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
