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
Sliced Denoising: A Physics-Informed Molecular Pre-Training Method Yuyan Ni Shikun Feng Wei-Ying Ma Zhiming Ma Yanyan Lan DiffM AI4CE 21 7 0 03 Nov 2023
Neural Atoms: Propagating Long-range Interaction in Molecular Graphs through Efficient Communication Channel Xuan Li Zhanke Zhou Jiangchao Yao Yu Rong Lu Zhang Bo Han 19 3 0 02 Nov 2023
$Generating QM1B with PySCF$_{\text{IPU}}$$ Generating QM1B with PySCF $_{\text{IPU}}$ Alexander Mathiasen Hatem Helal Kerstin Klaser Paul Balanca Josef Dean Carlo Luschi Dominique Beaini Andrew Fitzgibbon Dominic Masters 10 1 0 02 Nov 2023
UniMAP: Universal SMILES-Graph Representation Learning Shikun Feng Lixin Yang Wei-Ying Ma Yanyan Lan OffRL 11 4 0 22 Oct 2023
Large Language Models for Scientific Synthesis, Inference and Explanation Yizhen Zheng Huan Yee Koh Jiaxin Ju A. T. Nguyen Lauren T. May Geoffrey I. Webb Shirui Pan ELM 31 30 0 12 Oct 2023
Towards Foundational Models for Molecular Learning on Large-Scale Multi-Task Datasets Dominique Beaini Shenyang Huang Joao Alex Cunha Zhiyi Li Gabriela Moisescu-Pareja ... Thérence Bois Andrew Fitzgibbon Bla.zej Banaszewski Chad Martin Dominic Masters AI4CE 13 19 0 06 Oct 2023
Fragment-based Pretraining and Finetuning on Molecular Graphs Kha-Dinh Luong Ambuj Singh AI4CE 17 12 0 05 Oct 2023
3D-Mol: A Novel Contrastive Learning Framework for Molecular Property Prediction with 3D Information Taojie Kuang Yiming Ren Zhixiang Ren 6 7 0 28 Sep 2023
Genetic InfoMax: Exploring Mutual Information Maximization in High-Dimensional Imaging Genetics Studies Yaochen Xie Z. Xie Sheikh Muhammad Saiful Islam D. Zhi Shuiwang Ji MedIm 15 0 0 26 Sep 2023
Large-scale Pretraining Improves Sample Efficiency of Active Learning based Molecule Virtual Screening Zhonglin Cao Simone Sciabola Ye Wang 19 1 0 20 Sep 2023
3D Denoisers are Good 2D Teachers: Molecular Pretraining via Denoising and Cross-Modal Distillation Sungjun Cho Dae-Woong Jeong Sung Moon Ko Jinwoo Kim Sehui Han Seunghoon Hong Honglak Lee Moontae Lee AI4CE DiffM 20 1 0 08 Sep 2023
Geometry-aware Line Graph Transformer Pre-training for Molecular Property Prediction Peizhen Bai Xianyuan Liu Haiping Lu ViT AI4CE 21 1 0 01 Sep 2023
Current Methods for Drug Property Prediction in the Real World Jacob Green Cecilia Cabrera Diaz Maximilian A. H. Jakobs A. Dimitracopoulos Mark van der Wilk Ryan D. Greenhalgh 9 1 0 25 Jul 2023
Fractional Denoising for 3D Molecular Pre-training Shi Feng Yuyan Ni Yanyan Lan Zhiming Ma Wei-Ying Ma DiffM AI4CE 27 25 0 20 Jul 2023
Graph Positional and Structural Encoder Semih Cantürk Renming Liu Olivier Lapointe-Gagné Vincent Létourneau Guy Wolf Dominique Beaini Ladislav Rampášek 23 13 0 14 Jul 2023
Multimodal Molecular Pretraining via Modality Blending Qiying Yu Yudi Zhang Yuyan Ni Shi Feng Yanyan Lan Hao Zhou Jingjing Liu 21 12 0 12 Jul 2023
Symmetry-Informed Geometric Representation for Molecules, Proteins, and Crystalline Materials Shengchao Liu Weitao Du Yanjing Li Zhuoxinran Li Zhiling Zheng ... Anima Anandkumar C. Borgs J. Chayes Hongyu Guo Jian Tang AI4CE 26 17 0 15 Jun 2023
MUBen: Benchmarking the Uncertainty of Molecular Representation Models Yinghao Li Lingkai Kong Yuanqi Du Yue Yu Yuchen Zhuang Wenhao Mu Chao Zhang 17 8 0 14 Jun 2023
Automated 3D Pre-Training for Molecular Property Prediction Xu Wang Huan Zhao Weiwei Tu Quanming Yao AI4CE 19 35 0 13 Jun 2023
A Crystal-Specific Pre-Training Framework for Crystal Material Property Prediction Haomin Yu Yanru Song Jilin Hu Chenjuan Guo B. Yang AI4CE 19 4 0 08 Jun 2023
MolFM: A Multimodal Molecular Foundation Model Yi Luo Kai Yang Massimo Hong Xingyi Liu Zaiqing Nie 20 27 0 06 Jun 2023
Bi-level Contrastive Learning for Knowledge-Enhanced Molecule Representations Pengcheng Jiang Cao Xiao Tianfan Fu Jimeng Sun 20 3 0 02 Jun 2023
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning Xiangzhe Kong Wen-bing Huang Yang Liu 8 13 0 02 Jun 2023
A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining Shengchao Liu Weitao Du Zhiming Ma Hongyu Guo Jian Tang 22 29 0 28 May 2023
Atomic and Subgraph-aware Bilateral Aggregation for Molecular Representation Learning Jiahao Chen Yurou Liu Jiangmeng Li Bing-Huang Su Jirong Wen 6 0 0 22 May 2023
MolKD: Distilling Cross-Modal Knowledge in Chemical Reactions for Molecular Property Prediction Liang Zeng Lanqing Li Jian Li 30 3 0 03 May 2023
InstructBio: A Large-scale Semi-supervised Learning Paradigm for Biochemical Problems Fang Wu Huiling Qin Siyuan Li Stan Z. Li Xianyuan Zhan Jinbo Xu 6 5 0 08 Apr 2023
GeoTMI:Predicting quantum chemical property with easy-to-obtain geometry via positional denoising Hyeonsu Kim Jeheon Woo Seonghwan Kim Seokhyun Moon Jun Hyeong Kim Woo Youn Kim AI4CE 19 6 0 28 Mar 2023
Highly Accurate Quantum Chemical Property Prediction with Uni-Mol+ Shuqi Lu Zhifeng Gao Di He Linfeng Zhang Guolin Ke 19 24 0 16 Mar 2023
Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Language Philipp Seidl Andreu Vall Sepp Hochreiter G. Klambauer 55 35 0 06 Mar 2023
Denoise Pretraining on Nonequilibrium Molecules for Accurate and Transferable Neural Potentials Yuyang Wang Chang Xu Zijie Li A. Farimani AAML AI4CE 6 20 0 03 Mar 2023
MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation Clément Vignac Nagham Osman Laura Toni P. Frossard DiffM 30 49 0 17 Feb 2023
Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey from Precision to Interpretability Zhiqiang Zhong A. Barkova Davide Mottin 11 8 0 16 Feb 2023
Self-supervised Guided Hypergraph Feature Propagation for Semi-supervised Classification with Missing Node Features Chengxiang Lei Sichao Fu Yuetian Wang Wen-Qiang Qiu Yachen Hu Qinmu Peng Xinge You 17 3 0 16 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 23 8 0 06 Feb 2023
GFlowNets for AI-Driven Scientific Discovery Moksh Jain T. Deleu Jason S. Hartford Cheng-Hao Liu Alex Hernandez-Garcia Yoshua Bengio AI4CE 10 32 0 01 Feb 2023
Knowledge Distillation on Graphs: A Survey Yijun Tian Shichao Pei Xiangliang Zhang Chuxu Zhang Nitesh V. Chawla 8 28 0 01 Feb 2023
OrthoReg: Improving Graph-regularized MLPs via Orthogonality Regularization Hengrui Zhang Shen Wang V. Ioannidis Soji Adeshina Jiani Zhang Xiao Qin Christos Faloutsos Da Zheng George Karypis Philip S. Yu 24 2 0 31 Jan 2023
Task-Agnostic Graph Neural Network Evaluation via Adversarial Collaboration Xiangyu Zhao Hannes Stärk Dominique Beaini Yiren Zhao Pietro Lio' 10 0 0 27 Jan 2023
Coordinating Cross-modal Distillation for Molecular Property Prediction Hao Zhang N. Zhang Ruixin Zhang Lei Shen Yingyi Zhang Meng Liu 12 1 0 30 Nov 2022
BARTSmiles: Generative Masked Language Models for Molecular Representations Gayane Chilingaryan Hovhannes Tamoyan Ani Tevosyan N. Babayan L. Khondkaryan Karen Hambardzumyan Zaven Navoyan Hrant Khachatrian Armen Aghajanyan SSL 16 25 0 29 Nov 2022
Latent Graph Inference using Product Manifolds Haitz Sáez de Ocáriz Borde Anees Kazi Federico Barbero Pietro Lio' BDL 14 17 0 26 Nov 2022
A 3D-Shape Similarity-based Contrastive Approach to Molecular Representation Learning Austin O. Atsango N. Diamant Ziqing Lu Tommaso Biancalani Gabriele Scalia Kangway V Chuang 14 2 0 03 Nov 2022
A Systematic Survey of Chemical Pre-trained Models Jun-Xiong Xia Yanqiao Zhu Yuanqi Du Stan Z.Li AI4CE 46 50 0 29 Oct 2022
Improving Molecular Pretraining with Complementary Featurizations Yanqiao Zhu Dingshuo Chen Yuanqi Du Yingze Wang Qiang Liu Shu Wu AI4CE 28 6 0 29 Sep 2022
Graph Neural Networks for Molecules Yuyang Wang Zijie Li A. Farimani GNN AI4CE 41 20 0 12 Sep 2022
DPA-1: Pretraining of Attention-based Deep Potential Model for Molecular Simulation Duoduo Zhang Hangrui Bi Fu-Zhi Dai Wanrun Jiang Linfeng Zhang Han Wang AI4CE 14 35 0 17 Aug 2022
Energy-Motivated Equivariant Pretraining for 3D Molecular Graphs Rui Jiao Jiaqi Han Wenbing Huang Yu Rong Yang Liu AI4CE 17 45 0 18 Jul 2022
Unified 2D and 3D Pre-Training of Molecular Representations Jinhua Zhu Yingce Xia Lijun Wu Shufang Xie Tao Qin Wen-gang Zhou Houqiang Li Tie-Yan Liu AI4CE 46 67 0 14 Jul 2022
Graph-based Molecular Representation Learning Zhichun Guo Kehan Guo B. Nan Yijun Tian Roshni G. Iyer ... Olaf Wiest Xiangliang Zhang Wei Wang Chuxu Zhang Nitesh V. Chawla AI4CE 10 59 0 08 Jul 2022