NaFM: Pre-training a Foundation Model for Small-Molecule Natural Products

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NaFM: Pre-training a Foundation Model for Small-Molecule Natural Products

22 March 2025

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Papers citing "NaFM: Pre-training a Foundation Model for Small-Molecule Natural Products"

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Title
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 14 0 14 Jul 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
Does GNN Pretraining Help Molecular Representation? Ruoxi Sun Hanjun Dai Adams Wei Yu SSL AI4CE GNN 61 75 0 13 Jul 2022
Improving Molecular Contrastive Learning via Faulty Negative Mitigation and Decomposed Fragment Contrast Yuyang Wang Rishikesh Magar Chen Liang A. Farimani 81 78 0 18 Feb 2022
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 188 318 0 07 Oct 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
Visualization of Very Large High-Dimensional Data Sets as Minimum Spanning Trees Daniel Probst J. Reymond 63 210 0 16 Aug 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
Analyzing Learned Molecular Representations for Property Prediction Kevin Kaichuang Yang Kyle Swanson Wengong Jin Connor W. Coley Philipp Eiden ... Andrew Palmer Volker Settels Tommi Jaakkola K. Jensen Regina Barzilay 104 1,322 0 02 Apr 2019
How Powerful are Graph Neural Networks? Keyulu Xu Weihua Hu J. Leskovec Stefanie Jegelka GNN 243 7,681 0 01 Oct 2018
N-Gram Graph: Simple Unsupervised Representation for Graphs, with Applications to Molecules Shengchao Liu M. F. Demirel Yingyu Liang GNN NAI 54 195 0 24 Jun 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 1,076 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 722 132,199 0 12 Jun 2017
Molecular Graph Convolutions: Moving Beyond Fingerprints S. Kearnes Kevin McCloskey Marc Berndl Vijay S. Pande Patrick F. Riley GNN 151 1,449 0 02 Mar 2016
Learning to SMILE(S) Stanislaw Jastrzebski Damian Lesniak Wojciech M. Czarnecki 60 89 0 19 Feb 2016
Learning Phrase Representations using RNN Encoder-Decoder for Statistical Machine Translation Kyunghyun Cho B. V. Merrienboer Çağlar Gülçehre Dzmitry Bahdanau Fethi Bougares Holger Schwenk Yoshua Bengio AIMat 1.1K 23,370 0 03 Jun 2014