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A Systematic Survey of Chemical Pre-trained Models

29 October 2022

Papers citing "A Systematic Survey of Chemical Pre-trained Models"

32 / 32 papers shown

Title
3DMolFormer: A Dual-channel Framework for Structure-based Drug Discovery Xiuyuan Hu Guoqing Liu Can Chen Yang Zhao Jun Wang Xue Liu 99 2 0 07 Feb 2025
ChemDFM-X: Towards Large Multimodal Model for Chemistry Zihan Zhao B. Chen Jingpiao Li Lu Chen Liyang Wen ... Ziping Wan Yansi Li Zhongyang Dai Xin Chen Kai Yu AI4CE 206 5 0 03 Jan 2025
Large Language Models are In-Context Molecule Learners Jiatong Li Wei Liu Zhihao Ding Wenqi Fan Yuqiang Li Qing Li 106 6 0 07 Mar 2024
A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications Jiaqi Han Jiacheng Cen Liming Wu Zongzhao Li Xiangzhe Kong ... Zhewei Wei Deli Zhao Yu Rong Wenbing Huang Wenbing Huang AI4CE 130 23 0 01 Mar 2024
Unified 2D and 3D Pre-Training of Molecular Representations Jinhua Zhu Yingce Xia Lijun Wu Shufang Xie Tao Qin Wen-gang Zhou Houqiang Li Tie-Yan Liu AI4CE 100 70 0 14 Jul 2022
Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matching Shengchao Liu Hongyu Guo Jian Tang 64 80 0 27 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
Translation between Molecules and Natural Language Carl Edwards T. Lai Kevin Ros Garrett Honke Kyunghyun Cho Heng Ji 101 168 0 25 Apr 2022
Graph Self-supervised Learning with Accurate Discrepancy Learning Dongki Kim Jinheon Baek Sung Ju Hwang SSL 52 38 0 07 Feb 2022
Molecular Contrastive Learning with Chemical Element Knowledge Graph Yin Fang Qiang Zhang Haihong Yang Xiang Zhuang Shumin Deng Wen Zhang Minghai Qin Zhuo Chen Xiaohui Fan Huajun Chen 62 111 0 01 Dec 2021
InfoGCL: Information-Aware Graph Contrastive Learning Dongkuan Xu Wei Cheng Dongsheng Luo Haifeng Chen Xiang Zhang 61 200 0 28 Oct 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
ProGCL: Rethinking Hard Negative Mining in Graph Contrastive Learning Jun Xia Lirong Wu Ge Wang Jintao Chen Stan Z. Li 63 123 0 05 Oct 2021
Motif-based Graph Self-Supervised Learning for Molecular Property Prediction Zaixin Zhang Qi Liu Hao Wang Chengqiang Lu Chee-Kong Lee SSL AI4CE 83 259 0 03 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 58 450 0 11 Jun 2021
Graph Contrastive Learning Automated Yuning You Tianlong Chen Yang Shen Zhangyang Wang 81 479 0 10 Jun 2021
Self-supervised Graph-level Representation Learning with Local and Global Structure Minghao Xu Hang Wang Bingbing Ni Hongyu Guo Jian Tang SSL 47 211 0 08 Jun 2021
OGB-LSC: A Large-Scale Challenge for Machine Learning on Graphs Weihua Hu Matthias Fey Hongyu Ren Maho Nakata Yuxiao Dong J. Leskovec AI4CE 72 413 0 17 Mar 2021
E(n) Equivariant Graph Neural Networks Victor Garcia Satorras Emiel Hoogeboom Max Welling 113 1,033 0 19 Feb 2021
Equivariant message passing for the prediction of tensorial properties and molecular spectra Kristof T. Schütt Oliver T. Unke M. Gastegger 110 541 0 05 Feb 2021
Contrastive Multi-View Representation Learning on Graphs Kaveh Hassani Amir Hosein Khas Ahmadi SSL 232 1,305 0 10 Jun 2020
GEOM: Energy-annotated molecular conformations for property prediction and molecular generation Simon Axelrod Rafael Gómez-Bombarelli 3DV AI4CE 92 221 0 09 Jun 2020
Principal Neighbourhood Aggregation for Graph Nets Gabriele Corso Luca Cavalleri Dominique Beaini Pietro Lio Petar Velickovic GNN 114 672 0 12 Apr 2020
Learning to Simulate Complex Physics with Graph Networks Alvaro Sanchez-Gonzalez Jonathan Godwin Tobias Pfaff Rex Ying J. Leskovec Peter W. Battaglia PINN AI4CE 143 1,101 0 21 Feb 2020
SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery Shion Honda Shoi Shi H. Ueda MedIm 78 175 0 12 Nov 2019
InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization Fan-Yun Sun Jordan Hoffmann Vikas Verma Jian Tang SSL 153 864 0 31 Jul 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 116 1,409 0 29 May 2019
How Powerful are Graph Neural Networks? Keyulu Xu Weihua Hu J. Leskovec Stefanie Jegelka GNN 251 7,681 0 01 Oct 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
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 1,837 0 02 Mar 2017