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UniGEM: A Unified Approach to Generation and Property Prediction for Molecules

14 October 2024

Wei-Ying Ma

Papers citing "UniGEM: A Unified Approach to Generation and Property Prediction for Molecules"

44 / 44 papers shown

Title
Uni-3DAR: Unified 3D Generation and Understanding via Autoregression on Compressed Spatial Tokens Shuqi Lu Haowei Lin Lin Yao Zhifeng Gao Xiaohong Ji Weinan E Linfeng Zhang Guolin Ke 77 0 0 20 Mar 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 104 3 0 04 Mar 2025
Geometric Representation Condition Improves Equivariant Molecule Generation Zian Li Cai Zhou Xiyuan Wang Xingang Peng Muhan Zhang 85 2 0 04 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 59 16 0 14 Jul 2024
UniCorn: A Unified Contrastive Learning Approach for Multi-view Molecular Representation Learning Shikun Feng Yuyan Ni Minghao Li Yanwen Huang Zhiming Ma Wei-Ying Ma Yanyan Lan SSL 91 8 0 15 May 2024
Rethinking Specificity in SBDD: Leveraging Delta Score and Energy-Guided Diffusion Bowen Gao Minsi Ren Yuyan Ni Yanwen Huang Yiran Zhou Zhiming Ma Wei-Ying Ma Yanyan Lan 71 6 0 04 Mar 2024
Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design Andrew Campbell Jason Yim Regina Barzilay Tom Rainforth Tommi Jaakkola AI4CE 121 123 0 07 Feb 2024
Deconstructing Denoising Diffusion Models for Self-Supervised Learning Xinlei Chen Zhuang Liu Saining Xie Kaiming He DiffM 86 60 0 25 Jan 2024
Non-Denoising Forward-Time Diffusions Stefano Peluchetti DiffM 65 58 0 22 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
SODA: Bottleneck Diffusion Models for Representation Learning Drew A. Hudson Daniel Zoran Mateusz Malinowski Andrew Kyle Lampinen Andrew Jaegle James L. McClelland Loic Matthey Felix Hill Alexander Lerchner DiffM 95 56 0 29 Nov 2023
Sliced Denoising: A Physics-Informed Molecular Pre-Training Method Yuyan Ni Shikun Feng Wei-Ying Ma Zhiming Ma Yanyan Lan DiffM AI4CE 82 11 0 03 Nov 2023
UniMAP: Universal SMILES-Graph Representation Learning Shikun Feng Lixin Yang Wei-Ying Ma Yanyan Lan OffRL 59 6 0 22 Oct 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 101 31 0 29 Sep 2023
Bayesian Flow Networks Alex Graves R. Srivastava Timothy James Atkinson Faustino J. Gomez BDL 114 45 0 14 Aug 2023
Fractional Denoising for 3D Molecular Pre-training Shi Feng Yuyan Ni Yanyan Lan Zhiming Ma Wei-Ying Ma DiffM AI4CE 84 29 0 20 Jul 2023
A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining Shengchao Liu Weitao Du Zhiming Ma Hongyu Guo Jian Tang 85 33 0 28 May 2023
Geometric Latent Diffusion Models for 3D Molecule Generation Minkai Xu Alexander Powers R. Dror Stefano Ermon J. Leskovec DiffM AI4CE 130 150 0 02 May 2023
3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction Jiaqi Guan Wesley Wei Qian Xingang Peng Yufeng Su Jian-wei Peng Jianzhu Ma DiffM 97 177 0 06 Mar 2023
MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation Clément Vignac Nagham Osman Laura Toni P. Frossard DiffM 84 63 0 17 Feb 2023
Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics Marloes Arts Victor Garcia Satorras Chin-Wei Huang Daniel Zuegner Marco Federici C. Clementi Frank Noé Robert Pinsler Rianne van den Berg DiffM 109 92 0 01 Feb 2023
Equivariant Energy-Guided SDE for Inverse Molecular Design Fan Bao Min Zhao Zhongkai Hao Pei‐Yun Li Chongxuan Li Jun Zhu DiffM 260 67 0 30 Sep 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 223 277 0 22 Sep 2022
Diffusion-based Molecule Generation with Informative Prior Bridges Lemeng Wu Chengyue Gong Xingchao Liu Mao Ye Qiang Liu DiffM 97 116 0 02 Sep 2022
Understanding Diffusion Models: A Unified Perspective Calvin Luo DiffM 99 347 0 25 Aug 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
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 110 127 0 31 May 2022
GraphMAE: Self-Supervised Masked Graph Autoencoders Zhenyu Hou Xiao Liu Yukuo Cen Yuxiao Dong Hongxia Yang C. Wang Jie Tang SSL 99 586 0 22 May 2022
Equivariant Diffusion for Molecule Generation in 3D Emiel Hoogeboom Victor Garcia Satorras Clément Vignac Max Welling DiffM 133 623 0 31 Mar 2022
3D Infomax improves GNNs for Molecular Property Prediction Hannes Stärk Dominique Beaini Gabriele Corso Prudencio Tossou Christian Dallago Stephan Günnemann Pietro Lio AI4CE 92 208 0 08 Oct 2021
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 191 319 0 07 Oct 2021
GeomGCL: Geometric Graph Contrastive Learning for Molecular Property Prediction Shuangli Li Jingbo Zhou Tong Xu Dejing Dou Hui Xiong AI4CE 75 122 0 24 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 63 452 0 11 Jun 2021
Diffusion-Based Representation Learning K. Abstreiter Sarthak Mittal Stefan Bauer Bernhard Schölkopf Arash Mehrjou DiffM 80 58 0 29 May 2021
E(n) Equivariant Normalizing Flows Victor Garcia Satorras Emiel Hoogeboom F. Fuchs Ingmar Posner Max Welling BDL 87 181 0 19 May 2021
E(n) Equivariant Graph Neural Networks Victor Garcia Satorras Emiel Hoogeboom Max Welling 113 1,033 0 19 Feb 2021
Denoising Diffusion Probabilistic Models Jonathan Ho Ajay Jain Pieter Abbeel DiffM 742 18,364 0 19 Jun 2020
GEOM: Energy-annotated molecular conformations for property prediction and molecular generation Simon Axelrod Rafael Gómez-Bombarelli 3DV AI4CE 97 221 0 09 Jun 2020
Cormorant: Covariant Molecular Neural Networks Brandon M. Anderson Truong-Son Hy Risi Kondor 123 425 0 06 Jun 2019
Symmetry-adapted generation of 3d point sets for the targeted discovery of molecules Niklas W. A. Gebauer M. Gastegger Kristof T. Schütt 146 211 0 02 Jun 2019
Strategies for Pre-training Graph Neural Networks Weihua Hu Bowen Liu Joseph Gomes Marinka Zitnik Percy Liang Vijay S. Pande J. Leskovec SSL AI4CE 120 1,416 0 29 May 2019
Representation Learning with Contrastive Predictive Coding Aaron van den Oord Yazhe Li Oriol Vinyals DRL SSL 351 10,364 0 10 Jul 2018
Continuous-Time Flows for Efficient Inference and Density Estimation Changyou Chen Chunyuan Li Liquan Chen Wenlin Wang Yunchen Pu Lawrence Carin TPM 109 57 0 04 Sep 2017
Deep Unsupervised Learning using Nonequilibrium Thermodynamics Jascha Narain Sohl-Dickstein Eric A. Weiss Niru Maheswaranathan Surya Ganguli SyDa DiffM 312 7,031 0 12 Mar 2015