RefineGNN - Iterative refinement graph neural network for antibody sequence-structure co-design (RefineGNN)

Last update: Dec 31, 2022

Related tags

Deep Learning RefineGNN

Overview

Iterative refinement graph neural network for antibody sequence-structure co-design (RefineGNN)

This is the implementation of our ICLR 2022 paper: https://arxiv.org/pdf/2110.04624.pdf

Warning: this repo is still under construction...

Language model and CDR structure prediction (Section 4.1)

Antibody structure data is retreived from the Structural Antibody Database (SAbDab). The training, validation, and test sets are provided in data/sabdab. Please decompress the files in that folder. To train a generative model for CDR-H3, please run

python ab_train.py --cdr_type 3

Antigen-binding antibody design (Section 4.2)

antibody-antigen binding data is provided in data/rabd. To train a generative model, please run

python ab_train.py --train_path data/rabd/train.jsonl --val_path data/rabd/val.jsonl --test_path data/rabd/test.jsonl

Owner

Wengong Jin

GitHub Repository

PyTorchVideo is a deeplearning library with a focus on video understanding work

PyTorchVideo is a deeplearning library with a focus on video understanding work. PytorchVideo provides resusable, modular and efficient components needed to accelerate the video understanding researc

2.7k Jan 07, 2023

Cluttered MNIST Dataset

Cluttered MNIST Dataset A setup script will download MNIST and produce mnist/*.t7 files: luajit download_mnist.lua Example usage: local mnist_clutter

50 Jul 12, 2022

Google Landmark Recogntion and Retrieval 2021 Solutions

Google Landmark Recogntion and Retrieval 2021 Solutions In this repository you can find solution and code for Google Landmark Recognition 2021 and Goo

5 Nov 25, 2022

Pyramid Pooling Transformer for Scene Understanding

Pyramid Pooling Transformer for Scene Understanding Requirements: torch 1.6+ torchvision 0.7.0 timm==0.3.2 Validated on torch 1.6.0, torchvision 0.7.0

119 Dec 29, 2022

Source code for Adaptively Calibrated Critic Estimates for Deep Reinforcement Learning

Adaptively Calibrated Critic Estimates for Deep Reinforcement Learning Official implementation of ACC, described in the paper "Adaptively Calibrated C

3 Sep 16, 2022

Official code for Next Check-ins Prediction via History and Friendship on Location-Based Social Networks (MDM 2018)

MUC Next Check-ins Prediction via History and Friendship on Location-Based Social Networks (MDM 2018) Performance Details for Accuracy: | Dataset

3 Oct 09, 2022

Code accompanying the paper "ProxyFL: Decentralized Federated Learning through Proxy Model Sharing"

ProxyFL Code accompanying the paper "ProxyFL: Decentralized Federated Learning through Proxy Model Sharing" Authors: Shivam Kalra*, Junfeng Wen*, Jess

14 Dec 06, 2022

It's A ML based Web Site build with python and Django to find the breed of the dog

ML-Based-Dog-Breed-Identifier This is a Django Based Web Site To Identify the Breed of which your DOG belogs All You Need To Do is to Follow These Ste

2 Oct 12, 2022

Repository of continual learning papers

Continual learning paper repository This repository contains an incomplete (but dynamically updated) list of papers exploring continual learning in ma

29 Jan 05, 2023

ReLoss - Official implementation for paper "Relational Surrogate Loss Learning" ICLR 2022

Relational Surrogate Loss Learning (ReLoss) Official implementation for paper "R

31 Nov 22, 2022

Code for the SIGGRAPH 2022 paper "DeltaConv: Anisotropic Operators for Geometric Deep Learning on Point Clouds."

DeltaConv [Paper] [Project page] Code for the SIGGRAPH 2022 paper "DeltaConv: Anisotropic Operators for Geometric Deep Learning on Point Clouds" by Ru

98 Nov 26, 2022

Visual dialog agents with pre-trained vision-and-language encoders.

Learning Better Visual Dialog Agents with Pretrained Visual-Linguistic Representation Or READ-UP: Referring Expression Agent Dialog with Unified Pretr

7 Oct 08, 2022

Rax is a Learning-to-Rank library written in JAX

🦖 Rax: Composable Learning to Rank using JAX Rax is a Learning-to-Rank library written in JAX. Rax provides off-the-shelf implementations of ranking

247 Dec 27, 2022

Physical Anomalous Trajectory or Motion (PHANTOM) Dataset

Physical Anomalous Trajectory or Motion (PHANTOM) Dataset Description This dataset contains the six different classes as described in our paper[]. The

0 Dec 16, 2021

Patches desktop steam to look like the new steamdeck ui.

steam_deck_ui_patch The Deck UI patch will patch the regular desktop steam to look like the brand new SteamDeck UI. This patch tool currently works on

3 Aug 29, 2022

QilingLab challenge writeup

qiling lab writeup shielder 在 2021/7/21 發布了 QilingLab 來幫助學習 qiling framwork 的用法，剛好最近有用到，順手解了一下並寫了一下 writeup。前情提要 Qiling 是一款功能強大的模擬框架，和 qemu user mode

17 Nov 17, 2022

A highly efficient, fast, powerful and light-weight anime downloader and streamer for your favorite anime.

AnimDL - Download & Stream Your Favorite Anime AnimDL is an incredibly powerful tool for downloading and streaming anime. Core features Abuses the dev

759 Jan 08, 2023

Torchlight2 lan game server tool - A message forwarding tool for Torchlight 2 lan game

Torchlight 2 Lan Game Server Tool A message forwarding tool for Torchlight 2 lan

3 Nov 01, 2022

Code for: Gradient-based Hierarchical Clustering using Continuous Representations of Trees in Hyperbolic Space. Nicholas Monath, Manzil Zaheer, Daniel Silva, Andrew McCallum, Amr Ahmed. KDD 2019.

gHHC Code for: Gradient-based Hierarchical Clustering using Continuous Representations of Trees in Hyperbolic Space. Nicholas Monath, Manzil Zaheer, D

35 Nov 16, 2022

Code for "PVNet: Pixel-wise Voting Network for 6DoF Pose Estimation" CVPR 2019 oral

Good news! We release a clean version of PVNet: clean-pvnet, including how to train the PVNet on the custom dataset. Use PVNet with a detector. The tr

722 Dec 27, 2022