This repository provides a minimal example of distributed training using PyTorch's DistributedDataParallel on a Slurm-managed cluster

Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)

Prediction of binding residues for metal ions, nucleic acids, and small molecules.

Official repository for the paper "Tranception: Protein Fitness Prediction with Autoregressive Transformers and Inference-time Retrieval"

Code and Data for the paper: Multi-level Protein Structure Pre-training with Prompt Learning [ICLR 2023]

PyTorch implementation of the GradNorm

Google Research

Multi-Task Deep Neural Networks for Natural Language Understanding

A practical implementation of GradNorm, Gradient Normalization for Adaptive Loss Balancing, in Pytorch

This in my Demo of Chen et al. "GradNorm: Gradient Normalization for Adaptive Loss Balancing in Deep Multitask Networks" ICML 2018

This is the official repository of Prot2Token paper.

A Protein Large Language Model for Multi-Task Protein Language Processing

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

S-PLM: Structure-aware Protein Language Model via Contrastive Learning between Sequence and Structure

scBSP is a specialized package designed for processing biological data, specifically in the analysis of gene expression and cell coordinates. It efficiently computes p-values for a given set of gen…

Graph Network for protein-protein interface including language model features

A program fror inter-protein contact prediction from structures of interacting proteins

Run AlphaFold2 (and multimer) step by step

Open source code for AlphaFold 2.

State-of-the-Art Deep Learning scripts organized by models - easy to train and deploy with reproducible accuracy and performance on enterprise-grade infrastructure.

A dependency-free cross-platform swiss army knife for PDB files.

A Python 3 script for cleaning up the PDB file

A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files

A PyTorch implementation of "SimGNN: A Neural Network Approach to Fast Graph Similarity Computation" (WSDM 2019).

code for the SE3 Transformers paper: https://arxiv.org/abs/2006.10503