# BioBigBird: A Sparse Attention Model for Long-Range Dependency Processing in Biomedical Text

arXiv: https://arxiv.org/abs/2610.11430 · HTML: https://mlsanity.com/paper/2610.11430/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 5 of its 27 references that are in the map.
- First posted on arXiv 8 Oct 2026.

## Builds on (most cited first, 5 of 5)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [HuggingFace's Transformers: State-of-the-art Natural Language Processing](https://mlsanity.com/paper/1910.03771/) (2019)
- [Big Bird: Transformers for Longer Sequences](https://mlsanity.com/paper/2007.14062/) (2020)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)

## Abstract (arXiv)

While domain-specific Large Language Models (LLMs) have encoded vast biomedical knowledge, their limited context windows often hinder a deep understanding of nuanced relationships within and across texts. To address this limitation, we introduce BioBigBird, a bidirectional language model pre-trained on extensive biomedical literature and clinical data, specifically designed to handle long-range dependencies. BioBigBird leverages a sparse attention mechanism to process sequences up to 4096 tokens, and its training incorporates a multi-stage process to mitigate noise from the large-scale pre-training corpus. We further enhance its performance by employing a multi-task learning (MTL) framework that jointly optimizes for Named Entity Recognition and Relation Extraction. Comprehensive evaluations on the BLURB benchmark reveal that our MTL-enhanced BioBigBird achieves highly competitive results against state-of-the-art models. Our work contributes an effective methodology for developing powerful, long-context language models for specialized domains, demonstrating the value of extended sequence processing for complex text analysis. Our models are publicly available at https://huggingface.co/collections/bisectgroup/biobigbird.