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Geometric Representation Condition Improves Equivariant Molecule Generation

4 October 2024

Papers citing "Geometric Representation Condition Improves Equivariant Molecule Generation"

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Title
Scalable Autoregressive 3D Molecule Generation Austin H. Cheng Chong Sun Alán Aspuru-Guzik 100 1 0 20 May 2025
Straight-Line Diffusion Model for Efficient 3D Molecular Generation Yuyan Ni Shikun Feng Haohan Chi Bowen Zheng Huan-ang Gao Wei-Ying Ma Zhi-Ming Ma Yanyan Lan DiffM 112 3 0 04 Mar 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 122 7 0 14 Oct 2024
Pre-training with Fractional Denoising to Enhance Molecular Property Prediction Yuyan Ni Shikun Feng Xin Hong Yuancheng Sun Wei-Ying Ma Zhiming Ma Qiwei Ye Yanyan Lan AI4CE 81 18 0 14 Jul 2024
Unified Generative Modeling of 3D Molecules via Bayesian Flow Networks Yuxuan Song Jingjing Gong Yanru Qu Hao Zhou Mingyue Zheng Jingjing Liu Wei-Ying Ma 89 13 0 17 Mar 2024
On the Completeness of Invariant Geometric Deep Learning Models Zian Li Xiyuan Wang Shijia Kang Muhan Zhang 99 3 0 07 Feb 2024
Equivariant Flow Matching with Hybrid Probability Transport Yuxuan Song Jingjing Gong Minkai Xu Ziyao Cao Yanyan Lan Stefano Ermon Hao Zhou Wei-Ying Ma DiffM 87 57 0 12 Dec 2023
Guided Flows for Generative Modeling and Decision Making Qinqing Zheng Matt Le Neta Shaul Y. Lipman Aditya Grover Ricky T. Q. Chen 114 46 0 22 Nov 2023
Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation Tuan Le Julian Cremer Frank Noé Djork-Arné Clevert Kristof T. Schütt DiffM 131 31 0 29 Sep 2023
Fractional Denoising for 3D Molecular Pre-training Shi Feng Yuyan Ni Yanyan Lan Zhiming Ma Wei-Ying Ma DiffM AI4CE 109 29 0 20 Jul 2023
Reward-Directed Conditional Diffusion: Provable Distribution Estimation and Reward Improvement Hui Yuan Kaixuan Huang Chengzhuo Ni Minshuo Chen Mengdi Wang DiffM 94 37 0 13 Jul 2023
Geometric Latent Diffusion Models for 3D Molecule Generation Minkai Xu Alexander Powers R. Dror Stefano Ermon J. Leskovec DiffM AI4CE 160 152 0 02 May 2023
MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation Clément Vignac Nagham Osman Laura Toni P. Frossard DiffM 110 63 0 17 Feb 2023
Is Distance Matrix Enough for Geometric Deep Learning? Zian Li Xiyuan Wang Yinan Huang Muhan Zhang 73 19 0 11 Feb 2023
Geometry-Complete Diffusion for 3D Molecule Generation and Optimization Alex Morehead Jianlin Cheng DiffM 81 30 0 08 Feb 2023
Graph Generation with Diffusion Mixture Jaehyeong Jo Dongki Kim Sung Ju Hwang DiffM 106 23 0 07 Feb 2023
Fast Graph Generation via Spectral Diffusion Tianze Luo Zhanfeng Mo Sinno Jialin Pan DiffM 101 27 0 16 Nov 2022
Flow Matching for Generative Modeling Y. Lipman Ricky T. Q. Chen Heli Ben-Hamu Maximilian Nickel Matt Le OOD 311 1,394 0 06 Oct 2022
Sampling is as easy as learning the score: theory for diffusion models with minimal data assumptions Sitan Chen Sinho Chewi Jungshian Li Yuanzhi Li Adil Salim Anru R. Zhang DiffM 227 279 0 22 Sep 2022
Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flow Xingchao Liu Chengyue Gong Qiang Liu OOD 274 1,056 0 07 Sep 2022
Diffusion-based Molecule Generation with Informative Prior Bridges Lemeng Wu Chengyue Gong Xingchao Liu Mao Ye Qiang Liu DiffM 106 117 0 02 Sep 2022
Convergence of denoising diffusion models under the manifold hypothesis Valentin De Bortoli DiffM 100 171 0 10 Aug 2022
Classifier-Free Diffusion Guidance Jonathan Ho Tim Salimans FaML 210 3,982 0 26 Jul 2022
Energy-Motivated Equivariant Pretraining for 3D Molecular Graphs Rui Jiao Jiaqi Han Wenbing Huang Yu Rong Yang Liu AI4CE 101 49 0 18 Jul 2022
Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matching Shengchao Liu Hongyu Guo Jian Tang 116 80 0 27 Jun 2022
Pre-training via Denoising for Molecular Property Prediction Sheheryar Zaidi Michael Schaarschmidt James Martens Hyunjik Kim Yee Whye Teh Alvaro Sanchez-Gonzalez Peter W. Battaglia Razvan Pascanu Jonathan Godwin DiffM AI4CE 129 127 0 31 May 2022
Equivariant Diffusion for Molecule Generation in 3D Emiel Hoogeboom Victor Garcia Satorras Clément Vignac Max Welling DiffM 169 628 0 31 Mar 2022
GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation Minkai Xu Lantao Yu Yang Song Chence Shi Stefano Ermon Jian Tang BDL DiffM 169 524 0 06 Mar 2022
TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentials Philipp Thölke Gianni De Fabritiis AI4CE 129 197 0 05 Feb 2022
High-Resolution Image Synthesis with Latent Diffusion Models Robin Rombach A. Blattmann Dominik Lorenz Patrick Esser Bjorn Ommer 3DV 615 15,855 0 20 Dec 2021
Top-N: Equivariant set and graph generation without exchangeability Clément Vignac P. Frossard BDL 148 35 0 05 Oct 2021
Inverse design of 3d molecular structures with conditional generative neural networks Niklas W. A. Gebauer M. Gastegger Stefaan S. P. Hessmann Klaus-Robert Muller Kristof T. Schütt AI4CE 259 180 0 10 Sep 2021
ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction Xiaomin Fang Lihang Liu Jieqiong Lei Donglong He Shanzhuo Zhang Jingbo Zhou Fan Wang Hua Wu Haifeng Wang AI4CE 82 460 0 11 Jun 2021
E(n) Equivariant Normalizing Flows Victor Garcia Satorras Emiel Hoogeboom F. Fuchs Ingmar Posner Max Welling BDL 113 182 0 19 May 2021
An Empirical Study of Training Self-Supervised Vision Transformers Xinlei Chen Saining Xie Kaiming He ViT 185 1,875 0 05 Apr 2021
E(n) Equivariant Graph Neural Networks Victor Garcia Satorras Emiel Hoogeboom Max Welling 119 1,038 0 19 Feb 2021
Score-Based Generative Modeling through Stochastic Differential Equations Yang Song Jascha Narain Sohl-Dickstein Diederik P. Kingma Abhishek Kumar Stefano Ermon Ben Poole DiffM SyDa 559 6,606 0 26 Nov 2020
An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale Alexey Dosovitskiy Lucas Beyer Alexander Kolesnikov Dirk Weissenborn Xiaohua Zhai ... Matthias Minderer G. Heigold Sylvain Gelly Jakob Uszkoreit N. Houlsby ViT 772 41,877 0 22 Oct 2020
A Contrastive Learning Approach for Training Variational Autoencoder Priors J. Aneja Alex Schwing Jan Kautz Arash Vahdat DRL 124 83 0 06 Oct 2020
Denoising Diffusion Implicit Models Jiaming Song Chenlin Meng Stefano Ermon VLM DiffM 334 7,531 0 06 Oct 2020
GEOM: Energy-annotated molecular conformations for property prediction and molecular generation Simon Axelrod Rafael Gómez-Bombarelli 3DV AI4CE 120 222 0 09 Jun 2020
Language Models are Few-Shot Learners Tom B. Brown Benjamin Mann Nick Ryder Melanie Subbiah Jared Kaplan ... Christopher Berner Sam McCandlish Alec Radford Ilya Sutskever Dario Amodei BDL 1.2K 42,712 0 28 May 2020
Cormorant: Covariant Molecular Neural Networks Brandon M. Anderson Truong-Son Hy Risi Kondor 139 426 0 06 Jun 2019
Generating Diverse High-Fidelity Images with VQ-VAE-2 Ali Razavi Aaron van den Oord Oriol Vinyals DRL BDL 209 1,832 0 02 Jun 2019
Symmetry-adapted generation of 3d point sets for the targeted discovery of molecules Niklas W. A. Gebauer M. Gastegger Kristof T. Schütt 164 211 0 02 Jun 2019
Diagnosing and Enhancing VAE Models Bin Dai David Wipf DRL 101 381 0 14 Mar 2019
BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding Jacob Devlin Ming-Wei Chang Kenton Lee Kristina Toutanova VLM SSL SSeg 1.9K 95,604 0 11 Oct 2018
Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds Nathaniel Thomas Tess E. Smidt S. Kearnes Lusann Yang Li Li Kai Kohlhoff Patrick F. Riley 3DPC 152 980 0 22 Feb 2018
Neural Discrete Representation Learning Aaron van den Oord Oriol Vinyals Koray Kavukcuoglu BDL SSL OCL 259 5,093 0 02 Nov 2017
Attention Is All You Need Ashish Vaswani Noam M. Shazeer Niki Parmar Jakob Uszkoreit Llion Jones Aidan Gomez Lukasz Kaiser Illia Polosukhin 3DV 980 133,443 0 12 Jun 2017