A Multi-modal LLM-Knowledge Fusion Framework for Predicting Single-cell Genetic Perturbation Effects

scPert, a multi-modal transformer framework that integrates large language model embeddings with structured biological knowledge to predict single-cell transcriptomic responses to genetic perturbations. Through hierarchical fusion of knowledge graph representations, contextual embeddings from foundation models, and gene-specific encodings, scPert achieves significant performance improvements in both single-gene and combinatorial perturbations over existing methods. In cancer-relevant applications, scPert demonstrates the capability to reveal p53 pathway dynamics and immune checkpoint regulatory mechanisms. Systematic evaluation on 42 cancer dependency genes demonstrates scPert's ability to identify critical potential therapeutic targets. Our framework establishes a powerful computational foundation for virtual cell construction and accelerates drug target discovery.

Installation

Install PyG, and then do pip install scpert

Requirement

• anndata==0.9.2
• scanpy==1.9.8
• torch==2.3.0
• torch-geometric==2.6.1
• scvi-tools==0.20.3
• pandas==2.0.3
• numpy==1.24.4
• scipy==1.10.1
• cell-gears==0.0.2
• nvidia-cublas-cu12==12.1.3.1
• nvidia-cudnn-cu12==8.9.2.26
• flash_attn==0.2.8

Usage

embedding_dir: Directory containing gene embedding files (.npy)

data_path: Base directory for perturbation datasets

model_path: Pretrained model directory containing model.pt

pert_file:CSV file specifying perturbation pairs with columns: gene1,gene2

You can train scPert on your perturbation dataset simply running the Python script:

python ./scripts/train.py

You can use scPert to predict single gene or gene pairs perturbations by running the scripts:

python ./scripts/infer.py

Using API Interface:

from scpert import ProcePertdata,scPert

pertData = ProcePertdata(data_path)
pertData.load(DataName = 'norman')

# training
SCPert = scPert(pertData, device = 'cuda:0')
SCPert.model_initialize(hidden_size = 64)
SCPert.train(epochs = 20)

# saving or loading model
SCPert.save_model(model_path)
SCPert.load_pretrained(model_path)

# predict
SCPert.predict([['PRDM1+CBFA2T3'], ['FEV']])
SCPert.GI_predict(['CBL', 'CNN1'])

Cite Us

This work is currently under peer review.