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

International Conference on Learning Representations (ICLR), 2024

14 October 2024

Wei-Ying Ma

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

50 / 51 papers shown

Title
Chemistry-Enhanced Diffusion-Based Framework for Small-to-Large Molecular Conformation Generation Yifei Zhu J. Zhang Jiawei Peng Mengge Li Chao Xu Zhenggang Lan DiffM 96 0 0 15 Nov 2025
InertialAR: Autoregressive 3D Molecule Generation with Inertial Frames Haorui Li Weitao Du Yuqiang Li Hongyu Guo Shengchao Liu 124 1 0 31 Oct 2025
3D-GSRD: 3D Molecular Graph Auto-Encoder with Selective Re-mask Decoding Chang Wu Zhiyuan Liu Wen Shu Liang Wang Yanchen Luo Wenqiang Lei Yatao Bian Junfeng Fang Xiang Wang 92 0 0 19 Oct 2025
Unifying Polymer Modeling and Design via a Conformation-Centric Generative Foundation Model Fanmeng Wang Shan Mei Wentao Guo H. Wang Qi Ou Zhifeng Gao Hongteng Xu AI4CE 128 0 0 15 Oct 2025
Predictive Feature Caching for Training-free Acceleration of Molecular Geometry Generation Johanna Sommer John Rachwan Nils Fleischmann Stephan Günnemann Bertrand Charpentier 104 1 0 06 Oct 2025
NS-Pep: De novo Peptide Design with Non-Standard Amino Acids Tao Guo Junbo Yin Yu Wang Xin Gao 98 0 0 01 Oct 2025
Guiding Diffusion Models with Reinforcement Learning for Stable Molecule Generation Zhijian Zhou Junyi An Zongkai Liu Yunfei Shi Xuan Zhang Fenglei Cao Chao Qu Yuan Qi 165 0 0 22 Aug 2025
Unified Cross-Scale 3D Generation and Understanding via Autoregressive Modeling Shuqi Lu Haowei Lin Lin Yao Zhifeng Gao Xiaohong Ji Weinan E Weinan E Linfeng Zhang Guolin Ke 288 2 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 359 6 0 04 Mar 2025
Geometric Representation Condition Improves Equivariant Molecule Generation Zian Li Cai Zhou Xiyuan Wang Xingang Peng Muhan Zhang 415 6 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 187 26 0 14 Jul 2024
UniCorn: A Unified Contrastive Learning Approach for Multi-view Molecular Representation LearningInternational Conference on Machine Learning (ICML), 2024 Shikun Feng Yuyan Ni Minghao Li Yanwen Huang Zhiming Ma Wei-Ying Ma Yanyan Lan SSL 242 17 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 189 9 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 284 211 0 07 Feb 2024
Deconstructing Denoising Diffusion Models for Self-Supervised LearningInternational Conference on Learning Representations (ICLR), 2024 Xinlei Chen Zhuang Liu Saining Xie Kaiming He DiffM 248 84 0 25 Jan 2024
Non-Denoising Forward-Time Diffusions Stefano Peluchetti DiffM 224 82 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 205 11 0 06 Dec 2023
SODA: Bottleneck Diffusion Models for Representation LearningComputer Vision and Pattern Recognition (CVPR), 2023 Drew A. Hudson Daniel Zoran Mateusz Malinowski Andrew Kyle Lampinen Andrew Jaegle James L. McClelland Loic Matthey Felix Hill Alexander Lerchner DiffM 293 75 0 29 Nov 2023
Sliced Denoising: A Physics-Informed Molecular Pre-Training MethodInternational Conference on Learning Representations (ICLR), 2023 Yuyan Ni Shikun Feng Wei-Ying Ma Zhiming Ma Yanyan Lan DiffM AI4CE 209 17 0 03 Nov 2023
UniMAP: Universal SMILES-Graph Representation Learning Shikun Feng Lixin Yang Wei-Ying Ma Yanyan Lan OffRL 154 9 0 22 Oct 2023
Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule GenerationInternational Conference on Learning Representations (ICLR), 2023 Tuan Le Julian Cremer Frank Noé Djork-Arné Clevert Kristof T. Schütt DiffM 226 48 0 29 Sep 2023
Bayesian Flow Networks Alex Graves R. Srivastava Timothy James Atkinson Faustino J. Gomez BDL 518 59 0 14 Aug 2023
Fractional Denoising for 3D Molecular Pre-trainingInternational Conference on Machine Learning (ICML), 2023 Shi Feng Yuyan Ni Yanyan Lan Zhiming Ma Wei-Ying Ma DiffM AI4CE 309 39 0 20 Jul 2023
A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal PretrainingInternational Conference on Machine Learning (ICML), 2023 Shengchao Liu Weitao Du Zhiming Ma Hongyu Guo Jian Tang 270 39 0 28 May 2023
Geometric Latent Diffusion Models for 3D Molecule GenerationInternational Conference on Machine Learning (ICML), 2023 Minkai Xu Alexander Powers R. Dror Stefano Ermon J. Leskovec DiffM AI4CE 278 216 0 02 May 2023
3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity PredictionInternational Conference on Learning Representations (ICLR), 2023 Jiaqi Guan Wesley Wei Qian Xingang Peng Yufeng Su Jian-wei Peng Jianzhu Ma DiffM 175 241 0 06 Mar 2023
MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation Clément Vignac Nagham Osman Laura Toni P. Frossard DiffM 244 94 0 17 Feb 2023
Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular DynamicsJournal of Chemical Theory and Computation (JCTC), 2023 Marloes Arts Victor Garcia Satorras Chin-Wei Huang Daniel Zuegner Marco Federici C. Clementi Frank Noé Tian Xie Rianne van den Berg DiffM 315 112 0 01 Feb 2023
Equivariant Energy-Guided SDE for Inverse Molecular DesignInternational Conference on Learning Representations (ICLR), 2022 Fan Bao Min Zhao Zhongkai Hao Pei‐Yun Li Chongxuan Li Jun Zhu DiffM 980 77 0 30 Sep 2022
Sampling is as easy as learning the score: theory for diffusion models with minimal data assumptionsInternational Conference on Learning Representations (ICLR), 2022 Sitan Chen Sinho Chewi Jungshian Li Yuanzhi Li Adil Salim Anru R. Zhang DiffM 472 347 0 22 Sep 2022
Diffusion-based Molecule Generation with Informative Prior BridgesNeural Information Processing Systems (NeurIPS), 2022 Lemeng Wu Chengyue Gong Xingchao Liu Mao Ye Qiang Liu DiffM 262 139 0 02 Sep 2022
Understanding Diffusion Models: A Unified Perspective Calvin Luo DiffM 224 455 0 25 Aug 2022
Energy-Motivated Equivariant Pretraining for 3D Molecular GraphsAAAI Conference on Artificial Intelligence (AAAI), 2022 Rui Jiao Jiaqi Han Wenbing Huang Yu Rong Yang Liu AI4CE 283 59 0 18 Jul 2022
Pre-training via Denoising for Molecular Property PredictionInternational Conference on Learning Representations (ICLR), 2022 Sheheryar Zaidi Michael Schaarschmidt James Martens Hyunjik Kim Yee Whye Teh Alvaro Sanchez-Gonzalez Peter W. Battaglia Razvan Pascanu Jonathan Godwin DiffM AI4CE 409 143 0 31 May 2022
GraphMAE: Self-Supervised Masked Graph AutoencodersKnowledge Discovery and Data Mining (KDD), 2022 Zhenyu Hou Xiao Liu Yukuo Cen Yuxiao Dong Hongxia Yang C. Wang Jie Tang SSL 532 734 0 22 May 2022
Equivariant Diffusion for Molecule Generation in 3DInternational Conference on Machine Learning (ICML), 2022 Emiel Hoogeboom Victor Garcia Satorras Clément Vignac Max Welling DiffM 359 770 0 31 Mar 2022
3D Infomax improves GNNs for Molecular Property PredictionInternational Conference on Machine Learning (ICML), 2021 Hannes Stärk Dominique Beaini Gabriele Corso Prudencio Tossou Christian Dallago Stephan Günnemann Pietro Lio AI4CE 246 247 0 08 Oct 2021
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 382 399 0 07 Oct 2021
GeomGCL: Geometric Graph Contrastive Learning for Molecular Property PredictionAAAI Conference on Artificial Intelligence (AAAI), 2021 Shuangli Li Jingbo Zhou Tong Xu Dejing Dou Hui Xiong AI4CE 161 144 0 24 Sep 2021
ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property PredictionNature Machine Intelligence (Nat. Mach. Intell.), 2021 Xiaomin Fang Lihang Liu Jieqiong Lei Donglong He Shanzhuo Zhang Jingbo Zhou Fan Wang Hua Wu Haifeng Wang AI4CE 191 553 0 11 Jun 2021
Diffusion-Based Representation LearningInternational Conference on Machine Learning (ICML), 2021 K. Abstreiter Sarthak Mittal Stefan Bauer Bernhard Schölkopf Arash Mehrjou DiffM 152 66 0 29 May 2021
E(n) Equivariant Normalizing FlowsNeural Information Processing Systems (NeurIPS), 2021 Victor Garcia Satorras Emiel Hoogeboom F. Fuchs Ingmar Posner Max Welling BDL 422 213 0 19 May 2021
E(n) Equivariant Graph Neural NetworksInternational Conference on Machine Learning (ICML), 2021 Victor Garcia Satorras Emiel Hoogeboom Max Welling 418 1,272 0 19 Feb 2021
Denoising Diffusion Probabilistic Models Jonathan Ho Ajay Jain Pieter Abbeel DiffM 4.2K 25,036 0 19 Jun 2020
GEOM: Energy-annotated molecular conformations for property prediction and molecular generation Simon Axelrod Rafael Gómez-Bombarelli 3DV AI4CE 369 273 0 09 Jun 2020
Cormorant: Covariant Molecular Neural NetworksNeural Information Processing Systems (NeurIPS), 2019 Brandon M. Anderson Truong-Son Hy Risi Kondor 389 465 0 06 Jun 2019
Symmetry-adapted generation of 3d point sets for the targeted discovery of moleculesNeural Information Processing Systems (NeurIPS), 2019 Niklas W. A. Gebauer M. Gastegger Kristof T. Schütt 396 249 0 02 Jun 2019
Strategies for Pre-training Graph Neural NetworksInternational Conference on Learning Representations (ICLR), 2019 Weihua Hu Bowen Liu Joseph Gomes Marinka Zitnik Abigail Z. Jacobs Vijay S. Pande J. Leskovec SSL AI4CE 349 1,620 0 29 May 2019
Representation Learning with Contrastive Predictive Coding Aaron van den Oord Yazhe Li Oriol Vinyals DRL SSL 1.7K 12,021 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 258 59 0 04 Sep 2017

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

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