Python Protein-structure-prediction Resources

directory-structure Print a directory tree structure in your Python code. Download You can simply: pip install directory-structure Or you can also: Cl

MVGCN MVGCN: a novel multi-view graph convolutional network (MVGCN) framework for link prediction in biomedical bipartite networks. Developer: Fu Hait

CodeForces This repository is dedicated to my Python solutions for CodeForces problems. Feel free to copy, contribute and/or comment. If you find any

The code for our paper "NSP-BERT: A Prompt-based Zero-Shot Learner Through an Original Pre-training Task —— Next Sentence Prediction"

WTW-Dataset This is an official implementation for the WTW Dataset in "Parsing Table Structures in the Wild " on ICCV 2021. Here, you can download the

Riiid Answer Correctness Prediction Introduction This repository is the code that placed 78th in Riiid Answer Correctness Prediction competition. Requ

AutoLay AutoLay: Benchmarking Monocular Layout Estimation Kaustubh Mani, N. Sai Shankar, J. Krishna Murthy, and K. Madhava Krishna Abstract In this pa

(ACMMM 2021 Oral) SfM Face Reconstruction Based on Massive Landmark Bundle Adjustment This repository shows two tasks: Face landmark detection and Fac

Using a predicted aligned error matrix corresponding to an AlphaFold2 model , returns a series of lists of residue indices, where each list corresponds to a set of residues clustering together into a pseudo-rigid domain.

(ACMMM 2021 Oral) SfM Face Reconstruction Based on Massive Landmark Bundle Adjustment This repository shows two tasks: Face landmark detection and Fac

Rotate-Yolov5 This repository is based on Ultralytics/yolov5, with adjustments to enable rotate prediction boxes. Section I. Description The codes are

Torch-RGCN Torch-RGCN is a PyTorch implementation of the RGCN, originally proposed by Schlichtkrull et al. in Modeling Relational Data with Graph Conv

High-Resolution Transformer for Dense Prediction Introduction This is the official implementation of High-Resolution Transformer (HRT). We present a H

It is expected to develop a machine learning model that can predict customers who will leave the company.

An Effective Loss Function for Generating 3D Models from Single 2D Image without Rendering Papers with code | Paper Nikola Zubić Pietro Lio University

Note: This is an alpha (preview) version which is still under refining. nn-Meter is a novel and efficient system to accurately predict the inference l

Paint Transformer: Feed Forward Neural Painting with Stroke Prediction [Paper] [PaddlePaddle Implementation] Homepage of paper: Paint Transformer: Fee

VideoBERT This repo reproduces the results of VideoBERT (https://arxiv.org/pdf/1904.01766.pdf). Inspiration was taken from https://github.com/MDSKUL/M

How to Become More Salient? Surfacing Representation Biases of the Saliency Prediction Model

Text2Event An implementation for Text2Event: Controllable Sequence-to-Structure Generation for End-to-end Event Extraction Please contact Yaojie Lu (@

Panoptic Segmentation Forecasting Colin Graber, Grace Tsai, Michael Firman, Gabriel Brostow, Alexander Schwing - CVPR 2021 [Link to paper] We propose

ASAP-Net This project implements ASAP-Net of paper ASAP-Net: Attention and Structure Aware Point Cloud Sequence Segmentation (BMVC2020). Overview We i

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

Trajectory Prediction using Equivariant Continuous Convolution (ECCO) This is the codebase for the ICLR 2021 paper Trajectory Prediction using Equivar

Inductive entity representations from text via link prediction This repository contains the code used for the experiments in the paper "Inductive enti

Geometric Vector Perceptron Code to accompany Learning from Protein Structure with Geometric Vector Perceptrons by B Jing, S Eismann, P Suriana, RJL T

ParallelFold Author: Bozitao Zhong This is a modified version of DeepMind's Alphafold2 to divide CPU part (MSA and template searching) and GPU part (p

Implementation of Deep-Forecast using PyTorch Deep Forecast: Deep Learning-based Spatio-Temporal Forecasting Adapted from original implementation Setu

Visual-Interaction-Networks An implementation of Deepmind visual interaction networks in Pytorch. Introduction For the purpose of understanding the ch

LogDeep is an open source deeplearning-based log analysis toolkit for automated anomaly detection.

PlaneTR: Structure-Guided Transformers for 3D Plane Recovery This is the official implementation of our ICCV 2021 paper News There maybe some bugs in

Evidential Deep Learning for Guided Molecular Property Prediction and Discovery Ava Soleimany*, Alexander Amini*, Samuel Goldman*, Daniela Rus, Sangee

Deep Two-View Structure-from-Motion Revisited This repository provides the code for our CVPR 2021 paper Deep Two-View Structure-from-Motion Revisited.

Triangle Multiplicative Module - Pytorch Implementation of the Triangle Multiplicative module, used in Alphafold2 as an efficient way to mix rows or c

A MLP-like Architecture for Dense Prediction (arXiv) Updates (22/07/2021) Initial release. Model Zoo We provide CycleMLP models pretrained on ImageNet

This is a fork of Fairseq(-py) with implementations of the following models: Pervasive Attention - 2D Convolutional Neural Networks for Sequence-to-Se

PDFSyntax A Python tool to generate a static HTML file that represents the internal structure of a PDF file At some point the low-level functions deve

Clockwork VAEs in JAX/Flax Implementation of experiments in the paper Clockwork Variational Autoencoders (project website) using JAX and Flax, ported

You Don't Need a Bigger Boat An end-to-end (Metaflow-based) implementation of an intent prediction flow for kids who can't MLOps good and wanna learn

Invariant Point Attention - Pytorch Implementation of Invariant Point Attention as a standalone module, which was used in the structure module of Alph

Pytorch-MBNet A pytorch implementation of MBNET: MOS PREDICTION FOR SYNTHESIZED SPEECH WITH MEAN-BIAS NETWORK Training To train a new model, please ru

ManhattanSLAM Authors: Raza Yunus, Yanyan Li and Federico Tombari ManhattanSLAM is a real-time SLAM library for RGB-D cameras that computes the camera

Using python and scikit-learn to make stock predictions

Plug-and-play Module Plug and play transformer you can find network structure and official complete code by clicking List The following is to quickly

PyKEEN PyKEEN (Python KnowlEdge EmbeddiNgs) is a Python package designed to train and evaluate knowledge graph embedding models (incorporating multi-m

A selection of State Of The Art research papers (and code) on human trajectory prediction (forecasting). Papers marked with [W] are workshop papers.

Beyond Image to Depth: Improving Depth Prediction using Echoes (CVPR 2021) Kranti Kumar Parida, Siddharth Srivastava, Gaurav Sharma. We address the pr

Self-supervised Graph-level Representation Learning with Local and Global Structure Introduction This project is an implementation of ``Self-supervise

Polygon-Yolov5 This repository is based on Ultralytics/yolov5, with adjustments to enable polygon prediction boxes. Section I. Description The codes a

README clDice - a Novel Topology-Preserving Loss Function for Tubular Structure Segmentation CVPR 2021 Authors: Suprosanna Shit and Johannes C. Paetzo

ProGen - (wip) Implementation and replication of ProGen, Language Modeling for Protein Generation, in Pytorch and Jax (the weights will be made easily

SSAN Introduction This is the pytorch implementation of the SSAN model (see our AAAI2021 paper: Entity Structure Within and Throughout: Modeling Menti

pure-predict speeds up and slims down machine learning prediction applications. It is a foundational tool for serverless inference or small batch prediction with popular machine learning frameworks like scikit-learn and fasttext. It implements the predict methods of these frameworks in pure Python.

A ready-to-use framework of latest models for structured (tabular) data learning with PyTorch. Applications include recommendation, CRT prediction, healthcare analytics, and etc.

DeepCDR Cancer Drug Response Prediction via a Hybrid Graph Convolutional Network This work has been accepted to ECCB2020 and was also published in the

FitVid Video Prediction Model Implementation of FitVid video prediction model in JAX/Flax. If you find this code useful, please cite it in your paper:

Stox ⚡ A Python Module For The Stock Market ⚡ A Module to predict the "close price" for the next day and give "technical analysis". It uses a Neural N

LibTraffic is a unified, flexible and comprehensive traffic prediction library, which provides researchers with a credibly experimental tool and a convenient development framework. Our library is implemented based on PyTorch, and includes all the necessary steps or components related to traffic prediction into a systematic pipeline.

MolRep: A Deep Representation Learning Library for Molecular Property Prediction Summary MolRep is a Python package for fairly measuring algorithmic p

Waymo motion prediction challenge 2021: 3rd place solution 📜 Technical report 🗨️ Presentation 🎉 Announcement 🛆Motion Prediction Channel Website 🛆

This is a release of our VIMPAC paper to illustrate the implementations. The pretrained checkpoints and scripts will be soon open-sourced in HuggingFace transformers.

One2Set This repository contains the code for our ACL 2021 paper “One2Set: Generating Diverse Keyphrases as a Set”. Our implementation is built on the

Markup is an online annotation tool that can be used to transform unstructured documents into structured formats for NLP and ML tasks, such as named-entity recognition. Markup learns as you annotate in order to predict and suggest complex annotations. Markup also provides integrated access to existing and custom ontologies, enabling the prediction and suggestion of ontology mappings based on the text you're annotating.

We envision models that are pre-trained on a vast range of domain-relevant tasks to become key for molecule property prediction. This repository aims to give easy access to state-of-the-art pre-trained models.

Habitat: A Runtime-Based Computational Performance Predictor for Deep Neural Network Training Habitat is a tool that predicts a deep neural network's

kaggle-hpa-2021-7th-place-solution Code for 7th place solution of Human Protein Atlas - Single Cell Classification on Kaggle. A description of the met

SolvationAnalysis The macroscopic behavior of a liquid is determined by its microscopic structure. For ionic systems, like batteries and many enzymes,

Denoising Diffusion Probabilistic Model for Proteins Implementation of Denoising Diffusion Probabilistic Model in Pytorch. It is a new approach to gen

SpanNER: Named EntityRe-/Recognition as Span Prediction Overview | Demo | Installation | Preprocessing | Prepare Models | Running | System Combination

[TensorFlow] Protein Interface Prediction using Graph Convolutional Networks Unofficial TensorFlow implementation of Protein Interface Prediction usin

Sentance Parser Executing the Program Make sure Python 3.6+ is installed. Install requirements $ pip install requirements.txt Run the program:

ProteinLM We pretrain protein language model based on Megatron-LM framework, and then evaluate the pretrained model results on TAPE (Tasks Assessing P

ProteinBERT - Pytorch (wip) Implementation of ProteinBERT in Pytorch. Original Repository Install $ pip install protein-bert-pytorch Usage import torc

SumGNN: Multi-typed Drug Interaction Prediction via Efficient Knowledge Graph Summarization This is the code for our paper ``SumGNN: Multi-typed Drug

This is the repository for The Python Workshop, published by Packt. It contains all the supporting project files necessary to work through the course from start to finish.

ProteinBERT - Pytorch (wip) Implementation of ProteinBERT in Pytorch. Original Repository Install $ pip install protein-bert-pytorch Usage import torc

Stox A Module to predict the "close price" for the next day and give "technical analysis". It uses a Neural Network and the LSTM algorithm to predict

ProteinBERT is a universal protein language model pretrained on ~106M proteins from the UniRef90 dataset. Through its Python API, the pretrained model can be fine-tuned on any protein-related task in a matter of minutes. Based on our experiments with a wide range of benchmarks, ProteinBERT usually achieves state-of-the-art performance. ProteinBERT is built on TenforFlow/Keras.

DeepFRI Deep functional residue identification Citing @article {Gligorijevic2019, author = {Gligorijevic, Vladimir and Renfrew, P. Douglas and Koscio

The code for our newly accepted paper in Pattern Recognition 2020: "U^2-Net: Going Deeper with Nested U-Structure for Salient Object Detection."

DRO: Deep Recurrent Optimizer for Structure-from-Motion This is the official PyTorch implementation code for DRO-sfm. For technical details, please re

TANL: Structured Prediction as Translation between Augmented Natural Languages Code for the paper "Structured Prediction as Translation between Augmen

Torch-Struct: Structured Prediction Library A library of tested, GPU implementations of core structured prediction algorithms for deep learning applic

Graph-Based Protein Design This repo contains code for Generative Models for Graph-Based Protein Design by John Ingraham, Vikas Garg, Regina Barzilay

[Unofficial code-base] NeRF--: Neural Radiance Fields Without Known Camera Parameters [ Project | Paper | Official code base ] ⬅️ Thanks the original

Beyond Homophily in Graph Neural Networks: Current Limitations and Effective Designs Jiong Zhu, Yujun Yan, Lingxiao Zhao, Mark Heimann, Leman Akoglu,

Combining Events and Frames using Recurrent Asynchronous Multimodal Networks for Monocular Depth Prediction This is the code for the paper Combining E

AdelaiDepth is an open source toolbox for monocular depth prediction.

Structural basis for solubility in protein expression systems Large-scale protein production for biotechnology and biopharmaceutical applications rely

|Anaconda|_ MAPIE - Model Agnostic Prediction Interval Estimator MAPIE allows you to easily estimate prediction intervals using your favourite sklearn

Structure-Aware-BART This repo contains codes for the following paper: Jiaao Chen, Diyi Yang:Structure-Aware Abstractive Conversation Summarization vi

TalkNet 2 [WIP] TalkNet 2: Non-Autoregressive Depth-Wise Separable Convolutional Model for Speech Synthesis with Explicit Pitch and Duration Predictio

Few-shot Graph Learning for Molecular Property Prediction Introduction This is the source code and dataset for the following paper: Few-shot Graph Lea

bulbea "Deep Learning based Python Library for Stock Market Prediction and Modelling." Table of Contents Installation Usage Documentation Dependencies

StockPredictions Use classic tricks, neural networks, deep learning, genetic programming and other methods to predict stock and market movements. Both

Stock Price Prediction of Apple Inc. Using Recurrent Neural Network OHLC Average Prediction of Apple Inc. Using LSTM Recurrent Neural Network Dataset:

IntroNeuralNetworks in Python: A Template Project IntroNeuralNetworks is a project that introduces neural networks and illustrates an example of how o

AIAlpha: Multilayer neural network architecture for stock return prediction This project is meant to be an advanced implementation of stacked neural n

MachineLearningStocks in python: a starter project and guide EDIT as of Feb 2021: MachineLearningStocks is no longer actively maintained MachineLearni

STAR-FC This code is the implementation for the CVPR 2021 paper "Structure-Aware Face Clustering on a Large-Scale Graph with 10^7 Nodes" 🌟 🌟 . 🎓 Re