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Molecular Property Prediction (MPP) plays a pivotal role across diverse domains, spanning drug discovery, material science, and environmental chemistry. Fueled by the exponential growth of chemical data and the evolution of artificial…

Machine Learning · Computer Science 2024-08-23 Tanya Liyaqat , Tanvir Ahmad , Chandni Saxena

Research into deep learning models for molecular property prediction has primarily focused on the development of better Graph Neural Network (GNN) architectures. Though new GNN variants continue to improve performance, their modifications…

Quantitative Methods · Quantitative Biology 2021-11-23 Toni Sagayaraj , Carsten Eickhoff

Molecular property prediction with deep learning has gained much attention over the past years. Owing to the scarcity of labeled molecules, there has been growing interest in self-supervised learning methods that learn generalizable…

Machine Learning · Computer Science 2023-09-04 Peizhen Bai , Xianyuan Liu , Haiping Lu

We consider feature representation learning problem of molecular graphs. Graph Neural Networks have been widely used in feature representation learning of molecular graphs. However, most existing methods deal with molecular graphs…

Machine Learning · Computer Science 2022-06-08 Zhaoning Yu , Hongyang Gao

Graph Self-Supervised Learning (GSSL) provides a robust pathway for acquiring embeddings without expert labelling, a capability that carries profound implications for molecular graphs due to the staggering number of potential molecules and…

Machine Learning · Computer Science 2023-10-19 Hanchen Wang , Jean Kaddour , Shengchao Liu , Jian Tang , Joan Lasenby , Qi Liu

Predicting molecular properties with data-driven methods has drawn much attention in recent years. Particularly, Graph Neural Networks (GNNs) have demonstrated remarkable success in various molecular generation and prediction tasks. In…

Quantitative Methods · Quantitative Biology 2021-10-19 Zaixi Zhang , Qi Liu , Hao Wang , Chengqiang Lu , Chee-Kong Lee

Molecular property prediction is a fundamental task in computational chemistry with critical applications in drug discovery and materials science. While recent works have explored Large Language Models (LLMs) for this task, they primarily…

Computer Vision and Pattern Recognition · Computer Science 2025-07-08 Deepan Adak , Yogesh Singh Rawat , Shruti Vyas

Molecular representation learning is pivotal in predicting molecular properties and advancing drug design. Traditional methodologies, which predominantly rely on homogeneous graph encoding, are limited by their inability to integrate…

Machine Learning · Computer Science 2025-03-24 Mukun Chen , Jia Wu , Shirui Pan , Fu Lin , Bo Du , Xiuwen Gong , Wenbin Hu

How to produce expressive molecular representations is a fundamental challenge in AI-driven drug discovery. Graph neural network (GNN) has emerged as a powerful technique for modeling molecular data. However, previous supervised approaches…

Machine Learning · Computer Science 2020-12-22 Pengyong Li , Jun Wang , Yixuan Qiao , Hao Chen , Yihuan Yu , Xiaojun Yao , Peng Gao , Guotong Xie , Sen Song

Molecular property prediction has attracted substantial attention recently. Accurate prediction of drug properties relies heavily on effective molecular representations. The structures of chemical compounds are commonly represented as…

Machine Learning · Computer Science 2025-08-05 Anyin Zhao , Zuquan Chen , Zhengyu Fang , Xiaoge Zhang , Jing Li

Molecular property prediction is a key component of AI-driven drug discovery and molecular characterization learning. Despite recent advances, existing methods still face challenges such as limited ability to generalize, and inadequate…

Machine Learning · Computer Science 2024-09-26 Zexing Zhao , Guangsi Shi , Xiaopeng Wu , Ruohua Ren , Xiaojun Gao , Fuyi Li

Molecular property prediction is essential for drug discovery. In recent years, deep learning methods have been introduced to this area and achieved state-of-the-art performances. However, most of existing methods ignore the intrinsic…

Biomolecules · Quantitative Biology 2022-11-04 Yuancheng Sun , Yimeng Chen , Weizhi Ma , Wenhao Huang , Kang Liu , Zhiming Ma , Wei-Ying Ma , Yanyan Lan

Accurate and efficient prediction of polymer properties is of key importance for polymer design. Traditional experimental tools and density function theory (DFT)-based simulations for polymer property evaluation, are both expensive and…

Materials Science · Physics 2024-10-08 Cong Shen , Yipeng Zhang , Fei Han , Kelin Xia

Accurate molecular property prediction is a critical challenge with wide-ranging applications in chemistry, materials science, and drug discovery. Molecular representation methods, including fingerprints and graph neural networks (GNNs),…

Machine Learning · Computer Science 2025-08-13 Jiaxin Ju , Yizhen Zheng , Huan Yee Koh , Can Wang , Shirui Pan

The prediction of molecular properties is a crucial task in the field of material and drug discovery. The potential benefits of using deep learning techniques are reflected in the wealth of recent literature. Still, these techniques are…

Machine Learning · Computer Science 2023-09-06 Minghao Guo , Veronika Thost , Samuel W Song , Adithya Balachandran , Payel Das , Jie Chen , Wojciech Matusik

Molecular representation learning is vital for various downstream applications, including the analysis and prediction of molecular properties and side effects. While Graph Neural Networks (GNNs) have been a popular framework for modeling…

Machine Learning · Computer Science 2025-02-18 Pengcheng Jiang , Cao Xiao , Tianfan Fu , Parminder Bhatia , Taha Kass-Hout , Jimeng Sun , Jiawei Han

The crux of molecular property prediction is to generate meaningful representations of the molecules. One promising route is to exploit the molecular graph structure through Graph Neural Networks (GNNs). It is well known that both atoms and…

Quantitative Methods · Quantitative Biology 2020-06-15 Hehuan Ma , Yatao Bian , Yu Rong , Wenbing Huang , Tingyang Xu , Weiyang Xie , Geyan Ye , Junzhou Huang

Multi-label Recognition (MLR) involves assigning multiple labels to each data instance in an image, offering advantages over single-label classification in complex scenarios. However, it faces the challenge of annotating all relevant…

Machine Learning · Computer Science 2025-06-03 Ruhui Zhang , Hezhe Qiao , Pengcheng Xu , Mingsheng Shang , Lin Chen

Self-supervised graph representation learning (SSGRL) is a representation learning paradigm used to reduce or avoid manual labeling. An essential part of SSGRL is graph data augmentation. Existing methods usually rely on heuristics commonly…

Machine Learning · Computer Science 2024-12-25 Ahmed E. Samy , Zekarias T. Kefatoa , Sarunas Girdzijauskasa

Benefiting from the powerful expressive capability of graphs, graph-based approaches have achieved impressive performance in various biomedical applications. Most existing methods tend to define the adjacency matrix among samples manually…

Machine Learning · Computer Science 2021-07-02 Shuai Zheng , Zhenfeng Zhu , Zhizhe Liu , Zhenyu Guo , Yang Liu , Yao Zhao