Unified 2D and 3D Pre-Training of Molecular Representations

14 July 2022

Papers citing "Unified 2D and 3D Pre-Training of Molecular Representations"

37 / 37 papers shown

Title
Multi-Modal Molecular Representation Learning via Structure Awareness Rong Yin Ruyue Liu Xiaoshuai Hao Xingrui Zhou Y. Liu Can Ma Weiping Wang 22 0 0 09 May 2025
NaFM: Pre-training a Foundation Model for Small-Molecule Natural Products Yuheng Ding Yusong Wang Bo Qiang Jie Yu Qi Li Yiran Zhou Zhenmin Liu 53 0 0 22 Mar 2025
MolSpectra: Pre-training 3D Molecular Representation with Multi-modal Energy Spectra Liang Wang Shaozhen Liu Yu Rong Deli Zhao Qiang Liu Shu Wu Liang Wang MedIm 52 1 0 22 Feb 2025
Multi-view biomedical foundation models for molecule-target and property prediction Parthasarathy Suryanarayanan Yunguang Qiu Shreyans Sethi Diwakar Mahajan Hongyang Li ... Bum Chul Kwon Pablo Meyer Feixiong Cheng Jianying Hu Joseph A. Morrone AI4CE 19 0 0 25 Oct 2024
Beyond Efficiency: Molecular Data Pruning for Enhanced Generalization Dingshuo Chen Zhixun Li Yuyan Ni Guibin Zhang Ding Wang Qiang Liu Shu Wu Jeffrey Xu Yu Liang Wang 36 0 0 02 Sep 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 20 0 0 14 Jul 2024
Learning Multi-view Molecular Representations with Structured and Unstructured Knowledge Yizhen Luo Kai Yang Massimo Hong Xing Yi Liu Zikun Nie Hao Zhou Zaiqing Nie 33 2 0 14 Jun 2024
Medication Recommendation via Dual Molecular Modalities and Multi-Substructure Enhancement Shizhuo Mu Shunpan Liang Xiang Li 14 0 0 30 May 2024
Hi-GMAE: Hierarchical Graph Masked Autoencoders Chuang Liu Zelin Yao Yibing Zhan Xueqi Ma Dapeng Tao Jia Wu Wenbin Hu Shirui Pan Bo Du AI4CE 31 0 0 17 May 2024
ESM All-Atom: Multi-scale Protein Language Model for Unified Molecular Modeling Kangjie Zheng Siyu Long Tianyu Lu Junwei Yang Xinyu Dai Ming Zhang Zaiqing Nie Wei-Ying Ma Hao Zhou 20 5 0 05 Mar 2024
Impact of Domain Knowledge and Multi-Modality on Intelligent Molecular Property Prediction: A Systematic Survey Taojie Kuang Pengfei Liu Zhixiang Ren AI4CE 32 1 0 11 Feb 2024
GlycoNMR: Dataset and benchmarks for NMR chemical shift prediction of carbohydrates with graph neural networks Zizhang Chen R. P. Badman Lachele Foley Robert Woods Pengyu Hong 15 0 0 28 Nov 2023
Sliced Denoising: A Physics-Informed Molecular Pre-Training Method Yuyan Ni Shikun Feng Wei-Ying Ma Zhiming Ma Yanyan Lan DiffM AI4CE 16 7 0 03 Nov 2023
From Molecules to Materials: Pre-training Large Generalizable Models for Atomic Property Prediction Nima Shoghi Adeesh Kolluru John R. Kitchin Zachary W. Ulissi C. L. Zitnick Brandon M. Wood AI4CE 9 30 0 25 Oct 2023
Fragment-based Pretraining and Finetuning on Molecular Graphs Kha-Dinh Luong Ambuj Singh AI4CE 17 12 0 05 Oct 2023
Uncovering Neural Scaling Laws in Molecular Representation Learning Dingshuo Chen Yanqiao Zhu Jieyu Zhang Yuanqi Du Zhixun Li Qiang Liu Shu Wu Liang Wang 8 15 0 15 Sep 2023
3D Denoisers are Good 2D Teachers: Molecular Pretraining via Denoising and Cross-Modal Distillation Sungjun Cho Dae-Woong Jeong Sung Moon Ko Jinwoo Kim Sehui Han Seunghoon Hong Honglak Lee Moontae Lee AI4CE DiffM 15 1 0 08 Sep 2023
Geometry-aware Line Graph Transformer Pre-training for Molecular Property Prediction Peizhen Bai Xianyuan Liu Haiping Lu ViT AI4CE 14 1 0 01 Sep 2023
On Data Imbalance in Molecular Property Prediction with Pre-training Limin Wang Masatoshi Hanai Toyotaro Suzumura Shun Takashige Kenjiro Taura AI4CE 12 0 0 17 Aug 2023
Fractional Denoising for 3D Molecular Pre-training Shi Feng Yuyan Ni Yanyan Lan Zhiming Ma Wei-Ying Ma DiffM AI4CE 22 25 0 20 Jul 2023
Multimodal Molecular Pretraining via Modality Blending Qiying Yu Yudi Zhang Yuyan Ni Shi Feng Yanyan Lan Hao Zhou Jingjing Liu 15 12 0 12 Jul 2023
ChiENN: Embracing Molecular Chirality with Graph Neural Networks Piotr Gaiñski Michał Koziarski Jacek Tabor Marek Śmieja GNN 14 3 0 05 Jul 2023
Automated 3D Pre-Training for Molecular Property Prediction Xu Wang Huan Zhao Weiwei Tu Quanming Yao AI4CE 11 35 0 13 Jun 2023
Multi-task Bioassay Pre-training for Protein-ligand Binding Affinity Prediction Jiaxian Yan Zhaofeng Ye Ziyi Yang Chengqiang Lu Shengyu Zhang Qi Liu J. Qiu 22 11 0 08 Jun 2023
MolFM: A Multimodal Molecular Foundation Model Yi Luo Kai Yang Massimo Hong Xingyi Liu Zaiqing Nie 15 27 0 06 Jun 2023
Bi-level Contrastive Learning for Knowledge-Enhanced Molecule Representations Pengcheng Jiang Cao Xiao Tianfan Fu Jimeng Sun 18 3 0 02 Jun 2023
Shift-Robust Molecular Relational Learning with Causal Substructure Namkyeong Lee Kanghoon Yoon Gyoung S. Na Sein Kim Chanyoung Park 8 9 0 29 May 2023
A Comprehensive Survey on Deep Graph Representation Learning Wei Ju Zheng Fang Yiyang Gu Zequn Liu Qingqing Long ... Jingyang Yuan Yusheng Zhao Yifan Wang Xiao Luo Ming Zhang GNN AI4TS 20 138 0 11 Apr 2023
Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Language Philipp Seidl Andreu Vall Sepp Hochreiter G. Klambauer 50 35 0 06 Mar 2023
MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation Clément Vignac Nagham Osman Laura Toni P. Frossard DiffM 30 33 0 17 Feb 2023
Physics-Informed Machine Learning: A Survey on Problems, Methods and Applications Zhongkai Hao Songming Liu Yichi Zhang Chengyang Ying Yao Feng Hang Su Jun Zhu PINN AI4CE 8 87 0 15 Nov 2022
A Systematic Survey of Chemical Pre-trained Models Jun-Xiong Xia Yanqiao Zhu Yuanqi Du Stan Z.Li AI4CE 44 50 0 29 Oct 2022
Energy-Motivated Equivariant Pretraining for 3D Molecular Graphs Rui Jiao Jiaqi Han Wenbing Huang Yu Rong Yang Liu AI4CE 15 45 0 18 Jul 2022
Graph-based Molecular Representation Learning Zhichun Guo Kehan Guo B. Nan Yijun Tian Roshni G. Iyer ... Olaf Wiest Xiangliang Zhang Wei Wang Chuxu Zhang Nitesh V. Chawla AI4CE 10 59 0 08 Jul 2022
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 106 294 0 07 Oct 2021
Zero-Shot Text-to-Image Generation Aditya A. Ramesh Mikhail Pavlov Gabriel Goh Scott Gray Chelsea Voss Alec Radford Mark Chen Ilya Sutskever VLM 253 4,735 0 24 Feb 2021
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 152 1,748 0 02 Mar 2017