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

deep_image_prior_extension

Code for "Is Deep Image Prior in Need of a Good Education?" Project page: https://jleuschn.github.io/docs.educated_deep_image_prior/. Supplementary Ma

7 Jan 09, 2022

HALO: A Skeleton-Driven Neural Occupancy Representation for Articulated Hands

HALO: A Skeleton-Driven Neural Occupancy Representation for Articulated Hands Oral Presentation, 3DV 2021 Korrawe Karunratanakul, Adrian Spurr, Zicong

43 Oct 07, 2022

Explainable Zero-Shot Topic Extraction

Zero-Shot Topic Extraction with Common-Sense Knowledge Graph This repository contains the code for reproducing the results reported in the paper "Expl

56 Dec 14, 2022

Instance-wise Occlusion and Depth Orders in Natural Scenes (CVPR 2022)

Instance-wise Occlusion and Depth Orders in Natural Scenes Official source code. Appears at CVPR 2022 This repository provides a new dataset, named In

27 Dec 27, 2022

Python3 Implementation of (Subspace Constrained) Mean Shift Algorithm in Euclidean and Directional Product Spaces

(Subspace Constrained) Mean Shift Algorithms in Euclidean and/or Directional Product Spaces This repository contains Python3 code for the mean shift a

0 Oct 19, 2021

VISNOTATE: An Opensource tool for Gaze-based Annotation of WSI Data

VISNOTATE: An Opensource tool for Gaze-based Annotation of WSI Data Introduction Requirements Installation and Setup Supported Hardware and Software R

1 Jun 14, 2022

Rasterize with the least efforts for researchers.

utils3d Rasterize and do image-based 3D transforms with the least efforts for researchers. Based on numpy and OpenGL. It could be helpful when you wan

8 Dec 15, 2022

VLG-Net: Video-Language Graph Matching Networks for Video Grounding

VLG-Net: Video-Language Graph Matching Networks for Video Grounding Introduction Official repository for VLG-Net: Video-Language Graph Matching Networ

25 Dec 04, 2022

PyTorch implementation of UPFlow (unsupervised optical flow learning)

UPFlow: Upsampling Pyramid for Unsupervised Optical Flow Learning By Kunming Luo, Chuan Wang, Shuaicheng Liu, Haoqiang Fan, Jue Wang, Jian Sun Megvii

87 Dec 20, 2022

Official code for 'Robust Siamese Object Tracking for Unmanned Aerial Manipulator' and offical introduction to UAMT100 benchmark

SiamSA: Robust Siamese Object Tracking for Unmanned Aerial Manipulator Demo video 📹 Our video on Youtube and bilibili demonstrates the evaluation of

12 Dec 18, 2022

Deep Ensembling with No Overhead for either Training or Testing: The All-Round Blessings of Dynamic Sparsity

[ICLR 2022] Deep Ensembling with No Overhead for either Training or Testing: The All-Round Blessings of Dynamic Sparsity by Shiwei Liu, Tianlong Chen, Zahra Atashgahi, Xiaohan Chen, Ghada Sokar, Elen

18 Dec 31, 2022

Dense Prediction Transformers

Vision Transformers for Dense Prediction This repository contains code and models for our paper: Vision Transformers for Dense Prediction René Ranftl,

1.3k Dec 28, 2022

Deep Learning as a Cloud API Service.

Deep API Deep Learning as Cloud APIs. This project provides pre-trained deep learning models as a cloud API service. A web interface is available as w

4 Jan 06, 2023

An Empirical Investigation of Model-to-Model Distribution Shifts in Trained Convolutional Filters

CNN-Filter-DB An Empirical Investigation of Model-to-Model Distribution Shifts in Trained Convolutional Filters Paul Gavrikov, Janis Keuper Paper: htt

18 Dec 30, 2022

ML course - EPFL Machine Learning Course, Fall 2021

EPFL Machine Learning Course CS-433 Machine Learning Course, Fall 2021 Repository for all lecture notes, labs and projects - resources, code templates

1k Jan 04, 2023

Py-faster-rcnn - Faster R-CNN (Python implementation)

py-faster-rcnn has been deprecated. Please see Detectron, which includes an implementation of Mask R-CNN. Disclaimer The official Faster R-CNN code (w

7.8k Jan 03, 2023

SAGE: Sensitivity-guided Adaptive Learning Rate for Transformers

SAGE: Sensitivity-guided Adaptive Learning Rate for Transformers This repo contains our codes for the paper "No Parameters Left Behind: Sensitivity Gu

23 Nov 07, 2022

This codebase proposes modular light python and pytorch implementations of several LiDAR Odometry methods

pyLiDAR-SLAM This codebase proposes modular light python and pytorch implementations of several LiDAR Odometry methods, which can easily be evaluated

208 Dec 16, 2022

LAMDA: Label Matching Deep Domain Adaptation

LAMDA: Label Matching Deep Domain Adaptation This is the implementation of the paper LAMDA: Label Matching Deep Domain Adaptation which has been accep

9 Sep 06, 2022

Explaining neural decisions contrastively to alternative decisions.

Contrastive Explanations for Model Interpretability This is the repository for the paper "Contrastive Explanations for Model Interpretability", about

16 Oct 16, 2022