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Equivariant Diffusion for Molecule Generation in 3D

31 March 2022

Emiel Hoogeboom

Victor Garcia Satorras

Papers citing "Equivariant Diffusion for Molecule Generation in 3D"

50 / 404 papers shown

Title
Generative AI and Process Systems Engineering: The Next Frontier Benjamin Decardi-Nelson Abdulelah S. Alshehri Akshay Ajagekar Fengqi You AI4CE LLMAG 78 29 0 15 Feb 2024
Position: Topological Deep Learning is the New Frontier for Relational Learning Theodore Papamarkou Tolga Birdal Michael M. Bronstein Gunnar Carlsson Justin Curry ... Petar Velickovic Bei Wang Yusu Wang Guo-Wei Wei Ghada Zamzmi AI4CE 99 35 0 14 Feb 2024
Zero Shot Molecular Generation via Similarity Kernels Rokas Elijosius Fabian Zills Ilyes Batatia Sam Walton Norwood D. P. Kovács Christian Holm Gábor Csányi DiffM 68 4 0 13 Feb 2024
A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation Xiangru Tang Howard Dai Elizabeth Knight Fang Wu Yunyang Li Tianxiao Li Mark B. Gerstein 96 31 0 13 Feb 2024
Denoising Diffusion Restoration Tackles Forward and Inverse Problems for the Laplace Operator Amartya Mukherjee M. Stadt Lena Podina Mohammad Kohandel Jun Liu DiffM 51 0 0 13 Feb 2024
Iterated Denoising Energy Matching for Sampling from Boltzmann Densities Tara Akhound-Sadegh Jarrid Rector-Brooks A. Bose Sarthak Mittal Pablo Lemos ... Siamak Ravanbakhsh Gauthier Gidel Yoshua Bengio Nikolay Malkin Alexander Tong DiffM 105 58 0 09 Feb 2024
Social Physics Informed Diffusion Model for Crowd Simulation Hongyi Chen Jingtao Ding Yong Li Yue Wang Xiao-Ping Zhang AI4CE 76 15 0 08 Feb 2024
Pard: Permutation-Invariant Autoregressive Diffusion for Graph Generation Lingxiao Zhao Xueying Ding Leman Akoglu DiffM 90 10 0 06 Feb 2024
Constrained Synthesis with Projected Diffusion Models Jacob K Christopher Stephen Baek Ferdinando Fioretto DiffM 91 20 0 05 Feb 2024
Equivariant Symmetry Breaking Sets YuQing Xie Tess E. Smidt 68 4 0 05 Feb 2024
Overcoming Order in Autoregressive Graph Generation Edo Cohen-Karlik Eyal Rozenberg Daniel Freedman 75 1 0 04 Feb 2024
Diffusion Model-Based Multiobjective Optimization for Gasoline Blending Scheduling Wenxuan Fang Wei Du Renchu He Yang Tang Yaochu Jin Gary G. Yen DiffM 65 6 0 04 Feb 2024
Diffusion-based Graph Generative Methods Hongyang Chen Can Xu Lingyu Zheng Qiang Zhang Xuemin Lin DiffM MedIm 92 0 0 28 Jan 2024
FREED++: Improving RL Agents for Fragment-Based Molecule Generation by Thorough Reproduction Alexander Telepov Artem Tsypin Kuzma Khrabrov Sergey Yakukhnov Pavel Strashnov ... Egor Rumiantsev Daniel Ezhov Manvel Avetisian Olga Popova Artur Kadurin 72 5 0 18 Jan 2024
Binding-Adaptive Diffusion Models for Structure-Based Drug Design Zhilin Huang Ling Yang Zaixi Zhang Xiangxin Zhou Yu Bao Xiawu Zheng Yuwei Yang Yu Wang Wenming Yang DiffM 88 9 0 15 Jan 2024
Demystifying Variational Diffusion Models Fabio De Sousa Ribeiro Ben Glocker DiffM 88 0 0 11 Jan 2024
Reflected Schrödinger Bridge for Constrained Generative Modeling Wei Deng Yu Chen Nicole Tianjiao Yang Hengrong Du Qi Feng Ricky T. Q. Chen 62 8 0 06 Jan 2024
Geometric-Facilitated Denoising Diffusion Model for 3D Molecule Generation Can Xu Haosen Wang Weigang Wang Pengfei Zheng Hongyang Chen DiffM 102 8 0 05 Jan 2024
A Multi-Modal Contrastive Diffusion Model for Therapeutic Peptide Generation Yongkang Wang Xuan Liu Feng Huang Zhankun Xiong Wen Zhang 114 14 0 25 Dec 2023
Towards Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion Alex Morehead Jeffrey A. Ruffolo Aadyot Bhatnagar Ali Madani DiffM 76 10 0 21 Dec 2023
PolyDiff: Generating 3D Polygonal Meshes with Diffusion Models A. Alliegro Yawar Siddiqui Tatiana Tommasi Matthias Nießner 89 36 0 18 Dec 2023
Continuous Diffusion for Mixed-Type Tabular Data Markus Mueller Kathrin Gruber Dennis Fok DiffM 179 5 0 16 Dec 2023
Autoregressive fragment-based diffusion for pocket-aware ligand design Mahdi Ghorbani Leo Gendelev Paul Beroza Michael J. Keiser DiffM 59 10 0 15 Dec 2023
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 81 57 0 12 Dec 2023
One-Step Diffusion Distillation via Deep Equilibrium Models Zhengyang Geng Ashwini Pokle Trevor Killeen 75 33 0 12 Dec 2023
Spectroscopy-Guided Discovery of Three-Dimensional Structures of Disordered Materials with Diffusion Models H. Kwon Tim Hsu Wenyu Sun Wonseok Jeong Fikret Aydin ... Xiao Chen Matthew R. Carbone Deyu Lu Fei Zhou Tuan Anh Pham DiffM 92 11 0 09 Dec 2023
Molecule Joint Auto-Encoding: Trajectory Pretraining with 2D and 3D Diffusion Weitao Du Jiujiu Chen Xuecang Zhang Zhiming Ma Shengchao Liu DiffM 80 9 0 06 Dec 2023
Swallowing the Bitter Pill: Simplified Scalable Conformer Generation Yuyang Wang Ahmed A. A. Elhag Navdeep Jaitly J. Susskind Miguel Angel Bautista DiffM 105 26 0 27 Nov 2023
Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure Ian Dunn D. Koes DiffM GNN 63 3 0 22 Nov 2023
MonoDiffusion: Self-Supervised Monocular Depth Estimation Using Diffusion Model Shuwei Shao Zhongcai Pei Weihai Chen Dingchi Sun Peter C. Y. Chen Zhengguo Li MDE DiffM 77 8 0 13 Nov 2023
3DifFusionDet: Diffusion Model for 3D Object Detection with Robust LiDAR-Camera Fusion Xinhao Xiang Simon Dräger Jiawei Zhang 60 1 0 07 Nov 2023
STRIDE: Structure-guided Generation for Inverse Design of Molecules Shehtab Zaman D. Akhiyarov Mauricio Araya-Polo Kenneth Chiu 87 1 0 06 Nov 2023
Investigating the Behavior of Diffusion Models for Accelerating Electronic Structure Calculations D. Rothchild Andrew S. Rosen Eric Taw Connie Robinson Joseph E. Gonzalez Aditi S. Krishnapriyan DiffM 58 2 0 02 Nov 2023
The Blessing of Randomness: SDE Beats ODE in General Diffusion-based Image Editing Shen Nie Hanzhong Guo Cheng Lu Yuhao Zhou Chenyu Zheng Chongxuan Li DiffM 132 43 0 02 Nov 2023
Score Normalization for a Faster Diffusion Exponential Integrator Sampler Guoxuan Xia Duolikun Danier Ayan Das Stathi Fotiadis F. Nabiei Ushnish Sengupta A. Bernacchia DiffM 51 3 0 31 Oct 2023
Purify++: Improving Diffusion-Purification with Advanced Diffusion Models and Control of Randomness Boya Zhang Weijian Luo Zhihua Zhang 75 12 0 28 Oct 2023
Generative Fractional Diffusion Models Gabriel Nobis Maximilian Springenberg Marco Aversa Michael Detzel Rembert Daems ... Tolga Birdal Manfred Opper Christoph Knochenhauer Luis Oala Wojciech Samek DiffM 76 6 0 26 Oct 2023
Free-form Flows: Make Any Architecture a Normalizing Flow Felix Dräxler Peter Sorrenson Lea Zimmermann Armand Rousselot Ullrich Kothe TPM DRL AI4CE BDL 103 11 0 25 Oct 2023
Discriminator Guidance for Autoregressive Diffusion Models Filip Ekstrom Kelvinius Fredrik Lindsten DiffM 42 5 0 24 Oct 2023
AutoDiff: combining Auto-encoder and Diffusion model for tabular data synthesizing Namjoon Suh Xiaofeng Lin Din-Yin Hsieh Merhdad Honarkhah Guang Cheng 83 16 0 24 Oct 2023
Closed-Form Diffusion Models Christopher Scarvelis Haitz Sáez de Ocáriz Borde Justin Solomon DiffM 189 12 0 19 Oct 2023
Reflection-Equivariant Diffusion for 3D Structure Determination from Isotopologue Rotational Spectra in Natural Abundance Austin H. Cheng Alston Lo Santiago Miret Brooks H Pate Alán Aspuru-Guzik 74 6 0 17 Oct 2023
MOFDiff: Coarse-grained Diffusion for Metal-Organic Framework Design Xiang Fu Tian Xie Andrew S. Rosen Tommi Jaakkola Jake A. Smith DiffM 78 12 0 16 Oct 2023
From Continuous Dynamics to Graph Neural Networks: Neural Diffusion and Beyond Andi Han Dai Shi Lequan Lin Junbin Gao AI4CE GNN 95 24 0 16 Oct 2023
Data-Driven Score-Based Models for Generating Stable Structures with Adaptive Crystal Cells Arsen Sultanov J. Crivello Tabea Rebafka Nataliya Sokolovska DiffM 70 6 0 16 Oct 2023
Kernel-Elastic Autoencoder for Molecular Design Haote Li Yu Shee B. Allen F. Maschietto Victor S. Batista 71 7 0 12 Oct 2023
Observation-Guided Diffusion Probabilistic Models Junoh Kang Jinyoung Choi Sungik Choi Bohyung Han 56 1 0 06 Oct 2023
Deep Generative Models of Music Expectation Ninon Lizé Masclef T. A. Keller DiffM 22 2 0 05 Oct 2023
Fast, Expressive SE $(n)$ Equivariant Networks through Weight-Sharing in Position-Orientation Space Erik J. Bekkers Sharvaree P. Vadgama Rob D. Hesselink P. A. V. D. Linden David W. Romero 67 30 0 04 Oct 2023
SE(3)-Stochastic Flow Matching for Protein Backbone Generation A. Bose Tara Akhound-Sadegh Guillaume Huguet Kilian Fatras Jarrid Rector-Brooks Cheng-Hao Liu A. Nica Maksym Korablyov Michael M. Bronstein Alexander Tong DiffM 113 84 0 03 Oct 2023