Pre-training via Denoising for Molecular Property Prediction

31 May 2022

Sheheryar Zaidi

Michael Schaarschmidt

James Martens

Hyunjik Kim

Yee Whye Teh

Alvaro Sanchez-Gonzalez

Papers citing "Pre-training via Denoising for Molecular Property Prediction"

35 / 35 papers shown

Title
Multi-Modal Molecular Representation Learning via Structure Awareness Rong Yin Ruyue Liu Xiaoshuai Hao Xingrui Zhou Yang Liu Can Ma Weiping Wang 36 0 0 09 May 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 59 1 0 13 Mar 2025
Pre-training Graph Neural Networks with Structural Fingerprints for Materials Discovery Shuyi Jia Shitij Govil Manav Ramprasad Victor Fung AI4CE 70 1 0 03 Mar 2025
A Survey of Graph Transformers: Architectures, Theories and Applications Chaohao Yuan Kangfei Zhao Ercan Engin Kuruoglu Liang Wang Tingyang Xu Wenbing Huang Deli Zhao Hong Cheng Yu Rong 57 4 0 23 Feb 2025
Equivariant Masked Position Prediction for Efficient Molecular Representation Junyi An Chao Qu Yun-Fei Shi XinHao Liu Qianwei Tang Fenglei Cao Yuan Qi 45 0 0 12 Feb 2025
ChemDFM-X: Towards Large Multimodal Model for Chemistry Zihan Zhao B. Chen Jingpiao Li Lu Chen Liyang Wen ... Ziping Wan Yansi Li Zhongyang Dai Xin Chen Kai Yu AI4CE 67 3 0 03 Jan 2025
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 45 5 0 14 Oct 2024
Representation Alignment for Generation: Training Diffusion Transformers Is Easier Than You Think Sihyun Yu Sangkyung Kwak Huiwon Jang Jongheon Jeong Jonathan Huang Jinwoo Shin Saining Xie OCL 81 70 0 09 Oct 2024
Geometric Representation Condition Improves Equivariant Molecule Generation Zian Li Cai Zhou Xiyuan Wang Xingang Peng Muhan Zhang 50 2 0 04 Oct 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 55 12 0 19 Jun 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 51 23 0 01 Mar 2024
PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design Chuanrui Wang Bozitao Zhong Zuobai Zhang Narendra Chaudhary Sanchit Misra Jian Tang 30 5 0 30 Nov 2023
From Molecules to Materials: Pre-training Large Generalizable Models for Atomic Property Prediction Nima Shoghi Adeesh Kolluru John R. Kitchin Zachary W. Ulissi C. L. Zitnick Brandon M. Wood AI4CE 29 32 0 25 Oct 2023
Fractional Denoising for 3D Molecular Pre-training Shi Feng Yuyan Ni Yanyan Lan Zhiming Ma Wei-Ying Ma DiffM AI4CE 52 25 0 20 Jul 2023
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning Xiangzhe Kong Wen-bing Huang Yang Liu 37 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 34 31 0 28 May 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 47 6 0 28 Mar 2023
Denoise Pretraining on Nonequilibrium Molecules for Accurate and Transferable Neural Potentials Yuyang Wang Chang Xu Zijie Li A. Farimani AAML AI4CE 34 21 0 03 Mar 2023
SupSiam: Non-contrastive Auxiliary Loss for Learning from Molecular Conformers Michael R. Maser Ji Won Park J. Lin Jae Hyeon Lee Nathan C. Frey Andrew Watkins 24 5 0 15 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 48 8 0 06 Feb 2023
Implicit Geometry and Interaction Embeddings Improve Few-Shot Molecular Property Prediction Christopher Fifty Joseph M. Paggi Ehsan Amid J. Leskovec R. Dror AI4CE 25 0 0 04 Feb 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 34 23 0 18 Nov 2022
A simple, efficient and scalable contrastive masked autoencoder for learning visual representations Shlok Kumar Mishra Joshua Robinson Huiwen Chang David Jacobs Aaron Sarna Aaron Maschinot Dilip Krishnan DiffM 56 31 0 30 Oct 2022
Learned Force Fields Are Ready For Ground State Catalyst Discovery Michael Schaarschmidt M. Rivière A. Ganose J. Spencer Alex Gaunt J. Kirkpatrick Simon Axelrod Peter W. Battaglia Jonathan Godwin 49 10 0 26 Sep 2022
Graph Neural Networks for Molecules Yuyang Wang Zijie Li A. Farimani GNN AI4CE 52 21 0 12 Sep 2022
A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language Fuchun Sun Dazhao Du Zhao-Qing Yang Yujie Zhou Jiangmeng Li Anyi Rao Haoran Sun Zhiwu Lu Ji-Rong Wen 66 109 0 12 Sep 2022
Diffusion Models: A Comprehensive Survey of Methods and Applications Ling Yang Zhilong Zhang Yingxia Shao Shenda Hong Runsheng Xu Yue Zhao Wentao Zhang Bin Cui Ming-Hsuan Yang DiffM MedIm 226 1,320 0 02 Sep 2022
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 132 306 0 07 Oct 2021
Rapid training of deep neural networks without skip connections or normalization layers using Deep Kernel Shaping James Martens Andy Ballard Guillaume Desjardins G. Swirszcz Valentin Dalibard Jascha Narain Sohl-Dickstein S. Schoenholz 88 43 0 05 Oct 2021
Carbon Emissions and Large Neural Network Training David A. Patterson Joseph E. Gonzalez Quoc V. Le Chen Liang Lluís-Miquel Munguía D. Rothchild David R. So Maud Texier J. Dean AI4CE 253 647 0 21 Apr 2021
E(3)-Equivariant Graph Neural Networks for Data-Efficient and Accurate Interatomic Potentials Simon L. Batzner Albert Musaelian Lixin Sun Mario Geiger J. Mailoa M. Kornbluth N. Molinari Tess E. Smidt Boris Kozinsky 256 1,244 0 08 Jan 2021
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 232 508 0 20 Oct 2020
Dynamical Isometry and a Mean Field Theory of CNNs: How to Train 10,000-Layer Vanilla Convolutional Neural Networks Lechao Xiao Yasaman Bahri Jascha Narain Sohl-Dickstein S. Schoenholz Jeffrey Pennington 247 350 0 14 Jun 2018
Interaction Networks for Learning about Objects, Relations and Physics Peter W. Battaglia Razvan Pascanu Matthew Lai Danilo Jimenez Rezende Koray Kavukcuoglu AI4CE OCL PINN GNN 283 1,401 0 01 Dec 2016
Geometric deep learning: going beyond Euclidean data M. Bronstein Joan Bruna Yann LeCun Arthur Szlam P. Vandergheynst GNN 264 3,246 0 24 Nov 2016