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Protein Representation Learning by Geometric Structure Pretraining

International Conference on Learning Representations (ICLR), 2022

11 March 2022

Zuobai Zhang

Minghao Xu

Arian R. Jamasb

Vijil Chenthamarakshan

A. Lozano

Payel Das

Jian Tang

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Papers citing "Protein Representation Learning by Geometric Structure Pretraining"

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Title
When Structure Doesn't Help: LLMs Do Not Read Text-Attributed Graphs as Effectively as We Expected Haotian Xu Yuning You Tengfei Ma 96 0 0 20 Nov 2025
Protein Secondary Structure Prediction Using 3D Graphs and Relation-Aware Message Passing Transformers Disha Varshney Samarth Garg Sarthak Tyagi Deeksha Varshney Nayan Deep Asif Ekbal 64 0 0 17 Nov 2025
A Novel Framework for Multi-Modal Protein Representation Learning Runjie Zheng Zhen Wang Anjie Qiao Jiancong Xie Jiahua Rao Yuedong Yang 96 0 0 27 Oct 2025
MoRE-GNN: Multi-omics Data Integration with a Heterogeneous Graph Autoencoder Zhiyu Wang Sonia Koszut Pietro Lio Francesco Ceccarelli 64 0 0 08 Oct 2025
BioBlobs: Differentiable Graph Partitioning for Protein Representation Learning Xin Wang Carlos Oliver 80 0 0 02 Oct 2025
Can LLMs Reason Over Non-Text Modalities in a Training-Free Manner? A Case Study with In-Context Representation Learning Tianle Zhang Wanlong Fang Jonathan Woo Paridhi Latawa Deepak A.Subramanian Alvin Chan 169 1 0 22 Sep 2025
Tokenizing Loops of Antibodies Ada Fang Robert G. Alberstein Simon Kelow Frédéric A. Dreyer 56 1 0 10 Sep 2025
Topotein: Topological Deep Learning for Protein Representation Learning Zhiyu Wang Arian R. Jamasb Mustafa Hajij Alex Morehead Luke Braithwaite Pietro Lio 80 1 0 04 Sep 2025
Zero-Shot Learning with Subsequence Reordering Pretraining for Compound-Protein Interaction Hongzhi Zhang Zhonglie Liu Kun Meng Jiameng Chen Jia Wu Bo Du Di Lin Yan Che Wenbin Hu 89 1 0 28 Jul 2025
Demystify Protein Generation with Hierarchical Conditional Diffusion Models Zinan Ling Yi Shi Da Yan Yang Zhou Yang Zhou Bo Hui DiffM 219 0 0 24 Jul 2025
Modeling All-Atom Glycan Structures via Hierarchical Message Passing and Multi-Scale Pre-training Minghao Xu Jiaze Song Keming Wu Xiangxin Zhou Huang Leng Wentao Zhang 170 1 0 02 Jun 2025
PFMBench: Protein Foundation Model Benchmark Zhangyang Gao Hao Wang Cheng Tan Chenrui Xu Mengdi Liu Bozhen Hu Linlin Chao Xiaoming Zhang Stan Z. Li 226 3 0 01 Jun 2025
UniSim: A Unified Simulator for Time-Coarsened Dynamics of Biomolecules Ziyang Yu Wenbing Huang Yang Liu AI4CE 226 1 0 20 May 2025
Bidirectional Hierarchical Protein Multi-Modal Representation Learning Xuefeng Liu Songhao Jiang Chong Liu Jinfeng Xu Rick L. Stevens 144 3 0 07 Apr 2025
A Comprehensive Benchmark for RNA 3D Structure-Function Modeling Luis Wyss Vincent Mallet Wissam Karroucha Karsten Borgwardt Carlos Oliver 309 2 0 27 Mar 2025
Unified Cross-Scale 3D Generation and Understanding via Autoregressive Modeling Shuqi Lu Haowei Lin Lin Yao Zhifeng Gao Xiaohong Ji Weinan E Weinan E Linfeng Zhang Guolin Ke 316 2 0 20 Mar 2025
SCOPE-DTI: Semi-Inductive Dataset Construction and Framework Optimization for Practical Usability Enhancement in Deep Learning-Based Drug Target Interaction Prediction Emmanouil Benetos Xiang Ji Ziyue Zhang Yuming Zhou Yang-Chi-Dung Lin ... Yixian Huang Shidong Cui Shih-Chung Yen Ariel Warshel Hsien-Da Huang 193 1 0 12 Mar 2025
A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discovery Yiheng Zhu Mingyang Li Junlong Liu Kun Fu Jian Wu Yue Liu Mingze Yin Jieping Ye Jian Wu Xiping Hu 293 0 0 06 Mar 2025
Proteina: Scaling Flow-based Protein Structure Generative ModelsInternational Conference on Learning Representations (ICLR), 2025 Tomas Geffner Kieran Didi Zuobai Zhang Danny Reidenbach Zhonglin Cao ... Mario Geiger Christian Dallago E. Küçükbenli Arash Vahdat Karsten Kreis DiffM AI4CE 264 52 0 02 Mar 2025
Protein Large Language Models: A Comprehensive Survey Yijia Xiao Wanjia Zhao Junkai Zhang Yiqiao Jin Han Zhang ... Xiao Luo Yu Zhang James Zou Yizhou Sun Wei Wang LM&MA AI4CE 416 19 0 21 Feb 2025
Fast and Accurate Antibody Sequence Design via Structure Retrieval Xingyi Zhang Kun Xie Ningqiao Huang Wen Liu Peilin Zhao Sibo Wang Kangfei Zhao Biaobin Jiang 261 1 0 11 Feb 2025
UniZyme: A Unified Protein Cleavage Site Predictor Enhanced with Enzyme Active-Site Knowledge Chenao Li Shuo Yan Enyan Dai 350 1 0 10 Feb 2025
Docking-Aware Attention: Dynamic Protein Representations through Molecular Context Integration Amitay Sicherman Kira Radinsky 82 1 0 03 Feb 2025
SeqProFT: Sequence-only Protein Property Prediction with LoRA Finetuning Shuo Zhang Jian K. Liu 234 2 0 18 Nov 2024
MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification PredictionInternational Conference on Learning Representations (ICLR), 2024 Cheng Tan Zhenxiao Cao Zhangyang Gao Lirong Wu Siyuan Li Yufei Huang Jun Xia Bozhen Hu Stan Z. Li 254 4 0 04 Nov 2024
SFM-Protein: Integrative Co-evolutionary Pre-training for Advanced Protein Sequence Representation Liang He Peiran Jin Yaosen Min Shufang Xie Lijun Wu Tao Qin Xiaozhuan Liang Ran Bi Yuliang Jiang Tie-Yan Liu AI4TS 181 3 0 31 Oct 2024
FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational LearningNeural Information Processing Systems (NeurIPS), 2024 Sizhe Liu Jun Xia Lecheng Zhang Yuchen Liu Yue Liu ... Zhangyang Gao Bozhen Hu Cheng Tan Hongxin Xiang Stan Z. Li 183 4 0 19 Oct 2024
Bridging Large Language Models and Graph Structure Learning Models for Robust Representation Learning Guangxin Su Yifan Zhu Wenjie Zhang Hanchen Wang Ying Zhang 352 3 0 15 Oct 2024
Structure-Enhanced Protein Instruction Tuning: Towards General-Purpose Protein Understanding with LLMs Wei Wu Chao Wang L. Chen Mingze Yin Yiheng Zhu Kun Fu Jieping Ye Hui Xiong Zheng Wang 353 3 0 04 Oct 2024
EditRoom: LLM-parameterized Graph Diffusion for Composable 3D Room Layout EditingInternational Conference on Learning Representations (ICLR), 2024 Kaizhi Zheng Xiaotong Chen Xuehai He Jing Gu Linjie Li Zhengyuan Yang Kevin Qinghong Lin Jianfeng Wang Lijuan Wang Xin Eric Wang KELM DiffM 204 6 0 03 Oct 2024
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning Jiaqing Xie Yue Zhao 392 2 0 02 Oct 2024
EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics Chenqing Hua Yong Liu Dinghuai Zhang Odin Zhang Sitao Luan Kevin K. Yang Guy Wolf Doina Precup Shuangjia Zheng 208 10 0 01 Oct 2024
Recent advances in interpretable machine learning using structure-based protein representations L. Vecchietti Minji Lee Begench Hangeldiyev Hyunkyu Jung Hahnbeom Park Tae-Kyun Kim Meeyoung Cha Ho Min Kim AI4CE 319 1 0 26 Sep 2024
Reactzyme: A Benchmark for Enzyme-Reaction PredictionNeural Information Processing Systems (NeurIPS), 2024 Chenqing Hua Bozitao Zhong Sitao Luan Liang Hong Guy Wolf Doina Precup Shuangjia Zheng 210 12 0 24 Aug 2024
Advanced atom-level representations for protein flexibility prediction utilizing graph neural networks Sina Sarparast Aldo Zaimi Maximilian Ebert Michael-Rock Goldsmith AI4CE 134 1 0 22 Aug 2024
ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding Yijia Xiao Edward Sun Yiqiao Jin Qifan Wang Wei Wang 240 26 0 21 Aug 2024
DIVE: Subgraph Disagreement for Graph Out-of-Distribution GeneralizationKnowledge Discovery and Data Mining (KDD), 2024 Xin Sun Liang Wang Qiang Liu Shu Wu Zilei Wang Liang Wang OOD CML 297 11 0 08 Aug 2024
GOProteinGNN: Leveraging Protein Knowledge Graphs for Protein Representation Learning Dan Kalifa Uriel Singer Kira Radinsky 466 3 0 31 Jul 2024
Antibody DomainBed: Out-of-Distribution Generalization in Therapeutic Protein Design Natavsa Tagasovska Ji Won Park Matthieu Kirchmeyer Nathan C. Frey Andrew Watkins ... Arian R. Jamasb Edith Lee Tyler Bryson Stephen Ra Kyunghyun Cho OOD 254 8 0 15 Jul 2024
Protein Representation Learning with Sequence Information Embedding: Does it Always Lead to a Better Performance? Y. Tan Lirong Zheng Bozitao Zhong Liang Hong Bingxin Zhou 189 8 0 28 Jun 2024
Geometric Self-Supervised Pretraining on 3D Protein Structures using Subgraphs Michail Chatzianastasis George Dasoulas Michalis Vazirgiannis SSL 171 1 0 20 Jun 2024
Evaluating representation learning on the protein structure universe Arian R. Jamasb Alex Morehead Chaitanya K. Joshi Zuobai Zhang Kieran Didi ... Charles Harris Jian Tang Jianlin Cheng Pietro Lio Tom L. Blundell SSL 229 22 0 19 Jun 2024
FoldToken2: Learning compact, invariant and generative protein structure language Zhangyang Gao Cheng Tan Stan Z. Li 170 6 0 11 Jun 2024
Improving Paratope and Epitope Prediction by Multi-Modal Contrastive Learning and Interaction Informativeness Estimation Zhiwei Wang Yongkang Wang Wen Zhang 171 6 0 31 May 2024
Boosting Protein Language Models with Negative Sample Mining Yaoyao Xu Xinjian Zhao Xiaozhuang Song Benyou Wang Tianshu Yu 166 1 0 28 May 2024
GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning Minghao Xu Yunteng Geng Yihang Zhang Ling Yang Jian Tang Wentao Zhang 133 6 0 25 May 2024
ProtFAD: Introducing function-aware domains as implicit modality towards protein function perception Mingqing Wang Zhiwei Nie Yonghong He Zhixiang Ren 158 0 0 24 May 2024
E(n) Equivariant Topological Neural Networks Claudio Battiloro Ege Karaismailoglu Mauricio Tec George Dasoulas Michelle Audirac Francesca Dominici 513 17 0 24 May 2024
Bond Graphs for multi-physics informed Neural Networks for multi-variate time series Alexis-Raja Brachet Pierre-Yves Richard Céline Hudelot AI4CE 175 1 0 22 May 2024
UniCorn: A Unified Contrastive Learning Approach for Multi-view Molecular Representation LearningInternational Conference on Machine Learning (ICML), 2024 Shikun Feng Yuyan Ni Minghao Li Yanwen Huang Zhiming Ma Wei-Ying Ma Yanyan Lan SSL 282 17 0 15 May 2024