A Survey of Graph Transformers: Architectures, Theories and Applications

23 February 2025

Papers citing "A Survey of Graph Transformers: Architectures, Theories and Applications"

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Title
ASD Classification on Dynamic Brain Connectome using Temporal Random Walk with Transformer-based Dynamic Network Embedding Suchanuch Piriyasatit Chaohao Yuan Ercan Engin Kuruoglu 114 0 0 16 Mar 2025
Unifying Structural Proximity and Equivalence for Enhanced Dynamic Network Embedding Suchanuch Piriyasatit Chaohao Yuan Ercan Engin Kuruoglu 76 0 0 14 Mar 2025
MolSpectra: Pre-training 3D Molecular Representation with Multi-modal Energy Spectra Liang Wang Shaozhen Liu Yu Rong Deli Zhao Qiang Liu Shu Wu Liang Wang MedIm 103 3 0 22 Feb 2025
Biologically Plausible Brain Graph Transformer Ciyuan Peng Yuelong Huang Qichao Dong Shuo Yu Xiwei Xu Chengqi Zhang Yaochu Jin 101 1 0 13 Feb 2025
Bi-Level Graph Structure Learning for Next POI Recommendation Liang Wang Shu Wu Qiang Liu Yinlin Zhu Xiang Tao Hao Fei Liang Wang 77 6 0 02 Nov 2024
Pin-Tuning: Parameter-Efficient In-Context Tuning for Few-Shot Molecular Property Prediction Liang Wang Qiang Liu Shaozhen Liu Xin Sun Shu Wu Liang Wang 96 2 0 02 Nov 2024
Open Materials 2024 (OMat24) Inorganic Materials Dataset and Models Luis Barroso-Luque Muhammed Shuaibi Xiang Fu Brandon M. Wood Misko Dzamba Meng Gao Ammar Rizvi C. L. Zitnick Zachary W. Ulissi AI4CE PINN 69 20 0 16 Oct 2024
Leveraging Contrastive Learning for Enhanced Node Representations in Tokenized Graph Transformers Jinsong Chen Hanpeng Liu John E. Hopcroft Kun He 87 4 0 27 Jun 2024
Uni-Mol2: Exploring Molecular Pretraining Model at Scale Xiaohong Ji Zhen Wang Zhifeng Gao Hang Zheng Linfeng Zhang Guolin Ke Weinan E AI4CE 80 9 0 21 Jun 2024
Aligning Transformers with Weisfeiler-Leman Luis Muller Christopher Morris AI4TS 37 3 0 05 Jun 2024
What Improves the Generalization of Graph Transformers? A Theoretical Dive into the Self-attention and Positional Encoding Hongkang Li Meng Wang Tengfei Ma Sijia Liu Zaixi Zhang Pin-Yu Chen MLT AI4CE 102 11 0 04 Jun 2024
Distinguished In Uniform: Self Attention Vs. Virtual Nodes Eran Rosenbluth Jan Tönshoff Martin Ritzert Berke Kisin Martin Grohe 57 12 0 20 May 2024
Atomas: Hierarchical Alignment on Molecule-Text for Unified Molecule Understanding and Generation Yikun Zhang Geyan Ye Chaohao Yuan Bo Han Long-Kai Huang Jianhua Yao Wei Liu Yu Rong 109 3 0 23 Apr 2024
Functional Protein Design with Local Domain Alignment Chaohao Yuan Songyou Li Geyan Ye Yikun Zhang Long-Kai Huang Wenbing Huang Wei Liu Jianhua Yao Yu Rong 67 1 0 18 Apr 2024
VCR-Graphormer: A Mini-batch Graph Transformer via Virtual Connections Dongqi Fu Zhigang Hua Yan Xie Jin Fang Si Zhang Kaan Sancak Hao Wu Andrey Malevich Jingrui He Bo Long 102 25 0 24 Mar 2024
Complete and Efficient Graph Transformers for Crystal Material Property Prediction Keqiang Yan Cong Fu Xiaofeng Qian Xiaoning Qian Shuiwang Ji 99 22 0 18 Mar 2024
Polynormer: Polynomial-Expressive Graph Transformer in Linear Time Chenhui Deng Zichao Yue Zhiru Zhang 133 29 0 02 Mar 2024
A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications Jiaqi Han Jiacheng Cen Liming Wu Zongzhao Li Xiangzhe Kong ... Zhewei Wei Deli Zhao Yu Rong Wenbing Huang Wenbing Huang AI4CE 128 23 0 01 Mar 2024
Comparing Graph Transformers via Positional Encodings Mitchell Black Qingsong Wang Zhengchao Wan A. Nayyeri Yusu Wang 75 13 0 22 Feb 2024
Graph Mamba: Towards Learning on Graphs with State Space Models Ali Behrouz Farnoosh Hashemi AI4CE 160 66 0 13 Feb 2024
Triplet Interaction Improves Graph Transformers: Accurate Molecular Graph Learning with Triplet Graph Transformers Md Shamim Hussain Mohammed J Zaki D. Subramanian ViT 88 8 0 07 Feb 2024
A Graph is Worth $K$ Words: Euclideanizing Graph using Pure Transformer Zhangyang Gao Daize Dong Cheng Tan Jun Xia Bozhen Hu Stan Z. Li 66 7 0 04 Feb 2024
Position: Graph Foundation Models are Already Here Haitao Mao Zhikai Chen Wenzhuo Tang Jianan Zhao Yao Ma Tong Zhao Neil Shah Mikhail Galkin Jiliang Tang AI4CE 101 38 0 03 Feb 2024
Mamba: Linear-Time Sequence Modeling with Selective State Spaces Albert Gu Tri Dao Mamba 146 2,699 0 01 Dec 2023
Sliced Denoising: A Physics-Informed Molecular Pre-Training Method Yuyan Ni Shikun Feng Wei-Ying Ma Zhiming Ma Yanyan Lan DiffM AI4CE 80 11 0 03 Nov 2023
MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter Zhiyuan Liu Changhao Nai Yancheng Luo Hao Fei Yixin Cao Kenji Kawaguchi Xiang Wang Tat-Seng Chua 70 91 0 19 Oct 2023
SignGT: Signed Attention-based Graph Transformer for Graph Representation Learning Jinsong Chen Gaichao Li John E. Hopcroft Kun He SLR 68 5 0 17 Oct 2023
GSLB: The Graph Structure Learning Benchmark Zhixun Li Liang Wang Xin Sun Yifan Luo Yanqiao Zhu ... Xiangxin Zhou Qiang Liu Shu Wu Liang Wang Jeffrey Xu Yu 85 36 0 08 Oct 2023
On the Stability of Expressive Positional Encodings for Graphs Yinan Huang William Lu Joshua Robinson Yu Yang Muhan Zhang Stefanie Jegelka Pan Li 73 12 0 04 Oct 2023
TransGNN: Harnessing the Collaborative Power of Transformers and Graph Neural Networks for Recommender Systems Peiyan Zhang Yuchen Yan Xi Zhang Chaozhuo Li Senzhang Wang Feiran Huang Sunghun Kim 74 18 0 28 Aug 2023
SEGNO: Generalizing Equivariant Graph Neural Networks with Physical Inductive Biases Yang Liu Jiashun Cheng Haihong Zhao Tingyang Xu P. Zhao Fugee Tsung Jia Li Yu Rong AI4CE 86 19 0 25 Aug 2023
Fractional Denoising for 3D Molecular Pre-training Shi Feng Yuyan Ni Yanyan Lan Zhiming Ma Wei-Ying Ma DiffM AI4CE 76 27 0 20 Jul 2023
Multimodal Molecular Pretraining via Modality Blending Qiying Yu Yudi Zhang Yuyan Ni Shi Feng Yanyan Lan Hao Zhou Jingjing Liu 67 13 0 12 Jul 2023
EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations Yidong Liao Brandon M. Wood Abhishek Das Tess E. Smidt 85 153 0 21 Jun 2023
SGFormer: Simplifying and Empowering Transformers for Large-Graph Representations Qitian Wu Wen-Long Zhao Chenxiao Yang Hengrui Zhang Fan Nie Haitian Jiang Yatao Bian Junchi Yan AI4CE 111 92 0 19 Jun 2023
NodeFormer: A Scalable Graph Structure Learning Transformer for Node Classification Qitian Wu Wentao Zhao Zenan Li David Wipf Junchi Yan 54 222 0 14 Jun 2023
GCT-TTE: Graph Convolutional Transformer for Travel Time Estimation Vladimir Mashurov Vaagn Chopurian Vadim Porvatov Arseny Ivanov Natalia Semenova ViT 55 11 0 07 Jun 2023
Graph Inductive Biases in Transformers without Message Passing Liheng Ma Chen Lin Derek Lim Adriana Romero Soriano P. Dokania Mark Coates Philip Torr Ser-Nam Lim AI4CE 74 96 0 27 May 2023
Transformer-Based Hierarchical Clustering for Brain Network Analysis Wei Dai Hejie Cui Xuan Kan Ying Guo S. V. Rooij Carl Yang 86 12 0 06 May 2023
Multimodal Graph Transformer for Multimodal Question Answering Xuehai He Xin Eric Wang 76 9 0 30 Apr 2023
MUDiff: Unified Diffusion for Complete Molecule Generation Chenqing Hua Sitao Luan Minkai Xu Rex Ying Jie Fu Stefano Ermon Doina Precup DiffM 85 37 0 28 Apr 2023
SGFormer: Semantic Graph Transformer for Point Cloud-based 3D Scene Graph Generation Changsheng Lv Mengshi Qi Xia Li Zhengyuan Yang Huadong Ma 3DPC ViT 74 11 0 20 Mar 2023
Exphormer: Sparse Transformers for Graphs Hamed Shirzad A. Velingker B. Venkatachalam Danica J. Sutherland A. Sinop 37 114 0 10 Mar 2023
AMIGO: Sparse Multi-Modal Graph Transformer with Shared-Context Processing for Representation Learning of Giga-pixel Images Ramin Nakhli Puria Azadi Moghadam Haoyang Mi H. Farahani Alexander S. Baras B. Gilks A. Bashashati MedIm ViT 81 20 0 01 Mar 2023
Single-Cell Multimodal Prediction via Transformers Wenzhuo Tang Haifang Wen Renming Liu Jiayuan Ding Wei Jin Yuying Xie Hui Liu Jiliang Tang AI4CE 48 11 0 01 Mar 2023
Edgeformers: Graph-Empowered Transformers for Representation Learning on Textual-Edge Networks Bowen Jin Yu Zhang Yu Meng Jiawei Han 78 30 0 21 Feb 2023
MulGT: Multi-task Graph-Transformer with Task-aware Knowledge Injection and Domain Knowledge-driven Pooling for Whole Slide Image Analysis Weiqin Zhao Shujun Wang Maximus C. F. Yeung Tianye Niu Lequan Yu 112 9 0 21 Feb 2023
Attending to Graph Transformers Luis Muller Mikhail Galkin Christopher Morris Ladislav Rampášek 93 92 0 08 Feb 2023
Single Cells Are Spatial Tokens: Transformers for Spatial Transcriptomic Data Imputation Haifang Wen Wenzhuo Tang Wei Jin Jiayuan Ding Renming Liu Xinnan Dai Feng Shi Lulu Shang Jiliang Tang Yuying Xie 52 9 0 06 Feb 2023
Structure-informed Language Models Are Protein Designers Zaixiang Zheng Yifan Deng Dongyu Xue Yi Zhou YE Fei Quanquan Gu 86 95 0 03 Feb 2023