Implementation of the GVP-Transformer, which was used in the paper "Learning inverse folding from millions of predicted structures" for de novo protein design alongside Alphafold2

Overview

GVP Transformer (wip)

Implementation of the GVP-Transformer, which was used in the paper Learning inverse folding from millions of predicted structures for de novo protein design alongside Alphafold2. The base neural network consists of an invariant geometric network, GVP, combined with an encoder / decoder transformer.

It will also offer the tools for enabling autoregressive infilling

Citations

@article {Hsu2022.04.10.487779,
    author  = {Hsu, Chloe and Verkuil, Robert and Liu, Jason and Lin, Zeming and Hie, Brian and Sercu, Tom and Lerer, Adam and Rives, Alexander},
    title   = {Learning inverse folding from millions of predicted structures},
    elocation-id = {2022.04.10.487779},
    year    = {2022},
    doi     = {10.1101/2022.04.10.487779},
    publisher = {Cold Spring Harbor Laboratory},
    URL     = {https://www.biorxiv.org/content/early/2022/04/10/2022.04.10.487779},
    eprint  = {https://www.biorxiv.org/content/early/2022/04/10/2022.04.10.487779.full.pdf},
    journal = {bioRxiv}
}
Owner
Phil Wang
Working with Attention. It's all we need
Phil Wang
BasicVSR++: Improving Video Super-Resolution with Enhanced Propagation and Alignment

BasicVSR++: Improving Video Super-Resolution with Enhanced Propagation and Alignment

Holy Wu 35 Jan 01, 2023
Offical implementation for "Trash or Treasure? An Interactive Dual-Stream Strategy for Single Image Reflection Separation".

Trash or Treasure? An Interactive Dual-Stream Strategy for Single Image Reflection Separation (NeurIPS 2021) by Qiming Hu, Xiaojie Guo. Dependencies P

Qiming Hu 31 Dec 20, 2022
This code reproduces the results of the paper, "Measuring Data Leakage in Machine-Learning Models with Fisher Information"

Fisher Information Loss This repository contains code that can be used to reproduce the experimental results presented in the paper: Awni Hannun, Chua

Facebook Research 43 Dec 30, 2022
Implement the Pareto Optimizer and pcgrad to make a self-adaptive loss for multi-task

multi-task_losses_optimizer Implement the Pareto Optimizer and pcgrad to make a self-adaptive loss for multi-task 已经实验过了,不会有cuda out of memory情况 ##Par

14 Dec 25, 2022
Official PyTorch implementation of the paper "Deep Constrained Least Squares for Blind Image Super-Resolution", CVPR 2022.

Deep Constrained Least Squares for Blind Image Super-Resolution [Paper] This is the official implementation of 'Deep Constrained Least Squares for Bli

MEGVII Research 141 Dec 30, 2022
113 Nov 28, 2022
Deep Q-learning for playing chrome dino game

[PYTORCH] Deep Q-learning for playing Chrome Dino

Viet Nguyen 68 Dec 05, 2022
[CVPR 2022] Structured Sparse R-CNN for Direct Scene Graph Generation

Structured Sparse R-CNN for Direct Scene Graph Generation Our paper Structured Sparse R-CNN for Direct Scene Graph Generation has been accepted by CVP

Multimedia Computing Group, Nanjing University 44 Dec 23, 2022
The official implementation code of "PlantStereo: A Stereo Matching Benchmark for Plant Surface Dense Reconstruction."

PlantStereo This is the official implementation code for the paper "PlantStereo: A Stereo Matching Benchmark for Plant Surface Dense Reconstruction".

Wang Qingyu 14 Nov 28, 2022
Local Attention - Flax module for Jax

Local Attention - Flax Autoregressive Local Attention - Flax module for Jax Install $ pip install local-attention-flax Usage from jax import random fr

Phil Wang 16 Jun 16, 2022
Earthquake detection via fiber optic cables using deep learning

Earthquake detection via fiber optic cables using deep learning Author: Fantine Huot Getting started Update the submodules After cloning the repositor

Fantine 4 Nov 30, 2022
we propose a novel deep network, named feature aggregation and refinement network (FARNet), for the automatic detection of anatomical landmarks.

Feature Aggregation and Refinement Network for 2D Anatomical Landmark Detection Overview Localization of anatomical landmarks is essential for clinica

aoyueyuan 0 Aug 28, 2022
Object detection evaluation metrics using Python.

Object detection evaluation metrics using Python.

Louis Facun 2 Sep 06, 2022
Colab notebook for openai/glide-text2im.

GLIDE text2im on Colab This repository provides a Colab notebook to produce images conditioned on text prompts with GLIDE [1]. Usage Run text2im.ipynb

Wok 19 Oct 19, 2022
Go from graph data to a secure and interactive visual graph app in 15 minutes. Batteries-included self-hosting of graph data apps with Streamlit, Graphistry, RAPIDS, and more!

✔️ Linux ✔️ OS X ❌ Windows (#39) Welcome to graph-app-kit Turn your graph data into a secure and interactive visual graph app in 15 minutes! Why This

Graphistry 107 Jan 02, 2023
Learning Optical Flow from a Few Matches (CVPR 2021)

Learning Optical Flow from a Few Matches This repository contains the source code for our paper: Learning Optical Flow from a Few Matches CVPR 2021 Sh

Shihao Jiang (Zac) 159 Dec 16, 2022
OMAMO: orthology-based model organism selection

OMAMO: orthology-based model organism selection OMAMO is a tool that suggests the best model organism to study a biological process based on orthologo

Dessimoz Lab 5 Apr 22, 2022
LBK 35 Dec 26, 2022
How Effective is Incongruity? Implications for Code-mix Sarcasm Detection.

Code for the paper: How Effective is Incongruity? Implications for Code-mix Sarcasm Detection - ICON ACL 2021

2 Jun 05, 2022
Customer-Transaction-Analysis - This analysis is based on a synthesised transaction dataset containing 3 months worth of transactions for 100 hypothetical customers.

Customer-Transaction-Analysis - This analysis is based on a synthesised transaction dataset containing 3 months worth of transactions for 100 hypothetical customers. It contains purchases, recurring

Ayodeji Yekeen 1 Jan 01, 2022