3D Infomax improves GNNs for Molecular Property Prediction

8 October 2021

Stephan Günnemann

Papers citing "3D Infomax improves GNNs for Molecular Property Prediction"

50 / 114 papers shown

Title
Multi-Modal Molecular Representation Learning via Structure Awareness Rong Yin Ruyue Liu Xiaoshuai Hao Xingrui Zhou Y. Liu Can Ma Weiping Wang 22 0 0 09 May 2025
Uni-3DAR: Unified 3D Generation and Understanding via Autoregression on Compressed Spatial Tokens Shuqi Lu Haowei Lin Lin Yao Zhifeng Gao Xiaohong Ji W. Elwasif Linfeng Zhang Guolin Ke 41 0 0 20 Mar 2025
Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling Shuqi Lu Xiaohong Ji Bohang Zhang Lin Yao Siyuan Liu Zhifeng Gao Linfeng Zhang Guolin Ke AI4CE 35 1 0 13 Mar 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 55 0 0 06 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 55 1 0 22 Feb 2025
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation Zhiyuan Liu Yanchen Luo Han Huang Enzhi Zhang Sihang Li Junfeng Fang Yaorui Shi X. Wang Kenji Kawaguchi Tat-Seng Chua 90 3 0 18 Feb 2025
Membership Inference Risks in Quantized Models: A Theoretical and Empirical Study Eric Aubinais Philippe Formont Pablo Piantanida Elisabeth Gassiat 36 0 0 10 Feb 2025
Molecular Graph Contrastive Learning with Line Graph Xueyuan Chen Shangzhe Li Ruomei Liu Bowen Shi J. Liu Junran Wu Ke Xu 40 0 0 15 Jan 2025
Pre-training Graph Neural Networks on Molecules by Using Subgraph-Conditioned Graph Information Bottleneck Van Thuy Hoang O-Joun Lee AI4CE 65 1 0 20 Dec 2024
SMI-Editor: Edit-based SMILES Language Model with Fragment-level Supervision Kangjie Zheng Siyue Liang Junwei Yang Bin Feng Zequn Liu Wei Ju Zhiping Xiao Ming Zhang 70 1 0 07 Dec 2024
3D Interaction Geometric Pre-training for Molecular Relational Learning Namkyeong Lee Yunhak Oh Heewoong Noh Gyoung S. Na Minkai Xu Hanchen Wang Tianfan Fu Chanyoung Park AI4CE 67 0 0 04 Dec 2024
MolParser: End-to-end Visual Recognition of Molecule Structures in the Wild Xi Fang Jiankun Wang X. Cai Shangqian Chen Shuwen Yang Lin Yao Linfeng Zhang Guolin Ke Linfeng Zhang Guolin Ke 40 1 0 17 Nov 2024
GeomCLIP: Contrastive Geometry-Text Pre-training for Molecules Teng Xiao Chao Cui Huaisheng Zhu V. Honavar AI4CE CLIP 28 0 0 16 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 31 0 0 02 Nov 2024
UniGEM: A Unified Approach to Generation and Property Prediction for Molecules Shikun Feng Yuyan Ni Yan Lu Zhi-Ming Ma Wei-Ying Ma Yanyan Lan 34 4 0 14 Oct 2024
CrysAtom: Distributed Representation of Atoms for Crystal Property Prediction Shrimon Mukherjee Madhusudan Ghosh Partha Basuchowdhuri 24 0 0 07 Sep 2024
MaskMol: Knowledge-guided Molecular Image Pre-Training Framework for Activity Cliffs Zhixiang Cheng Hongxin Xiang Pengsen Ma Li Zeng Xin Jin ... Yang Deng Bosheng Song Xinxin Feng Changhui Deng Xiangxiang Zeng 14 0 0 02 Sep 2024
What Ails Generative Structure-based Drug Design: Expressivity is Too Little or Too Much? Rafał Karczewski Samuel Kaski Markus Heinonen Vikas K. Garg 25 0 0 12 Aug 2024
MolTRES: Improving Chemical Language Representation Learning for Molecular Property Prediction Jun-Hyung Park Yeachan Kim Mingyu Lee Hyuntae Park SangKeun Lee 30 0 0 09 Jul 2024
TopoGCL: Topological Graph Contrastive Learning Yuzhou Chen José Frías Yulia R. Gel 14 8 0 25 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 27 5 0 21 Jun 2024
MoleculeCLA: Rethinking Molecular Benchmark via Computational Ligand-Target Binding Analysis Shikun Feng Jiaxin Zheng Yinjun Jia Yanwen Huang Fengfeng Zhou Wei-Ying Ma Yanyan Lan 19 0 0 13 Jun 2024
Medication Recommendation via Dual Molecular Modalities and Multi-Substructure Enhancement Shizhuo Mu Shunpan Liang Xiang Li 19 0 0 30 May 2024
Adapting Differential Molecular Representation with Hierarchical Prompts for Multi-label Property Prediction Linjia Kang Songhua Zhou Shuyan Fang Shichao Liu Wen Zhang AI4CE 28 0 0 29 May 2024
Analysis of Atom-level pretraining with Quantum Mechanics (QM) data for Graph Neural Networks Molecular property models Jose A. Arjona-Medina Ramil I. Nugmanov AI4CE 16 1 0 23 May 2024
UniCorn: A Unified Contrastive Learning Approach for Multi-view Molecular Representation Learning Shikun Feng Yuyan Ni Minghao Li Yanwen Huang Zhiming Ma Wei-Ying Ma Yanyan Lan SSL 41 7 0 15 May 2024
SubGDiff: A Subgraph Diffusion Model to Improve Molecular Representation Learning Jiying Zhang Zijing Liu Yu Wang Yu Li DiffM 39 1 0 09 May 2024
On the Scalability of GNNs for Molecular Graphs Maciej Sypetkowski Frederik Wenkel Farimah Poursafaei Nia Dickson Karush Suri Philip Fradkin Dominique Beaini GNN AI4CE 26 11 0 17 Apr 2024
ESM All-Atom: Multi-scale Protein Language Model for Unified Molecular Modeling Kangjie Zheng Siyu Long Tianyu Lu Junwei Yang Xinyu Dai Ming Zhang Zaiqing Nie Wei-Ying Ma Hao Zhou 25 5 0 05 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 29 20 0 01 Mar 2024
Pretraining Strategy for Neural Potentials Zehua Zhang Zijie Li A. Farimani AI4CE 29 0 0 24 Feb 2024
Impact of Domain Knowledge and Multi-Modality on Intelligent Molecular Property Prediction: A Systematic Survey Taojie Kuang Pengfei Liu Zhixiang Ren AI4CE 32 1 0 11 Feb 2024
Triplet Interaction Improves Graph Transformers: Accurate Molecular Graph Learning with Triplet Graph Transformers Md Shamim Hussain Mohammed J. Zaki D. Subramanian ViT 14 4 0 07 Feb 2024
A Graph is Worth $K$ Words: Euclideanizing Graph using Pure Transformer Zhangyang Gao Daize Dong Cheng Tan Jun-Xiong Xia Bozhen Hu Stan Z. Li 41 6 0 04 Feb 2024
Structure-Aware E(3)-Invariant Molecular Conformer Aggregation Networks D. M. Nguyen Nina Lukashina Tai Nguyen An T. Le TrungTin Nguyen Nhat Ho Jan Peters Daniel Sonntag Viktor Zaverkin Mathias Niepert 18 1 0 03 Feb 2024
Graph Multi-Similarity Learning for Molecular Property Prediction Hao Xu Zhengyang Zhou Pengyu Hong 14 0 0 31 Jan 2024
MolTailor: Tailoring Chemical Molecular Representation to Specific Tasks via Text Prompts Haoqiang Guo Sendong Zhao Hao Wang Yanrui Du Bing Qin AI4CE 8 8 0 21 Jan 2024
Multi-Modal Representation Learning for Molecular Property Prediction: Sequence, Graph, Geometry Zeyu Wang Tianyi Jiang Jinhuan Wang Qi Xuan AI4CE 8 4 0 07 Jan 2024
Pre-training of Molecular GNNs via Conditional Boltzmann Generator Daiki Koge N. Ono Shigehiko Kanaya AI4CE 11 0 0 20 Dec 2023
SE(3)-Invariant Multiparameter Persistent Homology for Chiral-Sensitive Molecular Property Prediction Andac Demir Francis Prael B. Kiziltan 8 2 0 12 Dec 2023
Molecule Joint Auto-Encoding: Trajectory Pretraining with 2D and 3D Diffusion Weitao Du Jiujiu Chen Xuecang Zhang Zhiming Ma Shengchao Liu DiffM 25 9 0 06 Dec 2023
Enhancing Molecular Property Prediction via Mixture of Collaborative Experts Xu Yao Shuang Liang Songqiao Han Hailiang Huang 11 4 0 06 Dec 2023
Removing Biases from Molecular Representations via Information Maximization Chenyu Wang Sharut Gupta Caroline Uhler Tommi Jaakkola 8 4 0 01 Dec 2023
Improving Self-supervised Molecular Representation Learning using Persistent Homology Yuankai Luo Lei Shi Veronika Thost SSL 6 8 0 29 Nov 2023
MultiModal-Learning for Predicting Molecular Properties: A Framework Based on Image and Graph Structures Zhuoyuan Wang Jiacong Mi Shan Lu Jieyue He 11 1 0 28 Nov 2023
InstructMol: Multi-Modal Integration for Building a Versatile and Reliable Molecular Assistant in Drug Discovery He Cao Zijing Liu Xingyu Lu Yuan Yao Yu Li 12 56 0 27 Nov 2023
Stoichiometry Representation Learning with Polymorphic Crystal Structures Namkyeong Lee Heewoong Noh Gyoung S. Na Tianfan Fu Jimeng Sun Chanyoung Park 13 0 0 17 Nov 2023
Multiparameter Persistent Homology for Molecular Property Prediction Andac Demir B. Kiziltan 14 1 0 17 Nov 2023
Identifying Semantic Component for Robust Molecular Property Prediction Zijian Li Zunhong Xu Ruichu Cai Zhenhui Yang Yuguang Yan Zhifeng Hao Guan-Hong Chen Kun Zhang 10 9 0 08 Nov 2023
Weakly supervised cross-modal learning in high-content screening Gabriel Watkinson Ethan O. Cohen Nicolas Bourriez Ihab Bendidi Guillaume Bollot Auguste Genovesio 11 3 0 08 Nov 2023