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Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling

13 March 2025

Papers citing "Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling"

33 / 33 papers shown

Title
Let's Think Dot by Dot: Hidden Computation in Transformer Language Models Jacob Pfau William Merrill Samuel R. Bowman LRM 78 83 0 24 Apr 2024
GraphAlign: Enhancing Accurate Feature Alignment by Graph matching for Multi-Modal 3D Object Detection Ziying Song Haiyue Wei Lin Bai Lei Yang Caiyan Jia 3DPC 74 27 0 12 Oct 2023
Vision Transformers Need Registers Zilong Chen Maxime Oquab Julien Mairal Huaping Liu ViT 166 350 0 28 Sep 2023
Fractional Denoising for 3D Molecular Pre-training Shi Feng Yuyan Ni Yanyan Lan Zhiming Ma Wei-Ying Ma DiffM AI4CE 79 29 0 20 Jul 2023
Multimodal Molecular Pretraining via Modality Blending Qiying Yu Yudi Zhang Yuyan Ni Shi Feng Yanyan Lan Hao Zhou Jingjing Liu 67 13 0 12 Jul 2023
Virtual Sparse Convolution for Multimodal 3D Object Detection Hai Wu Chenglu Wen Shaoshuai Shi Xin Li Cheng-i Wang 3DPC 59 110 0 04 Mar 2023
Denoise Pretraining on Nonequilibrium Molecules for Accurate and Transferable Neural Potentials Yuyang Wang Chang Xu Zijie Li A. Farimani AAML AI4CE 69 22 0 03 Mar 2023
Energy-Motivated Equivariant Pretraining for 3D Molecular Graphs Rui Jiao Jiaqi Han Wenbing Huang Yu Rong Yang Liu AI4CE 92 49 0 18 Jul 2022
Does GNN Pretraining Help Molecular Representation? Ruoxi Sun Hanjun Dai Adams Wei Yu SSL AI4CE GNN 61 75 0 13 Jul 2022
ComENet: Towards Complete and Efficient Message Passing for 3D Molecular Graphs Limei Wang Yi Liu Yu-Ching Lin Hao Liu Shuiwang Ji GNN 79 94 0 17 Jun 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 100 127 0 31 May 2022
FlashAttention: Fast and Memory-Efficient Exact Attention with IO-Awareness Tri Dao Daniel Y. Fu Stefano Ermon Atri Rudra Christopher Ré VLM 237 2,272 0 27 May 2022
GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation Minkai Xu Lantao Yu Yang Song Chence Shi Stefano Ermon Jian Tang BDL DiffM 160 519 0 06 Mar 2022
Dense Voxel Fusion for 3D Object Detection Anas Mahmoud Jordan S. K. Hu Steven L. Waslander 3DPC 59 47 0 02 Mar 2022
Direct Molecular Conformation Generation Jinhua Zhu Yingce Xia Chang-Shu Liu Lijun Wu Shufang Xie ... Tao Qin Wen-gang Zhou Houqiang Li Haiguang Liu Tie-Yan Liu 83 42 0 03 Feb 2022
VPFNet: Improving 3D Object Detection with Virtual Point based LiDAR and Stereo Data Fusion Hanqi Zhu Jiajun Deng Yu Zhang Jianmin Ji Qiuyu Mao Houqiang Li Yanyong Zhang 3DPC 109 138 0 29 Nov 2021
Multimodal Virtual Point 3D Detection Tianwei Yin Xingyi Zhou Philipp Krahenbuhl 3DPC 210 250 0 12 Nov 2021
Masked Autoencoders Are Scalable Vision Learners Kaiming He Xinlei Chen Saining Xie Yanghao Li Piotr Dollár Ross B. Girshick ViT TPM 467 7,814 0 11 Nov 2021
3D Infomax improves GNNs for Molecular Property Prediction Hannes Stärk Dominique Beaini Gabriele Corso Prudencio Tossou Christian Dallago Stephan Günnemann Pietro Lio AI4CE 80 208 0 08 Oct 2021
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 188 319 0 07 Oct 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 58 450 0 11 Jun 2021
GemNet: Universal Directional Graph Neural Networks for Molecules Johannes Klicpera Florian Becker Stephan Günnemann AI4CE 97 464 0 02 Jun 2021
Learning Gradient Fields for Molecular Conformation Generation Chence Shi Shitong Luo Minkai Xu Jian Tang DiffM AI4CE 75 216 0 09 May 2021
RoFormer: Enhanced Transformer with Rotary Position Embedding Jianlin Su Yu Lu Shengfeng Pan Ahmed Murtadha Bo Wen Yunfeng Liu 284 2,521 0 20 Apr 2021
Learning Neural Generative Dynamics for Molecular Conformation Generation Minkai Xu Shitong Luo Yoshua Bengio Jian-wei Peng Jian Tang AI4CE 89 119 0 20 Feb 2021
Spherical Message Passing for 3D Graph Networks Yi Liu Limei Wang Meng Liu Xuan Zhang Bora Oztekin Shuiwang Ji GNN 61 204 0 09 Feb 2021
Directional Message Passing for Molecular Graphs Johannes Klicpera Janek Groß Stephan Günnemann 127 879 0 06 Mar 2020
Strategies for Pre-training Graph Neural Networks Weihua Hu Bowen Liu Joseph Gomes Marinka Zitnik Percy Liang Vijay S. Pande J. Leskovec SSL AI4CE 116 1,409 0 29 May 2019
Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds Nathaniel Thomas Tess E. Smidt S. Kearnes Lusann Yang Li Li Kai Kohlhoff Patrick F. Riley 3DPC 98 977 0 22 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 155 1,086 0 26 Jun 2017
Attention Is All You Need Ashish Vaswani Noam M. Shazeer Niki Parmar Jakob Uszkoreit Llion Jones Aidan Gomez Lukasz Kaiser Illia Polosukhin 3DV 730 132,199 0 12 Jun 2017
Neural Message Passing for Quantum Chemistry Justin Gilmer S. Schoenholz Patrick F. Riley Oriol Vinyals George E. Dahl 596 7,485 0 04 Apr 2017
MoleculeNet: A Benchmark for Molecular Machine Learning Zhenqin Wu Bharath Ramsundar Evan N. Feinberg Joseph Gomes C. Geniesse Aneesh S. Pappu K. Leswing Vijay S. Pande OOD 337 1,834 0 02 Mar 2017