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GitHub topics: graph-transformer

mims-harvard/ClinVec

ClinVec: Unified Embeddings of Clinical Codes Enable Knowledge-Grounded AI in Medicine

Language: Jupyter Notebook - Size: 17.5 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 59 - Forks: 6

BorgwardtLab/NeuralWalker

Official Pytorch implementation of NeuralWalker (ICLR 2025)

Language: Python - Size: 26.1 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 33 - Forks: 2

wehos/awesome-graph-transformer

Papers about graph transformers.

Size: 82 KB - Last synced at: 5 days ago - Pushed at: 3 months ago - Stars: 891 - Forks: 75

iMoonLab/DHGFormer

DHGFormer: Dynamic Hierarchical Graph Transformer for Disorder Brain Disease Diagnosis

Language: Python - Size: 4.28 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 2 - Forks: 0

HUBioDataLab/DeepResponse Fork of burakcan-izmirli/DeepResponse

DeepResponse: Large Scale Prediction of Cancer Cell Line Drug Response with Deep Learning Based Pharmacogenomic Modelling

Language: Python - Size: 322 KB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 1 - Forks: 2

soda-inria/carte

Repository for CARTE: Context-Aware Representation of Table Entries

Language: Python - Size: 161 MB - Last synced at: 4 days ago - Pushed at: 3 months ago - Stars: 130 - Forks: 14

burakcan-izmirli/DeepResponse

DeepResponse: Large Scale Prediction of Cancer Cell Line Drug Response with Deep Learning Based Pharmacogenomic Modelling

Language: Python - Size: 322 KB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 6 - Forks: 3

qitianwu/DIFFormer

The official implementation for ICLR23 spotlight paper "DIFFormer: Scalable (Graph) Transformers Induced by Energy Constrained Diffusion"

Language: Python - Size: 125 KB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 299 - Forks: 32

azminewasi/Awesome-Graph-Research-ICLR2024

It is a comprehensive resource hub compiling all graph papers accepted at the International Conference on Learning Representations (ICLR) in 2024.

Size: 1.93 MB - Last synced at: 1 day ago - Pushed at: 8 months ago - Stars: 95 - Forks: 6

lias-laboratory/biogitom

BioGITOM: Matching Biomedical Ontologies with Graph Isomorphism Transformer

Language: Jupyter Notebook - Size: 8.3 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 16 - Forks: 0

graphdeeplearning/graphtransformer

Graph Transformer Architecture. Source code for "A Generalization of Transformer Networks to Graphs", DLG-AAAI'21.

Language: Python - Size: 170 KB - Last synced at: 25 days ago - Pushed at: almost 4 years ago - Stars: 971 - Forks: 141

willyfh/graph-transformer

An unofficial implementation of Graph Transformer (Masked Label Prediction: Unified Message Passing Model for Semi-Supervised Classification) - IJCAI 2021

Language: Python - Size: 483 KB - Last synced at: 18 days ago - Pushed at: about 1 year ago - Stars: 33 - Forks: 6

Zehong-Wang/G2PM

Scalable Graph Generative Modeling via Substructure Sequences

Language: Python - Size: 2.7 MB - Last synced at: 10 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

messierandromeda/Bachelor-Thesis

This repository contains the graph neural networks built with PyTorch Geometric that are used in my bachelor thesis: "Drug-Drug GNN for Drug Combination Prediction and Explanations".

Language: Jupyter Notebook - Size: 2.94 MB - Last synced at: 21 days ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

BorgwardtLab/SAT

Official Pytorch code for Structure-Aware Transformer.

Language: Python - Size: 2.59 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 258 - Forks: 41

lsj2408/Transformer-M

[ICLR 2023] One Transformer Can Understand Both 2D & 3D Molecular Data (official implementation)

Language: Python - Size: 5.45 MB - Last synced at: about 2 months ago - Pushed at: about 2 years ago - Stars: 209 - Forks: 26

NSLab-CUK/Community-aware-Graph-Transformer

Community-aware Graph Transformer (CGT) is a novel Graph Transformer model that utilizes community structures to address node degree biases in message-passing mechanism and developed by NS Lab @ CUK based on pure PyTorch backend.

Language: Python - Size: 183 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 13 - Forks: 2

GRAPH-0/RGTN-NIE

Implementation for the paper: Representation Learning on Knowledge Graphs for Node Importance Estimation

Language: Python - Size: 12.6 MB - Last synced at: 2 months ago - Pushed at: almost 3 years ago - Stars: 37 - Forks: 14

yi-ding-cs/EmT

[TNNLS-2025] This is the pytorch implementation of EmT, a graph-transformer for EEG emotion recognition.

Language: Python - Size: 4.16 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 35 - Forks: 3

jiaqingxie/DeepProtein

Code base for the paper DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning, Accepted @ Bioinformatics 2025

Language: Jupyter Notebook - Size: 201 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 24 - Forks: 2

vijaydwivedi75/lrgb

Long Range Graph Benchmark, NeurIPS 2022 Track on D&B

Language: Jupyter Notebook - Size: 27.6 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 158 - Forks: 22

vijaydwivedi75/gnn-lspe

Source code for GNN-LSPE (Graph Neural Networks with Learnable Structural and Positional Representations), ICLR 2022

Language: Python - Size: 267 KB - Last synced at: 3 months ago - Pushed at: over 3 years ago - Stars: 253 - Forks: 36

THUNLP-MT/GET

This repo contains the codes for our paper "Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning" (ICML 2024).

Language: Python - Size: 2.13 MB - Last synced at: 3 months ago - Pushed at: 9 months ago - Stars: 30 - Forks: 3

snap-research/LargeGT

Graph Transformers for Large Graphs

Language: Python - Size: 132 KB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 21 - Forks: 4

sail-sg/VGT

Video Graph Transformer for Video Question Answering (ECCV'22)

Language: Python - Size: 454 KB - Last synced at: 20 days ago - Pushed at: about 2 years ago - Stars: 47 - Forks: 12

BorgwardtLab/PST

Protein Structure Transformer (PST): Endowing pretrained protein language models with structural knowledge

Language: Python - Size: 2.29 MB - Last synced at: 3 months ago - Pushed at: 9 months ago - Stars: 36 - Forks: 2

XuhanLiu/DrugEx

Deep learning toolkit for Drug Design with Pareto-based Multi-Objective optimization in Polypharmacology

Language: Python - Size: 88.2 MB - Last synced at: 5 months ago - Pushed at: almost 2 years ago - Stars: 203 - Forks: 68

ETH-DISCO/Benchmarking-PEs

Benchmarking Positional Encodings for GNNs and Graph Transformers

Language: Python - Size: 35.9 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 6 - Forks: 1

NSLab-CUK/Unified-Graph-Transformer

Unified Graph Transformer (UGT) is a novel Graph Transformer model specialised in preserving both local and global graph structures and developed by NS Lab @ CUK based on pure PyTorch backend.

Language: Python - Size: 1.65 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 25 - Forks: 5

NSLab-CUK/Graph-Neural-Networks-Fall-2024

Welcome to the Graph Neural Networks (06838-01) class repository for the Department of Artificial Intelligence at the Catholic University of Korea. This platform is dedicated to sharing and archiving lecture materials such as practices, assignments, and sample codes for the class.

Language: Jupyter Notebook - Size: 34.8 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 6 - Forks: 1

rampasek/GraphGPS

Recipe for a General, Powerful, Scalable Graph Transformer

Language: Python - Size: 12.6 MB - Last synced at: 7 months ago - Pushed at: 12 months ago - Stars: 674 - Forks: 121

LabyrinthineLeo/RDGT

[TKDE-2024] "RDGT: Enhancing Group Cognitive Diagnosis with Relation-Guided Dual-Side Graph Transformer"

Language: Python - Size: 743 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0

JinheonBaek/GMT

Official Code Repository for the paper "Accurate Learning of Graph Representations with Graph Multiset Pooling" (ICLR 2021)

Language: Python - Size: 34.1 MB - Last synced at: 7 months ago - Pushed at: over 3 years ago - Stars: 101 - Forks: 21

HKU-MedAI/HIGT

[MICCAI'23] HIGT: Hierarchical Interaction Graph-Transformer for Whole Slide Image Analysis

Language: Python - Size: 460 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 26 - Forks: 1

cornell-zhang/HOGA

Hop-Wise Graph Attention for Scalable and Generalizable Learning on Circuits

Language: Python - Size: 635 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 21 - Forks: 2

cvit-mip/chextriev

[MICCAI 2024] Official implementation of "CheXtriev: Anatomy-Centered Representation for Case-Based Retrieval of Chest Radiographs"

Language: Jupyter Notebook - Size: 99.6 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 3 - Forks: 0

StonyBrookDB/igt-wsi

Repository for "Integrative Graph-Transformer Framework for Histopathology Whole Slide Image Representation and Classification""

Size: 13.7 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 1 - Forks: 0

shamim-hussain/tgt

Triplet Graph Transformer

Language: Python - Size: 5.64 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 21 - Forks: 1

HKUDS/GFormer

[SIGIR'2023] "GFormer: Graph Transformer for Recommendation"

Language: Python - Size: 7.43 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 50 - Forks: 11

daiquocnguyen/Graph-Transformer

Universal Graph Transformer Self-Attention Networks (TheWebConf WWW 2022) (Pytorch and Tensorflow)

Language: Python - Size: 109 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 622 - Forks: 77

jw9730/lps

[NeurIPS'23 Spotlight] Learning Probabilistic Symmetrization for Architecture Agnostic Equivariance (LPS), in PyTorch

Language: Python - Size: 149 MB - Last synced at: 10 months ago - Pushed at: about 1 year ago - Stars: 26 - Forks: 3

DongqiFu/VCR-Graphormer

VCR-Graphormer: A Mini-batch Graph Transformer via Virtual Connections, ICLR 2024

Language: Python - Size: 24.1 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

NSLab-CUK/Graph-Neural-Networks-Fall-2023

Welcome to the Graph Neural Networks (06838-01) class repository for the Department of Artificial Intelligence at the Catholic University of Korea. This platform is dedicated to sharing and archiving lecture materials such as practices, assignments, and sample codes for the class.

Language: Jupyter Notebook - Size: 59.2 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 9 - Forks: 2

HySonLab/Multires-Graph-Transformer

Multiresolution Graph Transformers and Wavelet Positional Encoding for Learning Long-Range and Hierarchical Structures

Language: Python - Size: 7.22 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 12 - Forks: 3

NSLab-CUK/Connector

The Graph Representation Learning Framework developed by NS Lab @ CUK.

Language: Python - Size: 35.8 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 7 - Forks: 1

LARS-research/3D-PGT

KDD-23 Automated 3D Pre-Training for Molecular Property Prediction

Language: Python - Size: 1.57 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 5 - Forks: 2

meakbiyik/graphtester

Test graph isomorphism with 1-WL for different graph classes and labelings

Language: Python - Size: 711 KB - Last synced at: 2 months ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 0

LMissher/STWave

[ICDE'2023] When Spatio-Temporal Meet Wavelets: Disentangled Traffic Forecasting via Efficient Spectral Graph Attention Networks

Language: Python - Size: 130 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 52 - Forks: 4

qitianwu/NodeFormer

The official implementation of NeurIPS22 spotlight paper "NodeFormer: A Scalable Graph Structure Learning Transformer for Node Classification"

Language: Jupyter Notebook - Size: 353 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 255 - Forks: 25

MANDO-Project/ge-sc-transformer

MANDO-HGT is a framework for detecting smart contract vulnerabilities. Given either in source code or bytecode forms, MANDO-HGT adapts heterogeneous graph transformers with customized meta relations for graph nodes and edges to learn their embeddings and train classifiers for detecting various vulnerability types in the contracts' nodes and graphs.

Language: Solidity - Size: 1.93 GB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 10 - Forks: 5

felipelmc/Deep-Learning

Assignments and presentation developed in the scope of the Deep Learning discipline, lectured by Professor Dário Oliveira (FGV EMAp). Presentation was co-authored with @anacarolerthal

Language: Jupyter Notebook - Size: 17.8 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

minjiyoon/CGT

Scalable and privacy-enhanced graph generative models for benchmark graph neural networks

Language: Python - Size: 368 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 13 - Forks: 1

jcyk/gtos

Code for AAAI2020 paper "Graph Transformer for Graph-to-Sequence Learning"

Language: Python - Size: 721 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 183 - Forks: 26

ansonb/FeTA_TMLR

This repository reproduces the results in the paper "How expressive are transformers in spectral domain for graphs?"(published in TMLR)

Language: Python - Size: 938 KB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 9 - Forks: 0

alexanderkrauck/pretraining-graph-transformers

Pretraining Techniques for Graph Transformers

Language: Jupyter Notebook - Size: 46.8 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

cptq/SignNet-BasisNet

SignNet and BasisNet

Language: Python - Size: 2.55 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 72 - Forks: 13

qslim/PDF

Towards Better Graph Representation Learning with Parameterized Decomposition & Filtering

Language: Python - Size: 56.6 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 8 - Forks: 1

BUAABIGSCity/PDFormer

[AAAI2023] A PyTorch implementation of PDFormer: Propagation Delay-aware Dynamic Long-range Transformer for Traffic Flow Prediction.

Language: Python - Size: 8.33 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 74 - Forks: 16

sorrowyn/MGTN

2021 AAAI Modular Graph Transformer Networks for Multi-Label Image Classification; Official GitHub: https://github.com/ReML-AI/MGTN

Language: Python - Size: 2.14 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 18 - Forks: 1

luis-mueller/probing-graph-transformers Fork of rampasek/GraphGPS

Code for our paper "Attending to Graph Transformers"

Language: Python - Size: 12.6 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 28 - Forks: 1

luis-mueller/bottleneck Fork of tech-srl/bottleneck

Code for our paper "Attending to Graph Transformers"

Language: Python - Size: 859 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

ayushnoori/graph-bbb

Graph Molecular Learning to Predict BBB Penetration

Language: Jupyter Notebook - Size: 17.2 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

burcgokden/Power-Law-Graph-Transformer

Implementation of Power Law Graph Transformer for Machine Translation and Representation Learning.

Language: Python - Size: 5.12 MB - Last synced at: 4 months ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0

Related Keywords
graph-transformer 63 graph-neural-networks 31 graph-representation-learning 16 transformer 14 deep-learning 12 machine-learning 9 graph 8 gnn 8 pytorch 7 graph-neural-network 7 transformers 6 attention 4 pytorch-geometric 4 graph-deep-learning 4 graph-learning 4 neural-network 3 graph-convolutional-networks 3 graph-algorithms 3 text-classification 3 positional-encoding 3 node-classification 3 representation-learning 3 classification 2 computational-pathology 2 deep-neural-networks 2 graph-attention-networks 2 self-supervised-graph-learning 2 pretrained-graph-model 2 wavelet-transform 2 machine-translation 2 graphs 2 graph-machine-learning 2 aaai 2 graph-classification 2 transformer-networks 2 self-attention 2 long-range-dependence 2 transformer-models 2 message-passing 2 regression 2 multi-omics 2 over-squashing 2 xgboost 2 geometric-deep-learning 2 pretraining 2 image-classification 2 large-graph 2 drug-response-prediction 2 convolutional-neural-networks 2 cancer-research 2 molecular-property-prediction 2 whole-slide-image 2 artificial-intelligence 2 python 2 density-functional-theory 1 attention-mechanism 1 graph-embedding 1 vision-transformer 1 weisfeiler-lehman 1 graph-measures 1 weisfeier-leman 1 graph-isomorphism 1 amr 1 iclr2024 1 graph-multiset-transformer 1 graph-pooling 1 graph-reconstruction 1 graph-representation 1 multi-instance-learning 1 distributed-training 1 electronic-design-automation 1 logic-synthesis 1 anatomy-learning 1 chest-radiography 1 medical-image-retrieval 1 histopathology-image-analysis 1 multiple-instance-learning 1 weakly-supervised-learning 1 molecular-graphs 1 collaborative-filtering 1 recommender-systems 1 graph-embeddings 1 node-embeddings 1 equivariance 1 spectral-graph-theory 1 graph-data 1 tansformer 1 aaai2023 1 dtw 1 kshape 1 multivariate-time-series-prediction 1 spatio-temporal-prediction 1 traffic-flow-prediction 1 traffic-prediction 1 multi-label-image 1 blood-brain-barrier 1 machine-learning-algorithms 1 machine-learning-model 1 plga 1 plgt 1