ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction

11 June 2021

Xiaomin Fang

Fan Wang

Papers citing "ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction"

38 / 38 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 29 0 0 09 May 2025
Evaluating Effects of Augmented SELFIES for Molecular Understanding Using QK-LSTM Collin Beaudoin Swaroop Ghosh 33 0 0 29 Apr 2025
MolGround: A Benchmark for Molecular Grounding Jiaxin Wu Ting Zhang Rubing Chen Wengyu Zhang Chen Jason Zhang Xiaoyong Wei Li Qing 48 0 0 31 Mar 2025
Exploiting Edited Large Language Models as General Scientific Optimizers Qitan Lv T. Liu H. Wang 41 0 0 08 Mar 2025
Understanding Oversmoothing in GNNs as Consensus in Opinion Dynamics Keqin Wang Yulong Yang Ishan Saha Christine Allen-Blanchette 58 1 0 31 Jan 2025
MOL-Mamba: Enhancing Molecular Representation with Structural & Electronic Insights Jingjing Hu D. Guo Zhan Si Deguang Liu Yunfeng Diao J. Zhang Jinxing Zhou Meng Wang Mamba 98 1 0 21 Dec 2024
MolParser: End-to-end Visual Recognition of Molecule Structures in the Wild Xi Fang Jiankun Wang X. Cai Shangqian Chen Shuwen Yang Lin Yao Linfeng Zhang Guolin Ke Linfeng Zhang Guolin Ke 50 1 0 17 Nov 2024
UniGEM: A Unified Approach to Generation and Property Prediction for Molecules Shikun Feng Yuyan Ni Yan Lu Zhi-Ming Ma Wei-Ying Ma Yanyan Lan 38 5 0 14 Oct 2024
Geometric Representation Condition Improves Equivariant Molecule Generation Zian Li Cai Zhou Xiyuan Wang Xingang Peng Muhan Zhang 45 1 0 04 Oct 2024
MaskMol: Knowledge-guided Molecular Image Pre-Training Framework for Activity Cliffs Zhixiang Cheng Hongxin Xiang Pengsen Ma Li Zeng Xin Jin ... Yang Deng Bosheng Song Xinxin Feng Changhui Deng Xiangxiang Zeng 28 0 0 02 Sep 2024
A Bayesian Flow Network Framework for Chemistry Tasks Nianze Tao Minori Abe BDL 32 2 0 28 Jul 2024
TransMA: an explainable multi-modal deep learning model for predicting properties of ionizable lipid nanoparticles in mRNA delivery Kun Wu Zixu Wang Xiulong Yang Yangyang Chen Zhenqi Han Jialu Zhang Lizhuang Liu 28 0 0 08 Jul 2024
Knowledge-enhanced Relation Graph and Task Sampling for Few-shot Molecular Property Prediction Zeyu Wang Tianyi Jiang Yao Lu Xiaoze Bao Shanqing Yu Bin Wei Qi Xuan 42 1 0 24 May 2024
MAGE: Model-Level Graph Neural Networks Explanations via Motif-based Graph Generation Zhaoning Yu Hongyang Gao 44 3 0 21 May 2024
Triplet Interaction Improves Graph Transformers: Accurate Molecular Graph Learning with Triplet Graph Transformers Md Shamim Hussain Mohammed J. Zaki D. Subramanian ViT 28 5 0 07 Feb 2024
Towards 3D Molecule-Text Interpretation in Language Models Sihang Li Zhiyuan Liu Yancheng Luo Xiang Wang Xiangnan He Kenji Kawaguchi Tat-Seng Chua Qi Tian AI4CE 33 42 0 25 Jan 2024
Molecular Hypergraph Neural Networks Junwu Chen Philippe Schwaller GNN 41 10 0 20 Dec 2023
3D-Mol: A Novel Contrastive Learning Framework for Molecular Property Prediction with 3D Information Taojie Kuang Yiming Ren Zhixiang Ren 23 7 0 28 Sep 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 32 16 0 15 Sep 2023
Fractional Denoising for 3D Molecular Pre-training Shi Feng Yuyan Ni Yanyan Lan Zhiming Ma Wei-Ying Ma DiffM AI4CE 47 25 0 20 Jul 2023
PUFFIN: A Path-Unifying Feed-Forward Interfaced Network for Vapor Pressure Prediction Vinícius V. Santana C. Rebello Luana P. Queiroz A. M. Ribeiro Nadia Shardt Idelfonso B. R. Nogueira 22 6 0 06 Jul 2023
TransformerG2G: Adaptive time-stepping for learning temporal graph embeddings using transformers Alan John Varghese Aniruddha Bora Mengjia Xu George Karniadakis 36 5 0 05 Jul 2023
A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining Shengchao Liu Weitao Du Zhiming Ma Hongyu Guo Jian Tang 26 30 0 28 May 2023
MolXPT: Wrapping Molecules with Text for Generative Pre-training Zequn Liu Wei Zhang Yingce Xia Lijun Wu Shufang Xie Tao Qin M. Zhang Tie-Yan Liu 22 66 0 18 May 2023
An Equivariant Generative Framework for Molecular Graph-Structure Co-Design Zaixin Zhang Qi Liu Cheekong Lee Chang-Yu Hsieh Enhong Chen 15 18 0 12 Apr 2023
SELFormer: Molecular Representation Learning via SELFIES Language Models Atakan Yüksel Erva Ulusoy Atabey Ünlü Tunca Dogan 25 55 0 10 Apr 2023
InstructBio: A Large-scale Semi-supervised Learning Paradigm for Biochemical Problems Fang Wu Huiling Qin Siyuan Li Stan Z. Li Xianyuan Zhan Jinbo Xu 21 5 0 08 Apr 2023
Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey from Precision to Interpretability Zhiqiang Zhong A. Barkova Davide Mottin 22 8 0 16 Feb 2023
Do Deep Learning Methods Really Perform Better in Molecular Conformation Generation? G. Zhou Zhifeng Gao Zhewei Wei Hang Zheng Guolin Ke OOD AI4CE BDL 27 15 0 14 Feb 2023
GPS++: Reviving the Art of Message Passing for Molecular Property Prediction Dominic Masters Josef Dean Kerstin Klaser Zhiyi Li Sam Maddrell-Mander ... D. Beker Andrew Fitzgibbon Shenyang Huang Ladislav Rampášek Dominique Beaini 30 8 0 06 Feb 2023
Implicit Geometry and Interaction Embeddings Improve Few-Shot Molecular Property Prediction Christopher Fifty Joseph M. Paggi Ehsan Amid J. Leskovec R. Dror AI4CE 18 0 0 04 Feb 2023
polyBERT: A chemical language model to enable fully machine-driven ultrafast polymer informatics Christopher Kuenneth R. Ramprasad 26 101 0 29 Sep 2022
Edge Direction-invariant Graph Neural Networks for Molecular Dipole Moments Prediction Yang Jeong Park GNN 23 1 0 26 Jun 2022
Evaluating Self-Supervised Learning for Molecular Graph Embeddings Hanchen Wang Jean Kaddour Shengchao Liu Jian Tang Joan Lasenby Qi Liu 27 20 0 16 Jun 2022
A Survey of Pretraining on Graphs: Taxonomy, Methods, and Applications Jun-Xiong Xia Yanqiao Zhu Yuanqi Du Stan Z. Li VLM 30 41 0 16 Feb 2022
Improving Molecular Representation Learning with Metric Learning-enhanced Optimal Transport Fang Wu Nicolas Courty Shuting Jin Stan Z. Li OOD OT 18 8 0 13 Feb 2022
Large-Scale Chemical Language Representations Capture Molecular Structure and Properties Jerret Ross Brian M. Belgodere Vijil Chenthamarakshan Inkit Padhi Youssef Mroueh Payel Das AI4CE 21 272 0 17 Jun 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 172 1,775 0 02 Mar 2017