README.md · hicai-zju/InstructBioMol-base at main

metadata

license: mit

InstructBioMol: A Multimodal LLM for Biomolecule Understanding and Design

Paper • Project • Quickstart • Citation

Model Description

InstructBioMol is a multimodal large language model that bridges natural language with biomolecules (proteins and small molecules). It achieves any-to-any alignment between natural language, molecules, and proteins through comprehensive instruction tuning.

For detailed information, please refer to our paper and code repository.

Released Variants

Model Name	Stage	Multimodal	Description
InstructBioMol-base (This Model)	Pretraining	❎	Continual pretrained model on molecular sequences, protein sequences, and scientific literature.
InstructBioMol-instruct-stage1	Instruction tuning (stage 1)	✅	Stage1 instruction-tuned model with biomolecular multimodal processing capabilities. (e.g., 3D molecules/proteins)
InstructBioMol-instruct	Instruction tuning (stage 1 and 2)	✅	Fully instruction-tuned model (stage1 & stage2) with biomolecular multimodal processing capabilities (e.g., 3D molecules/proteins)

Training Details

Base Architecture: LLaMA-2-7B

Training Data:

1. Molecular Sequences:

Format: SELFIES
Source: PubChem
Size: 100 million (100M) entries

2. Protein Sequences:

Format: FASTA-like, prefixed with  (e.g., MALW...).
Source: UniRef50
Size: 59 million (59M) entries

3. Natural Language Texts:

Source: Abstracts from PubMed, bioRxiv, and ChemRxiv
Size: 6 million (6M) abstracts

Training Objective: Causal language modeling (self-supervised)

Quick Start

from transformers import LlamaForCausalLM, LlamaTokenizer
import torch

model_name = "hicai-zju/InstructBioMol-base"  
tokenizer = LlamaTokenizer.from_pretrained(model_name)
model = LlamaForCausalLM.from_pretrained(model_name, device_map="cuda:0")

prompt = "<p>M"  # protein sequence
# prompt = "[C]"  # molecule sequence
# prompt = 'Scientific'  # natural language
inputs = tokenizer(prompt, return_tensors="pt").to(model.device)

with torch.no_grad():
    outputs = model.generate(
        **inputs,
        max_new_tokens=100, 
        temperature=0.7,     
        top_p=0.9,          
        do_sample=True     
    )

generated_text = tokenizer.decode(outputs[0], skip_special_tokens=True)
print(generated_text)

Citation

@article{zhuang2025advancing,
  author       = {Xiang Zhuang and
                  Keyan Ding and
                  Tianwen Lyu and
                  Yinuo Jiang and
                  Xiaotong Li and
                  Zhuoyi Xiang and
                  Zeyuan Wang and
                  Ming Qin and
                  Kehua Feng and
                  Jike Wang and
                  Qiang Zhang and
                  Huajun Chen},
  title={Advancing biomolecular understanding and design following human instructions},
  journal={Nature Machine Intelligence},
  pages={1--14},
  year={2025},
  publisher={Nature Publishing Group UK London}
}