150 Open source projects that are alternatives of or similar to ProteinGCN

This project is a collection of recent research in areas such as new infrastructure and urban computing, including white papers, academic papers, AI lab and dataset etc.

ProtVec can be used in protein interaction predictions, structure prediction, and protein data visualization.

📚 🔬 PIA - Protein Inference Algorithms

A graph-based deep learning framework for life science

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

Awesome Graph Self-Supervised Learning

From Random Walks to Transformer for Learning Node Embeddings (ECML-PKDD 2020) (In Pytorch and Tensorflow)

Pytorch differentiable molecular dynamics

[ACL 2021] KGPool: Dynamic Knowledge Graph Context Selection for Relation Extraction

Implementation of "GNNAutoScale: Scalable and Expressive Graph Neural Networks via Historical Embeddings" in PyTorch

This is an open-source toolkit for Heterogeneous Graph Neural Network(OpenHGNN) based on DGL.

Code of the NeurIPS 2021 paper: Language and Visual Entity Relationship Graph for Agent Navigation

Geometric Deep Learning for Flux

Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Joint collaboration between the Marks lab and the OATML group.

GemNet model in PyTorch, as proposed in "GemNet: Universal Directional Graph Neural Networks for Molecules" (NeurIPS 2021)

Differentiable molecular simulation of proteins with a coarse-grained potential

Resources for the paper titled "EEG-GCNN: Augmenting Electroencephalogram-based Neurological Disease Diagnosis using a Domain-guided Graph Convolutional Neural Network". Accepted for publication (with an oral spotlight!) at ML4H Workshop, NeurIPS 2020.

Summary of social recommendation papers and codes

This is a paper list about Resource Allocation in Network Functions Virtualization (NFV) and Software-Defined Networking (SDN).

Context-Aware Visual Compatibility Prediction (https://arxiv.org/abs/1902.03646)

Pytorch/Python3 implementation of DeepAccNet, protein model accuracy evaluator.

[IJCAI 2019] Source code and datasets for "Hierarchical Graph Convolutional Networks for Semi-supervised Node Classification"

Official implementation of Neural Bellman-Ford Networks (NeurIPS 2021)

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

Code for the paper 'An Efficient Graph Convolutional Network Technique for the Travelling Salesman Problem' (INFORMS Annual Meeting Session 2019)

Implementation of the KDD 2020 paper "Graph Structure Learning for Robust Graph Neural Networks"

Graph-based machine learning for chemical property prediction

waka waka

A Context-aware Visual Attention-based training pipeline for Object Detection from a Webpage screenshot!

Code for the CHAMPS Predicting Molecular Properties Kaggle competition

🔨 🍇 💻 🚀 GraphScope: A One-Stop Large-Scale Graph Computing System from Alibaba 来自阿里巴巴的一站式大规模图计算系统 图分析 图查询 图机器学习

The official code and datasets for "Zero-Shot Multi-View Indoor Localization via Graph Location Networks" (ACMMM 2020)

Smart Contract Vulnerability Detection Using Graph Neural Networks (IJCAI-20 Accepted)

codes of Deep Spatio-Temporal Graph Convolutional Network for Traffic Accident Prediction

The PyTorch implementation of Directed Graph Contrastive Learning (DiGCL), NeurIPS-2021

Visualization tool for Graph Neural Networks

🧬 An R package for visualizing molecular data in 3D

Demo of RouteNet in ACM SIGCOMM'19

Message Passing Neural Networks for Simplicial and Cell Complexes

Code for the paper "How Attentive are Graph Attention Networks?" (ICLR'2022)

Supervised community detection with line graph neural networks

Making self-supervised learning work on molecules by using their 3D geometry to pre-train GNNs. Implemented in DGL and Pytorch Geometric.

⚡ Using deep learning (MLP, CNN, Graph CNN) to classify text in TensorFlow.

A suite of tools to explore protein structures with Protein Blocks 🐍

Tensorflow Implementation of the paper "Topology Adaptive Graph Convolutional Networks" (Du et al., 2017)

Knowledge Graph Alignment Network with Gated Multi-hop Neighborhood Aggregation, AAAI 2020

Locally Private Graph Neural Networks (ACM CCS 2021)

Revisiting Graph based Collaborative Filtering: A Linear Residual Graph Convolutional Network Approach, AAAI2020

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

Official git repository for Biopython (originally converted from CVS)

A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

[COLING 2020] Jointly Learning Aspect-Focused and Inter-Aspect Relations with Graph Convolutional Networks for Aspect Sentiment Analysis

web-based protein structure viewer and analysis tool interactively or in batch mode

This is a Pytorch implementation of GraphLIME

Official code for "InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization" (ICLR 2020, spotlight)

A simplified drug discovery pipeline -- generating SMILE molecular with AlphaSMILES, predicting protein structure with AlphaFold, and checking the druggability with fpocket/Amber.

Evolutionary couplings from protein and RNA sequence alignments

Implementation of TheWebConf 2021 -- Few-shot Network Anomaly Detection via Cross-network Meta-learning

Official repository for the paper "Learning Local Neighboring Structure for Robust 3D Shape Representation"

A spherical CNN for weather forecasting