qshao's repositories
ArchR
ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
Awesome-Diffusion-Models
A collection of resources and papers on Diffusion Models
awesome-graph-transformer
Papers about graph transformers.
Awesome-SBDD
Papers about Structure-based Drug Design (SBDD)
ColossalAI
Colossal-AI: A Unified Deep Learning System for Big Model Era
d2l-en
Interactive deep learning book with multi-framework code, math, and discussions. Adopted at 300 universities from 55 countries including Stanford, MIT, Harvard, and Cambridge.
ddim
Denoising Diffusion Implicit Models
dpm-solver
Official code for "DPM-Solver: A Fast ODE Solver for Diffusion Probabilistic Model Sampling in Around 10 Steps" (Neurips 2022 Oral)
DynamicBind
repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model
DynamO
An event-driven particle simulator and visualisation code. Please see the website below for more information.
GNN_IAC
This repository contains the training routines and the experiments presented in the paper "Graph Neural Networks for the prediction of infinite dilution activity coefficients"
gromacs
Public/backup repository of the gromacs molecular simulation toolkit
learning3d
This is a complete package of recent deep learning methods for 3D point clouds in pytorch (with pretrained models).
Machine-learning-for-proteins
Listing of papers about machine learning for proteins.
nanoGPT
The simplest, fastest repository for training/finetuning medium-sized GPTs.
NeuralPLexer
NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
OLMo
Modeling, training, eval, and inference code for OLMo
openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
papers_for_protein_design_using_DL
List of papers about Proteins Design using Deep Learning
plumed2
Development version of plumed 2
S-PLM
S-PLM: Structure-aware Protein Language Model via Contrastive Learning between Sequence and Structure
stable-baselines3
PyTorch version of Stable Baselines, reliable implementations of reinforcement learning algorithms.
TankBind
Open source code for TankBind. Galixir Tenchnologies
Transformer-Explainability
[CVPR 2021] Official PyTorch implementation for Transformer Interpretability Beyond Attention Visualization, a novel method to visualize classifications by Transformer based networks.
tuning_playbook
A playbook for systematically maximizing the performance of deep learning models.
webdataset
A high-performance Python-based I/O system for large (and small) deep learning problems, with strong support for PyTorch.