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Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements…

Machine Learning · Computer Science 2021-10-14 Dhananjay Bhaskar , Jackson D. Grady , Michael A. Perlmutter , Smita Krishnaswamy

Graph Neural Networks (GNNs) have been widely employed for feature representation learning in molecular graphs. Therefore, it is crucial to enhance the expressiveness of feature representation to ensure the effectiveness of GNNs. However, a…

Machine Learning · Computer Science 2024-09-16 Chengyu Yao , Hong Huang , Hang Gao , Fengge Wu , Haiming Chen , Junsuo Zhao

Molecular property prediction is crucial for drug discovery and materials science, yet existing approaches suffer from limited interpretability, poor cross-task generalization, and lack of chemical reasoning capabilities. Traditional…

Machine Learning · Computer Science 2025-10-20 Jiaxi Zhuang , Yaorui Shi , Jue Hou , Yunong He , Mingwei Ye , Mingjun Xu , Yuming Su , Linfeng Zhang , Ying Qian , Linfeng Zhang , Guolin Ke , Hengxing Cai

The limited extrapolative power of structure-based machine learning (ML) models is a critical bottleneck in chemical discovery, particularly for industrial R&D, where navigating uncharted chemical space to find next-generation materials or…

In the field of chemistry, the objective is to create novel molecules with desired properties, facilitating accurate property predictions for applications such as material design and drug screening. However, existing graph deep learning…

Machine Learning · Computer Science 2024-08-28 Sakhinana Sagar Srinivas , Venkataramana Runkana

In this study, a versatile methodology for initiating polymerization from monomers in highly cross-linked materials is investigated. As polymerization progresses, force-field parameters undergo continuous modification due to the formation…

Computational Engineering, Finance, and Science · Computer Science 2024-01-15 Wonseok Lee , Sanggyu Chong , Jihan Kim

Machine learning has emerged as an attractive alternative to experiments and simulations for predicting material properties. Usually, such an approach relies on specific domain knowledge for feature design: each learning target requires…

Materials Science · Physics 2020-03-10 Aditi S. Krishnapriyan , Maciej Haranczyk , Dmitriy Morozov

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

Predicting material properties has always been a challenging task in materials science. With the emergence of machine learning methodologies, new avenues have opened up. In this study, we build upon our recently developed Graph Neural…

Materials Science · Physics 2024-04-25 Si-Da Xue , Qi-Jun Hong

Recently, the study of graph neural network (GNN) has attracted much attention and achieved promising performance in molecular property prediction. Most GNNs for molecular property prediction are proposed based on the idea of learning the…

Machine Learning · Computer Science 2021-04-15 Yingfang Yuan , Wenjun Wang , Wei Pang

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…

Machine learning (ML) is widely used to explore crystal materials and predict their properties. However, the training is time-consuming for deep-learning models, and the regression process is a black box that is hard to interpret. Also, the…

Materials Science · Physics 2023-08-22 Xinyu Jiang , Haofan Sun , Kamal Choudhary , Houlong Zhuang , Qiong Nian

Accurate and efficient prediction of polymer properties is of great significance in polymer design. Conventionally, expensive and time-consuming experiments or simulations are required to evaluate polymer functions. Recently, Transformer…

Machine Learning · Computer Science 2023-04-27 Changwen Xu , Yuyang Wang , Amir Barati Farimani

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

Artificial intelligence (AI) has been widely applied in drug discovery with a major task as molecular property prediction. Despite booming techniques in molecular representation learning, key elements underlying molecular property…

Quantitative Methods · Quantitative Biology 2023-09-06 Jianyuan Deng , Zhibo Yang , Hehe Wang , Iwao Ojima , Dimitris Samaras , Fusheng Wang

Polymers are large macromolecules composed of repeating structural units known as monomers and are widely applied in fields such as energy storage, construction, medicine, and aerospace. However, existing graph neural network methods,…

Machine Learning · Computer Science 2026-01-06 Yihan Zhu , Gang Liu , Eric Inae , Tengfei Luo , Meng Jiang

Effective molecular representation learning is of great importance to facilitate molecular property prediction, which is a fundamental task for the drug and material industry. Recent advances in graph neural networks (GNNs) have shown great…

Machine Learning · Computer Science 2022-05-17 Xiaomin Fang , Lihang Liu , Jieqiong Lei , Donglong He , Shanzhuo Zhang , Jingbo Zhou , Fan Wang , Hua Wu , Haifeng Wang

The quest for accurate prediction of drug molecule properties poses a fundamental challenge in the realm of Artificial Intelligence Drug Discovery (AIDD). An effective representation of drug molecules emerges as a pivotal component in this…

Machine Learning · Computer Science 2024-04-22 Zhuoyuan Wang , Jiacong Mi , Shan Lu , Jieyue He

In drug discovery, it is vital to confirm the predictions of pharmaceutical properties from computational models using costly wet-lab experiments. Hence, obtaining reliable uncertainty estimates is crucial for prioritizing drug molecules…

Machine Learning · Computer Science 2023-10-19 Siddhartha Laghuvarapu , Zhen Lin , Jimeng Sun

Effective thermal conductivity is an important property of composites for different thermal management applications. Although physics-based methods, such as effective medium theory and solving partial differential equation, dominate the…

Computational Physics · Physics 2019-04-15 Qingyuan Rong , Han Wei , Hua Bao
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