Learning Flexible Forward Trajectories for Masked Molecular Diffusion

22 May 2025

Papers citing "Learning Flexible Forward Trajectories for Masked Molecular Diffusion"

50 / 56 papers shown

Title
Improving Equivariant Networks with Probabilistic Symmetry Breaking Hannah Lawrence Vasco Portilheiro Yan Zhang Sékou-Oumar Kaba 90 5 0 27 Mar 2025
Simplified and Generalized Masked Diffusion for Discrete Data Jiaxin Shi Kehang Han Zehao Wang Arnaud Doucet Michalis K. Titsias DiffM 115 80 0 17 Jan 2025
Efficient Diversity-Preserving Diffusion Alignment via Gradient-Informed GFlowNets Zhen Liu Tim Z. Xiao Weiyang Liu Yoshua Bengio Dinghuai Zhang 151 5 0 10 Dec 2024
XMOL: Explainable Multi-property Optimization of Molecules Aye Phyu Phyu Aung Jay Chaudhary Ji Wei Yoon Senthilnath Jayavelu 37 1 0 12 Sep 2024
Training-Free Guidance for Discrete Diffusion Models for Molecular Generation Thomas J. Kerby Kevin R. Moon 62 3 0 11 Sep 2024
Efficient Evolutionary Search Over Chemical Space with Large Language Models Haorui Wang Marta Skreta C. Ser Wenhao Gao Lingkai Kong ... Yanqiao Zhu Yuanqi Du Alán Aspuru-Guzik Kirill Neklyudov Chao Zhang 72 17 0 23 Jun 2024
LLMatDesign: Autonomous Materials Discovery with Large Language Models Shuyi Jia Chao Zhang Victor Fung 66 11 0 19 Jun 2024
Simple and Effective Masked Diffusion Language Models Subham Sekhar Sahoo Marianne Arriola Yair Schiff Aaron Gokaslan Edgar Marroquin Justin T Chiu Alexander M. Rush Volodymyr Kuleshov DiffM 80 91 0 11 Jun 2024
Data-Efficient Molecular Generation with Hierarchical Textual Inversion Seojin Kim Jaehyun Nam Sihyun Yu Younghoon Shin Jinwoo Shin 71 3 0 05 May 2024
SiT: Exploring Flow and Diffusion-based Generative Models with Scalable Interpolant Transformers Nanye Ma Mark Goldstein M. S. Albergo Nicholas M. Boffi Eric Vanden-Eijnden Saining Xie DiffM 72 186 0 16 Jan 2024
Diffusion Models With Learned Adaptive Noise Subham Sekhar Sahoo Aaron Gokaslan Christopher De Sa Volodymyr Kuleshov DiffM 61 10 0 20 Dec 2023
A Simple and Scalable Representation for Graph Generation Yunhui Jang Seul Lee SungSoo Ahn 40 5 0 04 Dec 2023
Autoregressive Diffusion Model for Graph Generation Lingkai Kong Jiaming Cui Haotian Sun Yuchen Zhuang B. Prakash Chao Zhang DiffM 37 66 0 17 Jul 2023
A Comprehensive Overview of Large Language Models Humza Naveed Asad Ullah Khan Shi Qiu Muhammad Saqib Saeed Anwar Muhammad Usman Naveed Akhtar Nick Barnes Ajmal Mian OffRL 83 564 0 12 Jul 2023
Graph Inductive Biases in Transformers without Message Passing Liheng Ma Chen Lin Derek Lim Adriana Romero Soriano P. Dokania Mark Coates Philip Torr Ser-Nam Lim AI4CE 65 91 0 27 May 2023
MUDiff: Unified Diffusion for Complete Molecule Generation Chenqing Hua Sitao Luan Minkai Xu Rex Ying Jie Fu Stefano Ermon Doina Precup DiffM 75 36 0 28 Apr 2023
Diffusion Bridge Mixture Transports, Schrödinger Bridge Problems and Generative Modeling Stefano Peluchetti OT DiffM 37 51 0 03 Apr 2023
Diffusion Schrödinger Bridge Matching Yuyang Shi Valentin De Bortoli Andrew Campbell Arnaud Doucet DiffM OT 85 75 0 29 Mar 2023
Sample-efficient Multi-objective Molecular Optimization with GFlowNets Yiheng Zhu Jialun Wu Chaowen Hu Jiahuan Yan Chang-Yu Hsieh Tingjun Hou Jian Wu 62 35 0 08 Feb 2023
Graph Generation with Diffusion Mixture Jaehyeong Jo Dongki Kim Sung Ju Hwang DiffM 41 21 0 07 Feb 2023
Muse: Text-To-Image Generation via Masked Generative Transformers Huiwen Chang Han Zhang Jarred Barber AJ Maschinot José Lezama ... Kevin Patrick Murphy William T. Freeman Michael Rubinstein Yuanzhen Li Dilip Krishnan DiffM 224 537 0 02 Jan 2023
Scalable Diffusion Models with Transformers William S. Peebles Saining Xie GNN 62 2,182 0 19 Dec 2022
DiffuSeq: Sequence to Sequence Text Generation with Diffusion Models Shansan Gong Mukai Li Jiangtao Feng Zhiyong Wu Lingpeng Kong 77 325 0 17 Oct 2022
Classifier-Free Diffusion Guidance Jonathan Ho Tim Salimans FaML 75 3,786 0 26 Jul 2022
Exploring Chemical Space with Score-based Out-of-distribution Generation Seul Lee Jaehyeong Jo Sung Ju Hwang OODD 66 78 0 06 Jun 2022
A Continuous Time Framework for Discrete Denoising Models Andrew Campbell Joe Benton Valentin De Bortoli Tom Rainforth George Deligiannidis Arnaud Doucet DiffM 208 152 0 30 May 2022
Diffusion-LM Improves Controllable Text Generation Xiang Lisa Li John Thickstun Ishaan Gulrajani Percy Liang Tatsunori B. Hashimoto AI4CE 204 802 0 27 May 2022
MaskGIT: Masked Generative Image Transformer Huiwen Chang Han Zhang Lu Jiang Ce Liu William T. Freeman ViT 83 656 0 08 Feb 2022
Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations Jaehyeong Jo Seul Lee Sung Ju Hwang DiffM 46 219 0 05 Feb 2022
High-Resolution Image Synthesis with Latent Diffusion Models Robin Rombach A. Blattmann Dominik Lorenz Patrick Esser Bjorn Ommer 3DV 250 15,081 0 20 Dec 2021
Graph Neural Networks with Learnable Structural and Positional Representations Vijay Prakash Dwivedi Anh Tuan Luu T. Laurent Yoshua Bengio Xavier Bresson GNN 241 318 0 15 Oct 2021
Differentiable Scaffolding Tree for Molecular Optimization Tianfan Fu Wenhao Gao Cao Xiao Jacob Yasonik Connor W. Coley Jimeng Sun 62 78 0 22 Sep 2021
Structured Denoising Diffusion Models in Discrete State-Spaces Jacob Austin Daniel D. Johnson Jonathan Ho Daniel Tarlow Rianne van den Berg DiffM 100 900 0 07 Jul 2021
Diffusion Schrödinger Bridge with Applications to Score-Based Generative Modeling Valentin De Bortoli James Thornton J. Heng Arnaud Doucet DiffM OT 69 448 0 01 Jun 2021
Diffusion Models Beat GANs on Image Synthesis Prafulla Dhariwal Alex Nichol 130 7,639 0 11 May 2021
MARS: Markov Molecular Sampling for Multi-objective Drug Discovery Yutong Xie Chence Shi Hao Zhou Yuwei Yang Weinan Zhang Yong Yu Lei Li 63 142 0 18 Mar 2021
Improved Denoising Diffusion Probabilistic Models Alex Nichol Prafulla Dhariwal DiffM 169 3,599 0 18 Feb 2021
Argmax Flows and Multinomial Diffusion: Learning Categorical Distributions Emiel Hoogeboom Didrik Nielsen P. Jaini Patrick Forré Max Welling DiffM 263 414 0 10 Feb 2021
GraphDF: A Discrete Flow Model for Molecular Graph Generation Youzhi Luo Keqiang Yan Shuiwang Ji DRL 204 195 0 01 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 262 6,293 0 26 Nov 2020
Goal-directed Generation of Discrete Structures with Conditional Generative Models Amina Mollaysa Brooks Paige Alexandros Kalousis 51 9 0 05 Oct 2020
Denoising Diffusion Probabilistic Models Jonathan Ho Ajay Jain Pieter Abbeel DiffM 279 17,550 0 19 Jun 2020
MoFlow: An Invertible Flow Model for Generating Molecular Graphs Chengxi Zang Fei Wang BDL 108 289 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 44 266 0 02 Mar 2020
Decision-Making with Auto-Encoding Variational Bayes Romain Lopez Pierre Boyeau Nir Yosef Michael I. Jordan Jeffrey Regier BDL 182 10,591 0 17 Feb 2020
GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation Chence Shi Minkai Xu Zhaocheng Zhu Weinan Zhang Ming Zhang Jian Tang 150 434 0 26 Jan 2020
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 221 42,038 0 03 Dec 2019
Fast Graph Representation Learning with PyTorch Geometric Matthias Fey J. E. Lenssen 3DH GNN 3DPC 155 4,289 0 06 Mar 2019
Latent Normalizing Flows for Discrete Sequences Zachary M. Ziegler Alexander M. Rush BDL DRL 57 126 0 29 Jan 2019
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation Jiaxuan You Bowen Liu Rex Ying Vijay S. Pande J. Leskovec GNN 262 895 0 07 Jun 2018