Runze Ma's repositories
exper
Exper is a Python package designed for personal use by the author to streamline the execution of PyTorch-based deep learning experiments. This framework is specifically crafted to support Distributed Data Parallel (DDP) training and provides a convenient mechanism for saving experiment logs.
torchdrug
A powerful and flexible machine learning platform for drug discovery
biopython
Official git repository for Biopython (originally converted from CVS)
esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
GearNet
GearNet and Geometric Pretraining Methods for Protein Structure Representation Learning (https://arxiv.org/abs/2203.06125)
mlx-examples
Examples in the MLX framework
MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
nobelium
A static blog build on top of Notion and NextJS, deployed on Vercel.
openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
PaddleHelix
Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集
pymol-open-source
Open-source foundation of the user-sponsored PyMOL molecular visualization system.
pytorch_geometric
Graph Neural Network Library for PyTorch
RDKit
some scripts for RDKit