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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…

机器学习 · 计算机科学 2023-09-06 Minghao Guo , Veronika Thost , Samuel W Song , Adithya Balachandran , Payel Das , Jie Chen , Wojciech Matusik

Discovering molecules with desirable molecular properties, including ADMET profiles, is of great importance in drug discovery. Existing approaches typically employ deep learning models, such as Graph Neural Networks (GNNs) and Transformers,…

生物大分子 · 定量生物学 2025-05-13 Huiyang Hong , Xinkai Wu , Hongyu Sun , Chaoyang Xie , Qi Wang , Yuquan Li

High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and properties that result from…

化学物理 · 物理学 2016-11-22 Sandip De , Felix Musil , Teresa Ingram , Carsten Baldauf , Michele Ceriotti

Large language models possess strong chemical reasoning capabilities, making them effective molecular editors. However, property-relevant information is implicitly entangled across their dense hidden states, providing no explicit handle for…

机器学习 · 计算机科学 2026-05-12 Mingxu Zhang , Yuhan Li , Lujundong Li , Dazhong Shen , Hui Xiong , Ying Sun

Molecular property is usually observed with a limited number of samples, and researchers have considered property prediction as a few-shot problem. One important fact that has been ignored by prior works is that each molecule can be…

机器学习 · 计算机科学 2023-06-30 Xiang Zhuang , Qiang Zhang , Bin Wu , Keyan Ding , Yin Fang , Huajun Chen

Molecule generation is a task made very difficult by the complex ways in which we represent molecules computationally. A common technique used in molecular generative modeling is to use SMILES strings with recurrent neural networks built…

生物大分子 · 定量生物学 2024-02-28 Divahar Sivanesan

Molecule-and-text cross-modal representation learning has emerged as a promising direction for enhancing the quality of molecular representation, thereby improving performance in various scientific fields. However, most approaches employ a…

定量方法 · 定量生物学 2025-03-04 Yikun Zhang , Geyan Ye , Chaohao Yuan , Bo Han , Long-Kai Huang , Jianhua Yao , Wei Liu , Yu Rong

Molecular representation learning, a cornerstone for downstream tasks like molecular captioning and molecular property prediction, heavily relies on Graph Neural Networks (GNN). However, GNN suffers from the over-smoothing problem, where…

机器学习 · 计算机科学 2025-08-13 Zihang Shao , Wentao Lei , Lei Wang , Wencai Ye , Li Liu

Developing an effective molecular generation framework even with a limited number of molecules is often important for its practical deployment, e.g., drug discovery, since acquiring task-related molecular data requires expensive and…

机器学习 · 计算机科学 2024-07-17 Seojin Kim , Jaehyun Nam , Sihyun Yu , Younghoon Shin , Jinwoo Shin

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…

定量方法 · 定量生物学 2023-09-06 Jianyuan Deng , Zhibo Yang , Hehe Wang , Iwao Ojima , Dimitris Samaras , Fusheng Wang

The recent advance in neural network architecture and training algorithms have shown the effectiveness of representation learning. The neural network-based models generate better representation than the traditional ones. They have the…

计算与语言 · 计算机科学 2018-05-29 Kamal Al-Sabahi , Zhang Zuping , Mohammed Nadher

Architectures for sparse hierarchical representation learning have recently been proposed for graph-structured data, but so far assume the absence of edge features in the graph. We close this gap and propose a method to pool graphs with…

Accurate prediction of molecular properties is crucial in drug discovery. Traditional methods often overlook that real-world molecules typically exhibit multiple property labels with complex correlations. To this end, we propose a novel…

定量方法 · 定量生物学 2024-08-13 Linjia Kang , Songhua Zhou , Shuyan Fang , Shichao Liu

Molecular property prediction plays a fundamental role in drug discovery to identify candidate molecules with target properties. However, molecular property prediction is essentially a few-shot problem which makes it hard to use regular…

机器学习 · 计算机科学 2021-11-12 Yaqing Wang , Abulikemu Abuduweili , Quanming Yao , Dejing Dou

Elucidating and accurately predicting the druggability and bioactivities of molecules plays a pivotal role in drug design and discovery and remains an open challenge. Recently, graph neural networks (GNN) have made remarkable advancements…

机器学习 · 计算机科学 2022-08-31 Weimin Zhu , Yi Zhang , DuanCheng Zhao , Jianrong Xu , Ling Wang

We compare the ability of a simulated annealing program and an evolutionary algorithm to find molecules with large molecular average hyperpolarizabilities. This property is an important component of nonlinear optical materials. Both…

计算物理 · 物理学 2026-02-19 Dominic Mashak , S. A. Alexander

Accurate molecular property prediction (MPP) is a critical step in modern drug development. However, the scarcity of experimental validation data poses a significant challenge to AI-driven research paradigms. Under few-shot learning…

机器学习 · 计算机科学 2025-05-20 Yifan Dai , Xuanbai Ren , Tengfei Ma , Qipeng Yan , Yiping Liu , Yuansheng Liu , Xiangxiang Zeng

Pre-trained Language Models have emerged as promising tools for predicting molecular properties, yet their development is in its early stages, necessitating further research to enhance their efficacy and address challenges such as…

Transformative innovations in model architectures have introduced hierarchical embedding augmentation as a means to redefine the representation of tokens through multi-level semantic structures, offering enhanced adaptability to complex…

计算与语言 · 计算机科学 2025-08-11 Derek Yotheringhay , Alistair Kirkland , Humphrey Kirkbride , Josiah Whitesteeple

Attribute recognition is a crucial but challenging task due to viewpoint changes, illumination variations and appearance diversities, etc. Most of previous work only consider the attribute-level feature embedding, which might perform poorly…

计算机视觉与模式识别 · 计算机科学 2020-05-26 Jie Yang , Jiarou Fan , Yiru Wang , Yige Wang , Weihao Gan , Lin Liu , Wei Wu
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