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Molecular representation learning is crucial for the problem of molecular property prediction, where graph neural networks (GNNs) serve as an effective solution due to their structure modeling capabilities. Since labeled data is often…

Machine Learning · Computer Science 2023-09-26 Cameron Diao , Kaixiong Zhou , Zirui Liu , Xiao Huang , Xia Hu

Recently, a novel two-phase framework named mol-infer for inference of chemical compounds with prescribed abstract structures and desired property values has been proposed. The framework mol-infer is primarily based on using mixed integer…

Machine Learning · Computer Science 2025-07-08 Jianshen Zhu , Naveed Ahmed Azam , Kazuya Haraguchi , Liang Zhao , Tatsuya Akutsu

Graph Neural Networks (GNNs) have gained traction in the complex domain of drug discovery because of their ability to process graph-structured data such as drug molecule models. This approach has resulted in a myriad of methods and models…

Machine Learning · Computer Science 2025-09-10 Katherine Berry , Liang Cheng

Machine learning (ML) models have emerged as powerful tools for accelerating materials discovery and design by enabling accurate predictions of properties from compositional and structural data. These capabilities are vital for developing…

Graph neural networks are currently leading the performance charts in learning-based molecule property prediction and classification. Computational chemistry has, therefore, become the a prominent testbed for generic graph neural networks,…

Machine Learning · Computer Science 2020-02-04 Eliya Nachmani , Lior Wolf

Machine Learning (ML) has the potential to accelerate discovery of new materials and shed light on useful properties of existing materials. A key difficulty when applying ML in Materials Science is that experimental datasets of material…

Recent advancements in Graph Neural Networks (GNNs) have spurred an upsurge of research dedicated to enhancing the explainability of GNNs, particularly in critical domains such as medicine. A promising approach is the self-explaining…

Machine Learning · Computer Science 2024-08-15 Jingyu Peng , Qi Liu , Linan Yue , Zaixi Zhang , Kai Zhang , Yunhao Sha

Graph networks are a new machine learning (ML) paradigm that supports both relational reasoning and combinatorial generalization. Here, we develop universal MatErials Graph Network (MEGNet) models for accurate property prediction in both…

Materials Science · Physics 2019-04-29 Chi Chen , Weike Ye , Yunxing Zuo , Chen Zheng , Shyue Ping Ong

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

Few-shot molecular property prediction (FSMPP) is essential in drug discovery and materials design, where high-quality labeled data are often scarce and expensive to obtain. Despite the promising performance of existing methods, especially…

Computational Engineering, Finance, and Science · Computer Science 2026-05-14 Zeyu Wang , Xin Zheng , Yao Lu , Shanqing Yu , Qi Xuan , Shirui Pan

Graph Neural Networks (GNNs) have emerged as a prominent class of data-driven methods for molecular property prediction. However, a key limitation of typical GNN models is their inability to quantify uncertainties in the predictions. This…

Machine Learning · Computer Science 2024-07-02 Shengli Jiang , Shiyi Qin , Reid C. Van Lehn , Prasanna Balaprakash , Victor M. Zavala

Machine learning (ML) based materials discovery has emerged as one of the most promising approaches for breakthroughs in materials science. While heuristic knowledge based descriptors have been combined with ML algorithms to achieve good…

Materials Science · Physics 2021-09-28 Sadman Sadeed Omee , Steph-Yves Louis , Nihang Fu , Lai Wei , Sourin Dey , Rongzhi Dong , Qinyang Li , Jianjun Hu

Various machine learning models have been used to predict the properties of polycrystalline materials, but none of them directly consider the physical interactions among neighboring grains despite such microscopic interactions critically…

Materials Science · Physics 2021-07-16 Minyi Dai , Mehmet F. Demirel , Yingyu Liang , Jia-Mian Hu

The goal of few-shot learning is to learn a classifier that generalizes well even when trained with a limited number of training instances per class. The recently introduced meta-learning approaches tackle this problem by learning a generic…

Machine Learning · Computer Science 2019-02-11 Yanbin Liu , Juho Lee , Minseop Park , Saehoon Kim , Eunho Yang , Sung Ju Hwang , Yi Yang

Molecular structure-property relationships are key to molecular engineering for materials and drug discovery. The rise of deep learning offers a new viable solution to elucidate the structure-property relationships directly from chemical…

Machine Learning · Computer Science 2018-10-09 Seongok Ryu , Jaechang Lim , Seung Hwan Hong , Woo Youn Kim

Multi-task learning for molecular property prediction is becoming increasingly important in drug discovery. However, in contrast to other domains, the performance of multi-task learning in drug discovery is still not satisfying as the…

Biomolecules · Quantitative Biology 2022-10-07 Shengchao Liu , Meng Qu , Zuobai Zhang , Huiyu Cai , Jian Tang

Many modern deep-learning techniques do not work without enormous datasets. At the same time, several fields demand methods working in scarcity of data. This problem is even more complex when the samples have varying structures, as in the…

Machine Learning · Computer Science 2024-10-31 Donato Crisostomi , Simone Antonelli , Valentino Maiorca , Luca Moschella , Riccardo Marin , Emanuele Rodolà

Graph neural networks (GNNs) have been proposed for a wide range of graph-related learning tasks. In particular, in recent years, an increasing number of GNN systems were applied to predict molecular properties. However, a direct impediment…

Biomolecules · Quantitative Biology 2021-04-23 Yingfang Yuan , Wenjun Wang , Wei Pang

Link prediction for knowledge graphs aims to predict missing connections between entities. Prevailing methods are limited to a transductive setting and hard to process unseen entities. The recent proposed subgraph-based models provided…

Machine Learning · Computer Science 2021-08-03 Shuangjia Zheng , Sijie Mai , Ya Sun , Haifeng Hu , Yuedong Yang

Most graph-network-based meta-learning approaches model instance-level relation of examples. We extend this idea further to explicitly model the distribution-level relation of one example to all other examples in a 1-vs-N manner. We propose…

Computer Vision and Pattern Recognition · Computer Science 2020-04-02 Ling Yang , Liangliang Li , Zilun Zhang , Xinyu Zhou , Erjin Zhou , Yu Liu
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