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Over the past six years, molecular transformer models have become key tools in drug discovery. Most existing models are pre-trained on large, unlabeled datasets such as ZINC or ChEMBL. However, the extent to which large-scale pre-training…

Machine Learning · Computer Science 2025-05-23 Afnan Sultan , Max Rausch-Dupont , Shahrukh Khan , Olga Kalinina , Dietrich Klakow , Andrea Volkamer

The increasing global prevalence of mental disorders, such as depression and PTSD, requires objective and scalable diagnostic tools. Traditional clinical assessments often face limitations in accessibility, objectivity, and consistency.…

Audio and Speech Processing · Electrical Eng. & Systems 2025-04-03 Abdelrahaman A. Hassan , Abdelrahman A. Ali , Aya E. Fouda , Radwa J. Hanafy , Mohammed E. Fouda

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

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

Pretrained language models (LMs) showcase significant capabilities in processing molecular text, while concurrently, message passing neural networks (MPNNs) demonstrate resilience and versatility in the domain of molecular science. Despite…

Machine Learning · Computer Science 2025-06-17 Jiaqing Xie , Ziheng Chi

Small molecules are essential to drug discovery, and graph-language models hold promise for learning molecular properties and functions from text. However, existing molecule-text datasets are limited in scale and informativeness,…

Biomolecules · Quantitative Biology 2025-06-03 Yihan Zhu , Gang Liu , Eric Inae , Meng Jiang

Accurate cancer survival prediction is crucial for assisting clinical doctors in formulating treatment plans. Multimodal data, including histopathological images and genomic data, offer complementary and comprehensive information that can…

Computer Vision and Pattern Recognition · Computer Science 2024-08-09 Hui Luo , Jiashuang Huang , Hengrong Ju , Tianyi Zhou , Weiping Ding

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular…

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

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

Modeling the joint distribution of data samples and their properties allows to construct a single model for both data generation and property prediction, with synergistic benefits reaching beyond purely generative or predictive models.…

Accurate molecular property prediction requires integrating complementary information from molecular structure and chemical semantics. In this work, we propose LGM-CL, a local-global multimodal contrastive learning framework that jointly…

Machine Learning · Computer Science 2026-02-02 Xiayu Liu , Zhengyi Lu , Yunhong Liao , Chan Fan , Hou-biao 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

In the field of chemical structure recognition, the task of converting molecular images into machine-readable data formats such as SMILES string stands as a significant challenge, primarily due to the varied drawing styles and conventions…

Computer Vision and Pattern Recognition · Computer Science 2025-03-12 Yufan Chen , Ching Ting Leung , Yong Huang , Jianwei Sun , Hao Chen , Hanyu Gao

Chemical representation learning has gained increasing interest due to the limited availability of supervised data in fields such as drug and materials design. This interest particularly extends to chemical language representation learning,…

Chemical Physics · Physics 2024-08-06 Jun-Hyung Park , Yeachan Kim , Mingyu Lee , Hyuntae Park , SangKeun Lee

Many vision-related tasks benefit from reasoning over multiple modalities to leverage complementary views of data in an attempt to learn robust embedding spaces. Most deep learning-based methods rely on a late fusion technique whereby…

Computer Vision and Pattern Recognition · Computer Science 2020-03-04 Austin Reiter , Menglin Jia , Pu Yang , Ser-Nam Lim

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

Glasses offer a broad range of tunable thermophysical properties that are linked to their compositions. However, it is challenging to establish a universal composition-property relation of glasses due to their enormous composition and…

Soft Condensed Matter · Physics 2023-08-23 Kumar Ayush , Pooja Sahu , Sk Musharaf Ali , Tarak K Patra

Machine learning (ML) can be used to construct surrogate models for the fast prediction of a property of interest. ML can thus be applied to chemical projects, where the usual experimentation or calculation techniques can take hours or days…

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…

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