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BioMamba: Domain-Adaptive Biomedical Language Models

Ling Yue, Mingzhi Zhu, Sixue Xing, Shaowu Pan, Vijil Chenthamarakshan, Yanbo Wang, Yunning Cao, Payel Das, Tianfan Fu · Aug 5, 2024 · Citations: 0

Automatic Metrics
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How to use this page

Low trust

Use this as background context only. Do not make protocol decisions from this page alone.

Best use

Background context only

What to verify

Validate the evaluation procedure and quality controls in the full paper before operational use.

Evidence quality

Low

Derived from extracted protocol signals and abstract evidence.

Abstract

Background: Biomedical language models should improve performance on biomedical text while retaining general-domain language ability. For Mamba-based models, this trade-off has not been clearly studied across biomedical literature and clinical text. Methods: We developed BioMamba, a family of biomedical models obtained by continued pretraining of public Mamba2 checkpoints on PubMed, with small amounts of general-domain data from the Colossal Clean Crawled Corpus (C4) and Wikipedia included to help preserve general-domain language ability. We evaluated language modeling and three downstream tasks across multiple model scales: clinical note completion, discharge summary generation, and biomedical yes/no question answering. Results: BioMamba consistently improved PubMed modeling, improved Wikipedia modeling, and left C4 performance largely unchanged. After supervised fine-tuning, BioMamba transferred well to both biomedical literature and clinical text, yielding strong results on completion, summarization, and question answering. On MIMIC-IV, BioMamba+SFT consistently matched or exceeded SFT from the corresponding base checkpoints across note completion and discharge summary generation. The strongest model achieved a PubMed perplexity of 5.28 and accuracies of 90.24% and 73.00% on BioASQ and PubMedQA, respectively. Conclusion: Balanced domain-adaptive pretraining strategy strengthens Mamba language models for both biomedical literature and clinical text, while preserving general-domain language capabilities, establishing BioMamba as a practical foundation for biomedical NLP applications.

Abstract-only analysis — low confidence

All signals on this page are inferred from the abstract only and may be inaccurate. Do not use this page as a primary protocol reference.

  • This paper looks adjacent to evaluation work, but not like a strong protocol reference.
  • The available metadata is too thin to trust this as a primary source.
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Should You Rely On This Paper?

This paper is adjacent to HFEPX scope and is best used for background context, not as a primary protocol reference.

Best use

Background context only

Use if you need

A secondary eval reference to pair with stronger protocol papers.

Main weakness

This paper looks adjacent to evaluation work, but not like a strong protocol reference.

Trust level

Low

Usefulness score

0/100 • Low

Treat as adjacent context, not a core eval-method reference.

Human Feedback Signal

Not explicit in abstract metadata

Evaluation Signal

Detected

Usefulness for eval research

Adjacent candidate

Extraction confidence 35%

If you are doing eval pipeline work, start here:

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What We Could Verify

These are the protocol signals we could actually recover from the available paper metadata. Use them to decide whether this paper is worth deeper reading.

Human Feedback Types

missing

None explicit

No explicit feedback protocol extracted.

"Background: Biomedical language models should improve performance on biomedical text while retaining general-domain language ability."

Evaluation Modes

partial

Automatic Metrics

Includes extracted eval setup.

"Background: Biomedical language models should improve performance on biomedical text while retaining general-domain language ability."

Quality Controls

missing

Not reported

No explicit QC controls found.

"Background: Biomedical language models should improve performance on biomedical text while retaining general-domain language ability."

Benchmarks / Datasets

missing

Not extracted

No benchmark anchors detected.

"Background: Biomedical language models should improve performance on biomedical text while retaining general-domain language ability."

Reported Metrics

partial

Perplexity

Useful for evaluation criteria comparison.

"The strongest model achieved a PubMed perplexity of 5.28 and accuracies of 90.24% and 73.00% on BioASQ and PubMedQA, respectively."

Human Feedback Details

  • Uses human feedback: No
  • Feedback types: None
  • Rater population: Not reported
  • Expertise required: Medicine

Evaluation Details

  • Evaluation modes: Automatic Metrics
  • Agentic eval: None
  • Quality controls: Not reported
  • Evidence quality: Low
  • Use this page as: Background context only

Protocol And Measurement Signals

Benchmarks / Datasets

No benchmark or dataset names were extracted from the available abstract.

Reported Metrics

perplexity

Research Brief

Metadata summary

Background: Biomedical language models should improve performance on biomedical text while retaining general-domain language ability.

Based on abstract + metadata only. Check the source paper before making high-confidence protocol decisions.

Key Takeaways

  • Background: Biomedical language models should improve performance on biomedical text while retaining general-domain language ability.
  • For Mamba-based models, this trade-off has not been clearly studied across biomedical literature and clinical text.
  • Methods: We developed BioMamba, a family of biomedical models obtained by continued pretraining of public Mamba2 checkpoints on PubMed, with small amounts of general-domain data from the Colossal Clean Crawled Corpus (C4) and Wikipedia included to help preserve general-domain language ability.

Researcher Actions

  • Compare this paper against nearby papers in the same arXiv category before using it for protocol decisions.
  • Check the full text for explicit evaluation design choices (raters, protocol, and metrics).
  • Use related-paper links to find stronger protocol-specific references.

Caveats

  • Generated from abstract + metadata only; no PDF parsing.
  • Signals below are heuristic and may miss details reported outside the abstract.

Recommended Queries

Research Summary

Contribution Summary

  • The strongest model achieved a PubMed perplexity of 5.28 and accuracies of 90.24% and 73.00% on BioASQ and PubMedQA, respectively.

Why It Matters For Eval

  • Abstract shows limited direct human-feedback or evaluation-protocol detail; use as adjacent methodological context.

Researcher Checklist

  • Gap: Human feedback protocol is explicit

    No explicit human feedback protocol detected.

  • Pass: Evaluation mode is explicit

    Detected: Automatic Metrics

  • Gap: Quality control reporting appears

    No calibration/adjudication/IAA control explicitly detected.

  • Gap: Benchmark or dataset anchors are present

    No benchmark/dataset anchor extracted from abstract.

  • Pass: Metric reporting is present

    Detected: perplexity

Related Papers

Papers are ranked by protocol overlap, extraction signal alignment, and semantic proximity.

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