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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

In recent years, artificial intelligence has played an important role on accelerating the whole process of drug discovery. Various of molecular representation schemes of different modals (e.g. textual sequence or graph) are developed. By…

Machine Learning · Computer Science 2022-11-28 Tianyu Wu , Yang Tang , Qiyu Sun , Luolin Xiong

Graphs are an essential data structure utilized to represent relationships in real-world scenarios. Prior research has established that Graph Neural Networks (GNNs) deliver impressive outcomes in graph-centric tasks, such as link prediction…

Machine Learning · Computer Science 2024-09-12 Xubin Ren , Jiabin Tang , Dawei Yin , Nitesh Chawla , Chao Huang

Molecular Machine Learning (ML) bears promise for efficient molecule property prediction and drug discovery. However, labeled molecule data can be expensive and time-consuming to acquire. Due to the limited labeled data, it is a great…

Machine Learning · Computer Science 2022-04-01 Yuyang Wang , Jianren Wang , Zhonglin Cao , Amir Barati Farimani

Multimodal Large Language Models (MLLMs) have demonstrated remarkable capabilities in representing and understanding diverse modalities. However, they typically focus on modality alignment in a pairwise manner while overlooking structural…

Machine Learning · Computer Science 2025-06-13 Jiajin Liu , Dongzhe Fan , Jiacheng Shen , Chuanhao Ji , Daochen Zha , Qiaoyu Tan

Molecular property prediction is of crucial importance in many disciplines such as drug discovery, molecular biology, or material and process design. The frequently employed quantitative structure-property/activity relationships…

Biomolecules · Quantitative Biology 2024-01-17 Jan G. Rittig , Qinghe Gao , Manuel Dahmen , Alexander Mitsos , Artur M. Schweidtmann

Prediction of molecular properties, including physico-chemical properties, is a challenging task in chemistry. Herein we present a new state-of-the-art multitask prediction method based on existing graph neural network models. We have used…

Machine Learning · Computer Science 2019-10-31 Fabio Capela , Vincent Nouchi , Ruud Van Deursen , Igor V. Tetko , Guillaume Godin

Molecule property prediction is a fundamental problem for computer-aided drug discovery and materials science. Quantum-chemical simulations such as density functional theory (DFT) have been widely used for calculating the molecule…

Machine Learning · Computer Science 2019-11-26 Hiroyuki Shindo , Yuji Matsumoto

Machine learning in materials science faces challenges due to limited experimental data, as generating synthesis data is costly and time-consuming, especially with in-house experiments. Mining data from existing literature introduces issues…

Computational Physics · Physics 2025-03-11 Devi Dutta Biswajeet , Sara Kadkhodaei

Integrating Pre-trained Language Models (PLMs) with Graph Neural Networks (GNNs) remains a central challenge in text-rich heterophilic graph learning. We propose a novel integration framework that enables effective fusion between powerful…

Computation and Language · Computer Science 2025-10-09 Aarush Sinha

Large Language Models (LLMs) have made great strides in areas such as language processing and computer vision. Despite the emergence of diverse techniques to improve few-shot learning capacity, current LLMs fall short in handling the…

Biomolecules · Quantitative Biology 2024-05-14 Xianggen Liu , Yan Guo , Haoran Li , Jin Liu , Shudong Huang , Bowen Ke , Jiancheng Lv

Learning on Graphs has attracted immense attention due to its wide real-world applications. The most popular pipeline for learning on graphs with textual node attributes primarily relies on Graph Neural Networks (GNNs), and utilizes shallow…

Machine Learning · Computer Science 2024-01-17 Zhikai Chen , Haitao Mao , Hang Li , Wei Jin , Hongzhi Wen , Xiaochi Wei , Shuaiqiang Wang , Dawei Yin , Wenqi Fan , Hui Liu , Jiliang Tang

Molecular property prediction is a critical task in computational drug discovery. While recent advances in Graph Neural Networks (GNNs) and Transformers have shown to be effective and promising, they face the following limitations:…

Deep neural networks show great potential for automating various visual quality inspection tasks in manufacturing. However, their applicability is limited in more volatile scenarios, such as remanufacturing, where the inspected products and…

Computer Vision and Pattern Recognition · Computer Science 2026-02-12 Johannes C. Bauer , Paul Geng , Stephan Trattnig , Petr Dokládal , Rüdiger Daub

Machine learning force fields (MLFFs) are gradually evolving towards enabling molecular dynamics simulations of molecules and materials with ab initio accuracy but at a small fraction of the computational cost. However, several challenges…

Multi-view multi-label feature selection aims to identify informative features from heterogeneous views, where each sample is associated with multiple interdependent labels. This problem is particularly important in machine learning…

Artificial Intelligence · Computer Science 2025-11-20 Zhiqi Chen , Yuzhou Liu , Jiarui Liu , Wanfu Gao

Machine learning plays an increasingly important role in many areas of chemistry and materials science, e.g. to predict materials properties, to accelerate simulations, to design new materials, and to predict synthesis routes of new…

In recent years, Graph Neural Networks (GNNs) have become successful in molecular property prediction tasks such as toxicity analysis. However, due to the black-box nature of GNNs, their outputs can be concerning in high-stakes…

Machine Learning · Computer Science 2024-10-22 Yinhan He , Zaiyi Zheng , Patrick Soga , Yaozhen Zhu , yushun Dong , Jundong Li

Large Language Models (LLMs) have demonstrated remarkable generalization and instruction-following capabilities with instruction tuning. The advancements in LLMs and instruction tuning have led to the development of Large Vision-Language…

Machine Learning · Computer Science 2024-11-05 Jinyoung Park , Minseong Bae , Dohwan Ko , Hyunwoo J. Kim

Foundation models, such as Large Language Models (LLMs) or Large Vision Models (LVMs), have emerged as one of the most powerful tools in the respective fields. However, unlike text and image data, graph data do not have a definitive…

Machine Learning · Computer Science 2025-04-28 Lecheng Kong , Jiarui Feng , Hao Liu , Chengsong Huang , Jiaxin Huang , Yixin Chen , Muhan Zhang