.com/paper/2204.06745/) (2022)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [Documenting Large Webtext Corpora: A Case Study on the Colossal Clean Crawled Corpus](https://mlsanity.com/paper/2104.08758/) (2021)
- [Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine](https://mlsanity.com/paper/2311.16452/) (2023)
- [BioMistral: A Collection of Open-Source Pretrained Large Language Models for Medical Domains](https://mlsanity.com/paper/2402.10373/) (2024)
- [MEDITRON-70B: Scaling Medical Pretraining for Large Language Models](https://mlsanity.com/paper/2311.16079/) (2023)
- [GatorTron: A Large Clinical Language Model to Unlock Patient Information from Unstructured Electronic Health Records](https://mlsanity.com/paper/2203.03540/) (2022)
- [LinkBERT: Pretraining Language Models with Document Links](https://mlsanity.com/paper/2203.15827/) (2022)
- [A Study of Generative Large Language Model for Medical Research and Healthcare](https://mlsanity.com/paper/2305.13523/) (2023)
- [SciFive: a text-to-text transformer model for biomedical literature](https://mlsanity.com/paper/2106.03598/) (2021)
- [Do We Still Need Clinical Language Models?](https://mlsanity.com/paper/2302.08091/) (2023)
- [PMC-LLaMA: Towards Building Open-source Language Models for Medicine](https://mlsanity.com/paper/2304.14454/) (2023)
- [BioMedLM: A 2.7B Parameter Language Model Trained On Biomedical Text](https://mlsanity.com/paper/2403.18421/) (2024)
- [BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model](https://mlsanity.com/paper/2204.03905/) (2022)
- [Benchmarking large language models for biomedical natural language processing applications and recommendations](https://mlsanity.com/paper/2305.16326/) (2023)
- [Reuse, Don't Retrain: A Recipe for Continued Pretraining of Language Models](https://mlsanity.com/paper/2407.07263/) (2024)
- [Clinical Camel: An Open Expert-Level Medical Language Model with Dialogue-Based Knowledge Encoding](https://mlsanity.com/paper/2305.12031/) (2023)

## Built on by (most cited first, 8 of 8)

- [Content-Aware Mamba for Learned Image Compression](https://mlsanity.com/paper/2508.02192/) (2025)
- [Instruction Tuning and CoT Prompting for Contextual Medical QA with LLMs](https://mlsanity.com/paper/2506.12182/) (2025)
- [Protein-Mamba: Biological Mamba Models for Protein Function Prediction](https://mlsanity.com/paper/2409.14617/) (2024)
- [Mamba-Based Graph Convolutional Networks: Tackling Over-smoothing with Selective State Space](https://mlsanity.com/paper/2501.15461/) (2025)
- [Technologies on Effectiveness and Efficiency: A Survey of State Spaces Models](https://mlsanity.com/paper/2503.11224/) (2025)
- [DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning](https://mlsanity.com/paper/2410.02023/) (2024)
- [MambaFormer: Token-Level Guided Routing Mixture-of-Experts for Accurate and Efficient Clinical Assistance](https://mlsanity.com/paper/2601.01260/) (2026)
- [Accelerated Markov Chain Monte Carlo Using Adaptive Weighting Scheme](https://mlsanity.com/paper/2408.12888/) (2024)

## Abstract (arXiv)

Background. Biomedical language models should improve performance on biomedical text while retaining general-language-modeling fluency. For Mamba-based models, this trade-off has not been systematically studied across biomedical literature and clinical text. Methods. We developed BioMamba, a family of biomedical Mamba2 models at five scales obtained by continued pretraining of released public Mamba2 checkpoints on a balanced 80%/10%/10% mixture of PubMed abstracts, the Colossal Clean Crawled Corpus (C4), and Wikipedia. The contribution is the adaptation recipe and the accompanying open-weight checkpoints. Results. Across five scales, BioMamba consistently lowered PubMed perplexity, improved Wikipedia-style held-out perplexity by 1.46-4.72 PPL, and left C4 perplexity essentially unchanged. On six out-of-domain multiple-choice benchmarks, BioMamba stayed within +/-3 percentage points of Mamba2 with no systematic regression. After supervised fine-tuning, BioMamba+SFT matched or exceeded Mamba2+SFT on MIMIC-IV note completion and discharge summary generation at every evaluated scale, and improved PubMedQA at every scale. The strongest model (BioMamba-2.7B) reached a PubMed perplexity of 5.28 and accuracies of 90.24% and 73.00% on BioASQ and PubMedQA, respectively. Conclusions. A balanced domain-adaptive continued pretraining recipe strengthens Mamba2 language models on biomedical literature and clinical text while preserving general-language-modeling fluency.