$Diffusion Models in $\textit{De Novo}$ Drug Design$

Diffusion Models in $\textit{De Novo}$ Drug Design

7 June 2024

Papers citing "Diffusion Models in $\textit{De Novo}$ Drug Design"

41 / 41 papers shown

Title
PILOT: Equivariant diffusion for pocket conditioned de novo ligand generation with multi-objective guidance via importance sampling Julian Cremer Tuan Le Frank Noé Djork-Arné Clevert Kristof T. Schütt DiffM 55 9 0 23 May 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 56 3 0 13 Feb 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 58 8 0 15 Jan 2024
MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter Zhiyuan Liu Changhao Nai Yancheng Luo Hao Fei Yixin Cao Kenji Kawaguchi Xiang Wang Tat-Seng Chua 60 89 0 19 Oct 2023
Adding Conditional Control to Text-to-Image Diffusion Models Lvmin Zhang Anyi Rao Maneesh Agrawala AI4CE 94 4,074 1 10 Feb 2023
DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding Haitao Lin Yufei Huang Odin Zhang Siqi Ma Meng Liu X. Li Lirong Wu Shuiwang Ji Tingjun Hou Stan Z. Li DiffM 51 65 0 21 Nov 2022
Fast Graph Generation via Spectral Diffusion Tianze Luo Zhanfeng Mo Sinno Jialin Pan DiffM 60 25 0 16 Nov 2022
Diffusion Models for Graphs Benefit From Discrete State Spaces K. Haefeli Karolis Martinkus Nathanael Perraudin Roger Wattenhofer DiffM 148 55 0 04 Oct 2022
Equivariant Energy-Guided SDE for Inverse Molecular Design Fan Bao Min Zhao Zhongkai Hao Pei‐Yun Li Chongxuan Li Jun Zhu DiffM 213 67 0 30 Sep 2022
State-specific protein-ligand complex structure prediction with a multi-scale deep generative model Zhuoran Qiao Weili Nie Arash Vahdat Thomas F. Miller Anima Anandkumar DiffM 73 90 0 30 Sep 2022
SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials Peter K. Eastman P. Behara David L. Dotson Raimondas Galvelis John E. Herr ... J. Chodera Benjamin P. Pritchard Yuanqing Wang Gianni De Fabritiis T. Markland 84 108 0 21 Sep 2022
Diffusion-based Molecule Generation with Informative Prior Bridges Lemeng Wu Chengyue Gong Xingchao Liu Mao Ye Qiang Liu DiffM 63 113 0 02 Sep 2022
Analog Bits: Generating Discrete Data using Diffusion Models with Self-Conditioning Ting-Li Chen Ruixiang Zhang Geoffrey E. Hinton DiffM 71 302 0 08 Aug 2022
MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields Ilyes Batatia D. P. Kovács G. Simm Christoph Ortner Gábor Csányi 66 470 0 15 Jun 2022
Exploring Chemical Space with Score-based Out-of-distribution Generation Seul Lee Jaehyeong Jo Sung Ju Hwang OODD 76 78 0 06 Jun 2022
DPM-Solver: A Fast ODE Solver for Diffusion Probabilistic Model Sampling in Around 10 Steps Cheng Lu Yuhao Zhou Fan Bao Jianfei Chen Chongxuan Li Jun Zhu DiffM 172 1,403 0 02 Jun 2022
Torsional Diffusion for Molecular Conformer Generation Bowen Jing Gabriele Corso Jeffrey Chang Regina Barzilay Tommi Jaakkola DiffM BDL 73 270 0 01 Jun 2022
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets Xingang Peng Shitong Luo Jiaqi Guan Qi Xie Jian-wei Peng Jianzhu Ma 52 187 0 15 May 2022
Equivariant Diffusion for Molecule Generation in 3D Emiel Hoogeboom Victor Garcia Satorras Clément Vignac Max Welling DiffM 94 606 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 125 511 0 06 Mar 2022
Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations Jaehyeong Jo Seul Lee Sung Ju Hwang DiffM 58 223 0 05 Feb 2022
Analytic-DPM: an Analytic Estimate of the Optimal Reverse Variance in Diffusion Probabilistic Models Fan Bao Chongxuan Li Jun Zhu Bo Zhang DiffM 74 343 0 17 Jan 2022
Improved Denoising Diffusion Probabilistic Models Alex Nichol Prafulla Dhariwal DiffM 274 3,648 0 18 Feb 2021
GraphDF: A Discrete Flow Model for Molecular Graph Generation Youzhi Luo Keqiang Yan Shuiwang Ji DRL 211 198 0 01 Feb 2021
A Generalization of Transformer Networks to Graphs Vijay Prakash Dwivedi Xavier Bresson AI4CE 98 747 0 17 Dec 2020
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 289 6,401 0 26 Nov 2020
MoFlow: An Invertible Flow Model for Generating Molecular Graphs Chengxi Zang Fei Wang BDL 114 292 0 17 Jun 2020
GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation Chence Shi Minkai Xu Zhaocheng Zhu Weinan Zhang Ming Zhang Jian Tang 158 437 0 26 Jan 2020
Generative Modeling by Estimating Gradients of the Data Distribution Yang Song Stefano Ermon SyDa DiffM 206 3,867 0 12 Jul 2019
GraphNVP: An Invertible Flow Model for Generating Molecular Graphs Kaushalya Madhawa Katushiko Ishiguro Kosuke Nakago Motoki Abe BDL 96 191 0 28 May 2019
Sliced Score Matching: A Scalable Approach to Density and Score Estimation Yang Song Sahaj Garg Jiaxin Shi Stefano Ermon 91 416 0 17 May 2019
Analyzing Learned Molecular Representations for Property Prediction Kevin Kaichuang Yang Kyle Swanson Wengong Jin Connor W. Coley Philipp Eiden ... Andrew Palmer Volker Settels Tommi Jaakkola K. Jensen Regina Barzilay 93 1,314 0 02 Apr 2019
Graph Neural Networks: A Review of Methods and Applications Jie Zhou Ganqu Cui Shengding Hu Zhengyan Zhang Cheng Yang Zhiyuan Liu Lifeng Wang Changcheng Li Maosong Sun AI4CE GNN 794 5,492 0 20 Dec 2018
Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models Daniil Polykovskiy Alexander Zhebrak Benjamín Sánchez-Lengeling Sergey Golovanov Oktai Tatanov ... Simon Johansson Hongming Chen Sergey I. Nikolenko Alán Aspuru-Guzik Alex Zhavoronkov ELM 243 647 0 29 Nov 2018
GuacaMol: Benchmarking Models for De Novo Molecular Design Nathan Brown Marco Fiscato Marwin H. S. Segler Alain C. Vaucher ELM 96 706 0 22 Nov 2018
Constrained Graph Variational Autoencoders for Molecule Design Qi Liu Miltiadis Allamanis Marc Brockschmidt Alexander L. Gaunt BDL 59 456 0 23 May 2018
NeVAE: A Deep Generative Model for Molecular Graphs Bidisha Samanta A. De G. Jana P. Chattaraj Niloy Ganguly Manuel Gomez Rodriguez GNN DRL BDL DiffM 58 217 0 14 Feb 2018
GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoders M. Simonovsky N. Komodakis GNN BDL 103 848 0 09 Feb 2018
SchNet: A continuous-filter convolutional neural network for modeling quantum interactions Kristof T. Schütt Pieter-Jan Kindermans Huziel Enoc Sauceda Felix Stefan Chmiela A. Tkatchenko K. Müller 134 1,074 0 26 Jun 2017
An Introduction to Convolutional Neural Networks K. O’Shea Ryan Nash FaML HAI 60 3,126 0 26 Nov 2015
Deep Unsupervised Learning using Nonequilibrium Thermodynamics Jascha Narain Sohl-Dickstein Eric A. Weiss Niru Maheswaranathan Surya Ganguli SyDa DiffM 238 6,875 0 12 Mar 2015

Diffusion Models in De Novo\textit{De Novo}De Novo Drug Design

Papers citing "Diffusion Models in $\textit{De Novo}$ Drug Design"

Diffusion Models in $\textit{De Novo}$ Drug Design