Benchmarking Graphormer on Large-Scale Molecular Modeling Datasets

9 March 2022

Papers citing "Benchmarking Graphormer on Large-Scale Molecular Modeling Datasets"

48 / 48 papers shown

Title
Unified Molecule Generation and Property Prediction Adam Izdebski Jan Olszewski Pankhil Gawade Krzysztof Koras Serra Korkmaz Valentin Rauscher Jakub M. Tomczak E. Szczurek 31 0 0 23 Apr 2025
A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discovery Yiheng Zhu Mingyang Li Junlong Liu Kun Fu J. Wu Q. Li Mingze Yin Jieping Ye Jian Wu Z. Wang 60 0 0 06 Mar 2025
CrystalFramer: Rethinking the Role of Frames for SE(3)-Invariant Crystal Structure Modeling Yusei Ito Tatsunori Taniai Ryo Igarashi Yoshitaka Ushiku K. Ono 60 0 0 04 Mar 2025
Stable and Accurate Orbital-Free DFT Powered by Machine Learning Roman Remme Tobias Kaczun Tim Ebert Christof A. Gehrig Dominik Geng ... Peter Lippmann Johannes S. Schmidt Simon Wagner A. Dreuw Fred A. Hamprecht 27 1 0 01 Mar 2025
Position: Graph Learning Will Lose Relevance Due To Poor Benchmarks Maya Bechler-Speicher Ben Finkelshtein Fabrizio Frasca Luis Muller Jan Tonshoff ... Michael M. Bronstein Mathias Niepert Bryan Perozzi Mikhail Galkin Christopher Morris OOD 97 2 0 21 Feb 2025
MVGT: A Multi-view Graph Transformer Based on Spatial Relations for EEG Emotion Recognition Yanjie Cui Xiaohong Liu Jing Liang Yamin Fu 57 1 0 17 Jan 2025
Bridging Geometric States via Geometric Diffusion Bridge Shengjie Luo Yixian Xu Di He Shuxin Zheng Tie-Yan Liu Liwei Wang 37 0 0 31 Oct 2024
Physical Consistency Bridges Heterogeneous Data in Molecular Multi-Task Learning Yuxuan Ren Dihan Zheng Chang-Shu Liu Peiran Jin Yu Shi Lin Huang Jiyan He Shengjie Luo Tao Qin Tie-Yan Liu AI4CE 32 1 0 14 Oct 2024
Structure-Enhanced Protein Instruction Tuning: Towards General-Purpose Protein Understanding Wei Yu Wu Chao Wang Liyi Chen Mingze Yin Yiheng Zhu Kun Fu Jieping Ye Hui Xiong Zheng Wang 28 1 0 04 Oct 2024
Contrastive Representation Learning for Dynamic Link Prediction in Temporal Networks Amirhossein Nouranizadeh Fatemeh Tabatabaei Far Mohammad Rahmati AI4TS 32 1 0 22 Aug 2024
Geometry Informed Tokenization of Molecules for Language Model Generation Xiner Li Limei Wang Youzhi Luo Carl N. Edwards Shurui Gui Yuchao Lin Heng Ji Shuiwang Ji 29 6 0 19 Aug 2024
Distribution Learning for Molecular Regression Nima Shoghi Pooya Shoghi Anuroop Sriram Abhishek Das OOD 21 0 0 30 Jul 2024
DTFormer: A Transformer-Based Method for Discrete-Time Dynamic Graph Representation Learning Xi Chen Yun Xiong Siwei Zhang Jiawei Zhang Yao Zhang Shiyang Zhou Xixi Wu Mingyang Zhang Tengfei Liu Weiqiang Wang AI4CE 28 1 0 26 Jul 2024
GeoMFormer: A General Architecture for Geometric Molecular Representation Learning Tianlang Chen Shengjie Luo Di He Shuxin Zheng Tie-Yan Liu Liwei Wang AI4CE 38 5 0 24 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 40 6 0 21 Jun 2024
Molecule Graph Networks with Many-body Equivariant Interactions Zetian Mao Jiawen Li Chen Liang Diptesh Das Masato Sumita Koji Tsuda Kelin Xia Koji Tsuda 35 1 0 19 Jun 2024
FlowerFormer: Empowering Neural Architecture Encoding using a Flow-aware Graph Transformer Dongyeong Hwang Hyunju Kim Sunwoo Kim Kijung Shin AI4CE 50 2 0 19 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 34 20 0 01 Mar 2024
Triplet Interaction Improves Graph Transformers: Accurate Molecular Graph Learning with Triplet Graph Transformers Md Shamim Hussain Mohammed J. Zaki D. Subramanian ViT 28 5 0 07 Feb 2024
Pre-Training Protein Bi-level Representation Through Span Mask Strategy On 3D Protein Chains Jiale Zhao Wanru Zhuang Jia Song Yaqi Li Shuqi Lu AI4CE 13 5 0 02 Feb 2024
Enabling Efficient Equivariant Operations in the Fourier Basis via Gaunt Tensor Products Shengjie Luo Tianlang Chen Aditi S. Krishnapriyan 25 19 0 18 Jan 2024
Exposition on over-squashing problem on GNNs: Current Methods, Benchmarks and Challenges Dai Shi Andi Han Lequan Lin Yi Guo Junbin Gao 47 12 0 13 Nov 2023
Lo-Hi: Practical ML Drug Discovery Benchmark Simon Steshin VLM 15 7 0 10 Oct 2023
iLoRE: Dynamic Graph Representation with Instant Long-term Modeling and Re-occurrence Preservation Siwei Zhang Yun Xiong Yao Zhang Xixi Wu Yiheng Sun Jiawei Zhang AI4TS 12 4 0 05 Sep 2023
Learning to Group Auxiliary Datasets for Molecule Ting Huang Ziniu Hu Rex Ying 11 0 0 08 Jul 2023
EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations Yidong Liao Brandon M. Wood Abhishek Das Tess E. Smidt 24 131 0 21 Jun 2023
Towards Predicting Equilibrium Distributions for Molecular Systems with Deep Learning Shuxin Zheng Jiyan He Chang-Shu Liu Yu Shi Ziheng Lu ... Peiran Jin Chi Chen Frank Noé Haiguang Liu Tie-Yan Liu AI4CE 19 41 0 08 Jun 2023
Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation Han Huang Leilei Sun Bowen Du Weifeng Lv DiffM 24 16 0 21 May 2023
Learning Large Graph Property Prediction via Graph Segment Training Kaidi Cao P. Phothilimthana Sami Abu-El-Haija Dustin Zelle Yanqi Zhou Charith Mendis J. Leskovec Bryan Perozzi 21 8 0 21 May 2023
Graph Propagation Transformer for Graph Representation Learning Zhe Chen Hao Hao Tan Tao Wang Tianrun Shen Tong Lu Qiuying Peng Cheng Cheng Yue Qi 27 11 0 19 May 2023
Highly Accurate Quantum Chemical Property Prediction with Uni-Mol+ Shuqi Lu Zhifeng Gao Di He Linfeng Zhang Guolin Ke 37 24 0 16 Mar 2023
DR-Label: Improving GNN Models for Catalysis Systems by Label Deconstruction and Reconstruction Bo-Lan Wang Chen Liang Jiaze Wang Furui Liu Shaogang Hao Dong Li Jianye Hao Guangyong Chen Xiaolong Zou Pheng-Ann Heng 41 3 0 06 Mar 2023
Diffusing Graph Attention Daniel Glickman Eran Yahav GNN 40 3 0 01 Mar 2023
3D Molecular Generation via Virtual Dynamics Shuqi Lu Lin Yao X. Chen Hang Zheng Di He Guolin Ke DiffM 24 7 0 12 Feb 2023
Attending to Graph Transformers Luis Muller Mikhail Galkin Christopher Morris Ladislav Rampášek 49 85 0 08 Feb 2023
GPS++: Reviving the Art of Message Passing for Molecular Property Prediction Dominic Masters Josef Dean Kerstin Klaser Zhiyi Li Sam Maddrell-Mander ... D. Beker Andrew Fitzgibbon Shenyang Huang Ladislav Rampášek Dominique Beaini 30 8 0 06 Feb 2023
Learning a Fourier Transform for Linear Relative Positional Encodings in Transformers K. Choromanski Shanda Li Valerii Likhosherstov Kumar Avinava Dubey Shengjie Luo Di He Yiming Yang Tamás Sarlós Thomas Weingarten Adrian Weller 31 8 0 03 Feb 2023
Molecular Geometry-aware Transformer for accurate 3D Atomic System modeling Zheng Yuan Yaoyun Zhang Chuanqi Tan Wei Wang Feiran Huang Songfang Huang AI4CE ViT 24 6 0 02 Feb 2023
On the Connection Between MPNN and Graph Transformer Chen Cai Truong Son-Hy Rose Yu Yusu Wang 33 51 0 27 Jan 2023
On the Expressive Power of Geometric Graph Neural Networks Chaitanya K. Joshi Cristian Bodnar Simon V. Mathis Taco Cohen Pietro Liò 50 83 0 23 Jan 2023
GPS++: An Optimised Hybrid MPNN/Transformer for Molecular Property Prediction Dominic Masters Josef Dean Kerstin Klaser Zhiyi Li Sam Maddrell-Mander Adam Sanders Hatem Helal D. Beker Ladislav Rampášek Dominique Beaini 26 23 0 18 Nov 2022
AutoML for Climate Change: A Call to Action Renbo Tu Nicholas Roberts Vishak Prasad Sibasis Nayak P. Jain Frederic Sala Ganesh Ramakrishnan Ameet Talwalkar W. Neiswanger Colin White 30 6 0 07 Oct 2022
Pure Transformers are Powerful Graph Learners Jinwoo Kim Tien Dat Nguyen Seonwoo Min Sungjun Cho Moontae Lee Honglak Lee Seunghoon Hong 40 189 0 06 Jul 2022
Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs Yi-Lun Liao Tess E. Smidt 80 213 0 23 Jun 2022
Long Range Graph Benchmark Vijay Prakash Dwivedi Ladislav Rampášek Mikhail Galkin Alipanah Parviz Guy Wolf A. Luu Dominique Beaini 26 195 0 16 Jun 2022
Your Transformer May Not be as Powerful as You Expect Shengjie Luo Shanda Li Shuxin Zheng Tie-Yan Liu Liwei Wang Di He 55 50 0 26 May 2022
Recipe for a General, Powerful, Scalable Graph Transformer Ladislav Rampášek Mikhail Galkin Vijay Prakash Dwivedi A. Luu Guy Wolf Dominique Beaini 57 514 0 25 May 2022
The Open Catalyst 2020 (OC20) Dataset and Community Challenges L. Chanussot Abhishek Das Siddharth Goyal Thibaut Lavril Muhammed Shuaibi ... Brandon M. Wood Junwoong Yoon Devi Parikh C. L. Zitnick Zachary W. Ulissi 226 503 0 20 Oct 2020