Exploring Chemical Space with Score-based Out-of-distribution Generation

6 June 2022

Papers citing "Exploring Chemical Space with Score-based Out-of-distribution Generation"

50 / 59 papers shown

Title
Learning Flexible Forward Trajectories for Masked Molecular Diffusion Hyunjin Seo Taewon Kim Sihyun Yu SungSoo Ahn DiffM AI4CE 100 0 0 22 May 2025
Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation Mohit Pandey G. Subbaraj Artem Cherkasov Martin Ester Emmanuel Bengio AI4CE 101 1 0 08 Mar 2025
MOLLM: Multi-Objective Large Language Model for Molecular Design -- Optimizing with Experts Nian Ran Yue Wang Richard Allmendinger 107 1 0 18 Feb 2025
GOLD: Graph Out-of-Distribution Detection via Implicit Adversarial Latent Generation Danny Wang Ruihong Qiu Guangdong Bai Zi Huang 306 2 0 09 Feb 2025
Bayesian Flow Is All You Need to Sample Out-of-Distribution Chemical Spaces Nianze Tao OOD OODD BDL 144 0 0 16 Dec 2024
MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning Peter Eckmann D. Wu G. Heinzelmann Michael K. Gilson Rose Yu AI4CE 59 0 0 15 Oct 2024
Chemistry-Inspired Diffusion with Non-Differentiable Guidance Yuchen Shen Chenhao Zhang Sijie Fu Chenghui Zhou Newell Washburn Barnabás Póczos 72 0 0 09 Oct 2024
Graph Representation Learning via Causal Diffusion for Out-of-Distribution Recommendation Chu Zhao Enneng Yang Yuliang Liang Pengxiang Lan Yuting Liu Jianzhe Zhao Guibing Guo Xingwei Wang OOD DiffM CML 173 7 0 01 Aug 2024
Design Editing for Offline Model-based Optimization Ye Yuan Youyuan Zhang Can Chen Haolun Wu Zixuan Li Jianmo Li James J. Clark Xue Liu 88 4 0 22 May 2024
Guided Multi-objective Generative AI to Enhance Structure-based Drug Design Amit Kadan Kevin Ryczko Erika Lloyd A. Roitberg Takeshi Yamazaki 114 1 0 20 May 2024
LIMO: Latent Inceptionism for Targeted Molecule Generation Peter Eckmann Kunyang Sun Bo Zhao Mudong Feng Michael K. Gilson Rose Yu BDL 58 46 0 17 Jun 2022
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets Xingang Peng Shitong Luo Jiaqi Guan Qi Xie Jian-wei Peng Jianzhu Ma 52 179 0 15 May 2022
Generating High Fidelity Data from Low-density Regions using Diffusion Models Vikash Sehwag C. Hazirbas Albert Gordo Firat Ozgenel Cristian Canton Ferrer DiffM 76 67 0 31 Mar 2022
Equivariant Diffusion for Molecule Generation in 3D Emiel Hoogeboom Victor Garcia Satorras Clément Vignac Max Welling DiffM 87 594 0 31 Mar 2022
A 3D Generative Model for Structure-Based Drug Design Shitong Luo Jiaqi Guan Jianzhu Ma Jian-wei Peng DiffM 86 181 0 20 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 120 502 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 53 220 0 05 Feb 2022
A Conditional Point Diffusion-Refinement Paradigm for 3D Point Cloud Completion Zhaoyang Lyu Zhifeng Kong Xudong Xu Liang Pan Dahua Lin DiffM BDL 237 121 0 07 Dec 2021
Solving Inverse Problems in Medical Imaging with Score-Based Generative Models Yang Song Liyue Shen Lei Xing Stefano Ermon DiffM SyDa OffRL MedIm 78 518 0 15 Nov 2021
DOCKSTRING: easy molecular docking yields better benchmarks for ligand design Miguel García-Ortegón G. Simm Austin Tripp José Miguel Hernández-Lobato A. Bender S. Bacallado 58 78 0 29 Oct 2021
Score-based diffusion models for accelerated MRI Hyungjin Chung Jong Chul Ye DiffM MedIm 74 413 0 08 Oct 2021
Hit and Lead Discovery with Explorative RL and Fragment-based Molecule Generation Soojung Yang Doyeong Hwang Seul Lee Seongok Ryu Sung Ju Hwang 61 72 0 04 Oct 2021
ILVR: Conditioning Method for Denoising Diffusion Probabilistic Models Jooyoung Choi Sungwon Kim Yonghyun Jeong Youngjune Gwon Sungroh Yoon DiffM 114 706 0 06 Aug 2021
Robust Compressed Sensing MRI with Deep Generative Priors A. Jalal Marius Arvinte Giannis Daras Eric Price A. Dimakis Jonathan I. Tamir MedIm 73 335 0 03 Aug 2021
Flow Network based Generative Models for Non-Iterative Diverse Candidate Generation Emmanuel Bengio Moksh Jain Maksym Korablyov Doina Precup Yoshua Bengio 73 325 0 08 Jun 2021
Learning Gradient Fields for Molecular Conformation Generation Chence Shi Shitong Luo Minkai Xu Jian Tang DiffM AI4CE 68 214 0 09 May 2021
SRDiff: Single Image Super-Resolution with Diffusion Probabilistic Models Haoying Li Yifan Yang Meng Chang H. Feng Zhi-hai Xu Qi Li Yue-ting Chen DiffM 61 627 0 30 Apr 2021
UNIT-DDPM: UNpaired Image Translation with Denoising Diffusion Probabilistic Models Hiroshi Sasaki Chris G. Willcocks T. Breckon DiffM 48 163 0 12 Apr 2021
MARS: Markov Molecular Sampling for Multi-objective Drug Discovery Yutong Xie Chence Shi Hao Zhou Yuwei Yang Weinan Zhang Yong Yu Lei Li 74 143 0 18 Mar 2021
GraphDF: A Discrete Flow Model for Molecular Graph Generation Youzhi Luo Keqiang Yan Shuiwang Ji DRL 209 195 0 01 Feb 2021
GraphEBM: Molecular Graph Generation with Energy-Based Models Meng Liu Keqiang Yan Bora Oztekin Shuiwang Ji 56 88 0 31 Jan 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 279 6,293 0 26 Nov 2020
Guiding Deep Molecular Optimization with Genetic Exploration SungSoo Ahn Junsup Kim Hankook Lee Jinwoo Shin 62 73 0 04 Jul 2020
Denoising Diffusion Probabilistic Models Jonathan Ho Ajay Jain Pieter Abbeel DiffM 401 17,550 0 19 Jun 2020
MoFlow: An Invertible Flow Model for Generating Molecular Graphs Chengxi Zang Fei Wang BDL 114 289 0 17 Jun 2020
Permutation Invariant Graph Generation via Score-Based Generative Modeling Chenhao Niu Yang Song Jiaming Song Shengjia Zhao Aditya Grover Stefano Ermon DiffM 61 269 0 02 Mar 2020
Hierarchical Generation of Molecular Graphs using Structural Motifs Wengong Jin Regina Barzilay Tommi Jaakkola 59 283 0 08 Feb 2020
GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation Chence Shi Minkai Xu Zhaocheng Zhu Weinan Zhang Ming Zhang Jian Tang 156 434 0 26 Jan 2020
Your Classifier is Secretly an Energy Based Model and You Should Treat it Like One Will Grathwohl Kuan-Chieh Wang J. Jacobsen David Duvenaud Mohammad Norouzi Kevin Swersky VLM 76 536 0 06 Dec 2019
PyTorch: An Imperative Style, High-Performance Deep Learning Library Adam Paszke Sam Gross Francisco Massa Adam Lerer James Bradbury ... Sasank Chilamkurthy Benoit Steiner Lu Fang Junjie Bai Soumith Chintala ODL 321 42,038 0 03 Dec 2019
Augmenting Genetic Algorithms with Deep Neural Networks for Exploring the Chemical Space AkshatKumar Nigam Pascal Friederich Mario Krenn Alán Aspuru-Guzik AI4CE 41 131 0 25 Sep 2019
Generative Modeling by Estimating Gradients of the Data Distribution Yang Song Stefano Ermon SyDa DiffM 200 3,803 0 12 Jul 2019
Generative Models for Automatic Chemical Design Daniel Schwalbe-Koda Rafael Gómez-Bombarelli MedIm AI4CE 55 81 0 02 Jul 2019
MolecularRNN: Generating realistic molecular graphs with optimized properties Mariya Popova Mykhailo Shvets Junier Oliva Olexandr Isayev GNN 66 166 0 31 May 2019
Optimization of Molecules via Deep Reinforcement Learning Zhenpeng Zhou S. Kearnes Li Li R. Zare Patrick F. Riley AI4CE 76 537 0 19 Oct 2018
Molecular generative model based on conditional variational autoencoder for de novo molecular design Jaechang Lim Seongok Ryu Jin Woo Kim W. Kim BDL DRL 49 332 0 15 Jun 2018
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation Jiaxuan You Bowen Liu Rex Ying Vijay S. Pande J. Leskovec GNN 272 895 0 07 Jun 2018
MolGAN: An implicit generative model for small molecular graphs Nicola De Cao Thomas Kipf GNN GAN 137 917 0 30 May 2018
Constrained Graph Variational Autoencoders for Molecule Design Qi Liu Miltiadis Allamanis Marc Brockschmidt Alexander L. Gaunt BDL 55 453 0 23 May 2018
Fréchet ChemNet Distance: A metric for generative models for molecules in drug discovery Kristina Preuer Philipp Renz Thomas Unterthiner Sepp Hochreiter Günter Klambauer MedIm 88 333 0 26 Mar 2018