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Releases: Bitbol-Lab/ProteomeLM

ProteomeLM v1.0.0

15 Aug 14:47
@CyrilMa CyrilMa
v1.0.0
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ProteomeLM v1.0.0 Latest
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ProteomeLM v1.0.0 - First Stable Release

ProteomeLM is a transformer-based language model that reasons on entire proteomes to enable ultra-fast protein-protein interaction prediction and gene essentiality analysis across the tree of life.

Key Features

  • Proteome-scale modeling: First language model to process entire proteomes across species
  • Ultra-fast PPI screening: Screen whole interactomes orders of magnitude faster than coevolution methods
  • Attention-based insights: Captures PPIs in attention coefficients without explicit training

Pre-trained Models

All models available on Hugging Face Hub:

  • ProteomeLM-XS (5.66M params, 11.3MB) - Ultra-lightweight
  • ProteomeLM-S (36.9M params, 73.8MB) - Speed/accuracy balance
  • ProteomeLM-M (112M params, 225MB) - Most applications
  • ProteomeLM-L (328M params, 656MB) - Maximum performance

Quick Start

git clone https://github.com/Bitbol-Lab/ProteomeLM.git
cd ProteomeLM
pip install -r requirements.txt

# Interactive PPI prediction
jupyter notebook notebooks/ppi_prediction.ipynb
Assets 3
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