# BioBridge: Bridging Proteins and Language for Enhanced Biological Reasoning with LLMs

arXiv: https://arxiv.org/abs/2602.17680 · HTML: https://mlsanity.com/paper/2602.17680/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 21 of its 32 references that are in the map.
- First posted on arXiv 4 Feb 2026.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)

## Builds on (most cited first, 21 of 21)

- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [BLIP-2: Bootstrapping Language-Image Pre-training with Frozen Image Encoders and Large Language Models](https://mlsanity.com/paper/2301.12597/) (2023)
- [Multitask Prompted Training Enables Zero-Shot Task Generalization](https://mlsanity.com/paper/2110.08207/) (2021)
- [Continual Lifelong Learning with Neural Networks: A Review](https://mlsanity.com/paper/1802.07569/) (2018)
- [Instruction Tuning with GPT-4](https://mlsanity.com/paper/2304.03277/) (2023)
- [Fine-tuned Language Models are Continual Learners](https://mlsanity.com/paper/2205.12393/) (2022)
- [TemporalWiki: A Lifelong Benchmark for Training and Evaluating Ever-Evolving Language Models](https://mlsanity.com/paper/2204.14211/) (2022)
- [Lifelong Pretraining: Continually Adapting Language Models to Emerging Corpora](https://mlsanity.com/paper/2110.08534/) (2021)
- [Diffusion Language Models Are Versatile Protein Learners](https://mlsanity.com/paper/2402.18567/) (2024)
- [ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts](https://mlsanity.com/paper/2301.12040/) (2023)
- [OntoProtein: Protein Pretraining With Gene Ontology Embedding](https://mlsanity.com/paper/2201.11147/) (2022)
- [xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering the Language of Protein](https://mlsanity.com/paper/2401.06199/) (2024)
- [CCPL: Contrastive Coherence Preserving Loss for Versatile Style Transfer](https://mlsanity.com/paper/2207.04808/) (2022)
- [BERN2: an advanced neural biomedical named entity recognition and normalization tool](https://mlsanity.com/paper/2201.02080/) (2022)
- [Prot2Text: Multimodal Protein's Function Generation with GNNs and Transformers](https://mlsanity.com/paper/2307.14367/) (2023)
- [ProtT3: Protein-to-Text Generation for Text-based Protein Understanding](https://mlsanity.com/paper/2405.12564/) (2024)
- [Recyclable Tuning for Continual Pre-training](https://mlsanity.com/paper/2305.08702/) (2023)
- [ConPET: Continual Parameter-Efficient Tuning for Large Language Models](https://mlsanity.com/paper/2309.14763/) (2023)
- [ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models](https://mlsanity.com/paper/2503.08179/) (2025)
- [PFMBench: Protein Foundation Model Benchmark](https://mlsanity.com/paper/2506.14796/) (2025)
- [Prot2Chat: Protein LLM with Early-Fusion of Text, Sequence and Structure](https://mlsanity.com/paper/2502.06846/) (2025)

## Abstract (arXiv)

Existing Protein Language Models (PLMs) often suffer from limited adaptability to multiple tasks and exhibit poor generalization across diverse biological contexts. In contrast, general-purpose Large Language Models (LLMs) lack the capability to interpret protein sequences and fall short in domain-specific knowledge, limiting their capacity for effective biosemantic reasoning. To combine the advantages of both, we propose BioBridge, a domain-adaptive continual pretraining framework for protein understanding. This framework employs Domain-Incremental Continual Pre-training (DICP) to infuse protein domain knowledge and general reasoning corpus into a LLM simultaneously, effectively mitigating catastrophic forgetting. Cross-modal alignment is achieved via a PLM-Projector-LLM pipeline, which maps protein sequence embeddings into the semantic space of the language model. Ultimately, an end-to-end optimization is adopted to uniformly support various tasks, including protein property prediction and knowledge question-answering. Our proposed BioBridge demonstrates performance comparable to that of mainstream PLMs on multiple protein benchmarks, such as EC and BindingDB. It also achieves results on par with LLMs on general understanding tasks like MMLU and RACE. This showcases its innovative advantage of combining domain-specific adaptability with general-purpose language competency.