KyGao

nanoT5

Fast & Simple repository for pre-training and fine-tuning T5-style models

MolGen

[ICLR 2024] Domain-Agnostic Molecular Generation with Chemical Feedback

alphafold_finetune

Python code for fine-tuning AlphaFold to perform protein-peptide binding predictions

AI2BMD

AI-powered ab initio biomolecular dynamics simulation

nanoGPT

The simplest, fastest repository for training/finetuning medium-sized GPTs.

AccGeoLDM

Accelerating Geometric Latent Diffusion Models for 3D Molecular Conformation Generation

sidechainnet

An all-atom protein structure dataset for machine learning.

llama3

The official Meta Llama 3 GitHub site

LDM-3DG

[ICLR 2024] "Latent 3D Graph Diffusion" by Yuning You, Ruida Zhou, Jiwoong Park, Haotian Xu, Chao Tian, Zhangyang Wang, Yang Shen

awesome-AI4MolConformation-MD

List of molecules (small molecules, RNA, peptide, protein, enzymes, antibody, and PPIs) conformations and molecular dynamics (force fields) using generative artificial intelligence and deep learning

iclr2024_learning_on_graphs

List of papers on ICLR 2024

Transformer-M

[ICLR 2023] One Transformer Can Understand Both 2D & 3D Molecular Data (official implementation)

DALL-E

PyTorch package for the discrete VAE used for DALL·E.

enhancing-transformers

An unofficial implementation of both ViT-VQGAN and RQ-VAE in Pytorch

VAR

[NeurIPS 2024 Oral][GPT beats diffusion🔥] [scaling laws in visual generation📈] Official impl. of "Visual Autoregressive Modeling: Scalable Image Generation via Next-Scale Prediction". An *ultra-simple, user-friendly yet state-of-the-art* codebase for autoregressive image generation!

tgt

Triplet Graph Transformer

BiPE

Two Stones Hit One Bird: Bilevel Positional Encoding for Better Length Extrapolation, ICML 2024

QuinNet

(NeurIPS 2023) QuinNet: Efficiently Incorporating Quintuple Interactions into Geometric Deep Learning Force Fields

sympy

A computer algebra system written in pure Python

ai4sci-research.github.io

DIG

A library for graph deep learning research

awesome-chemistry-datasets

overview of datasets for ML in chemistry

grok-1

Grok open release

DiffBindFR

Diffusion model based protein-ligand flexible docking method

PackDock

PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking

EDM-Dock

GeoDock

Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.

MARCEL

[ICLR 2024] MARCEL: Machine Learning over Molecular Conformer Ensembles

confidence-bootstrapping

Implementation of the Confidence Bootstrapping procedure for protein-ligand docking.

Awesome-Bio-Foundation-Models

A collection of awesome bio-foundation models, including protein, RNA, DNA, gene, single-cell, and so on.