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We present a generic framework for spatio-temporal (ST) data modeling, analysis, and forecasting, with a special focus on data that is sparse in both space and time. Our multi-scaled framework is a seamless coupling of two major components:…

Machine Learning · Computer Science 2018-04-04 Bao Wang , Xiyang Luo , Fangbo Zhang , Baichuan Yuan , Andrea L. Bertozzi , P. Jeffrey Brantingham

In multivariate time series (MTS) forecasting, many deep learning based methods have been proposed for modeling dependencies at multiple spatial (inter-variate) or temporal (intra-variate) scales. However, existing methods may fail to model…

Machine Learning · Computer Science 2025-09-03 Binqing Wu , Jianlong Huang , Zongjiang Shang , Ling Chen

Spatial transcriptomics (ST) technologies not only offer an unprecedented opportunity to interrogate intact biological samples in a spatially informed manner, but also set the stage for integration with other imaging-based modalities.…

Quantitative Methods · Quantitative Biology 2025-07-31 Levin M Moser , Ahmad Kamal Hamid , Esteban Miglietta , Nodar Gogoberidze , Beth A Cimini

PET imaging is widely employed for observing biological metabolic activities within the human body. However, numerous benign conditions can cause increased uptake of radiopharmaceuticals, confounding differentiation from malignant tumors.…

Image and Video Processing · Electrical Eng. & Systems 2024-10-31 Ran Hong , Yuxia Huang , Lei Liu , Zhonghui Wu , Bingxuan Li , Xuemei Wang , Qiegen Liu

Land surface temperature (LST) is a fundamental parameter in thermal infrared remote sensing, while current LST products are often constrained by the trade-off between spatial and temporal resolutions. To mitigate this limitation, numerous…

Geophysics · Physics 2025-11-11 Huanyu Zhang , Bo-Hui Tang , Tian Hu , Yun Jiang , Zhao-Liang Li

Spatially resolved transcriptomics is a fast-developing set of technologies that enables the measurement of localized gene expression across spatial locations in a sample. Detecting spatially varying genes is critical for analyzing such…

Applications · Statistics 2026-04-22 Pritam Dey , Rajarshi Guhaniyogi , Yang Ni , Bani K. Mallick

Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have…

Quantitative Methods · Quantitative Biology 2024-01-29 Dexiong Chen , Philip Hartout , Paolo Pellizzoni , Carlos Oliver , Karsten Borgwardt

Spatio-Temporal predictive Learning is a self-supervised learning paradigm that enables models to identify spatial and temporal patterns by predicting future frames based on past frames. Traditional methods, which use recurrent neural…

Computer Vision and Pattern Recognition · Computer Science 2024-11-18 Andrea Alfarano , Alberto Alfarano , Linda Friso , Andrea Bacciu , Irene Amerini , Fabrizio Silvestri

Although new vision foundation models such as Segment Anything Model 2 (SAM2) have significantly enhanced zero-shot image segmentation capabilities, reliance on human-provided prompts poses significant challenges in adapting SAM2 to medical…

Computer Vision and Pattern Recognition · Computer Science 2025-06-25 Yang Xing , Jiong Wu , Yuheng Bu , Kuang Gong

Graph neural networks (GNNs) have gained considerable attention in recent years for traffic flow prediction due to their ability to learn spatio-temporal pattern representations through a graph-based message-passing framework. Although GNNs…

Machine Learning · Computer Science 2025-03-12 Qianru Zhang , Xinyi Gao , Haixin Wang , Siu-Ming Yiu , Hongzhi Yin

Spatio-Temporal Graph (STG) forecasting is a fundamental task in many real-world applications. Spatio-Temporal Graph Neural Networks have emerged as the most popular method for STG forecasting, but they often struggle with temporal…

Machine Learning · Computer Science 2023-09-26 Yutong Xia , Yuxuan Liang , Haomin Wen , Xu Liu , Kun Wang , Zhengyang Zhou , Roger Zimmermann

Spatial transcriptomics (ST) measures mRNA expression while preserving spatial organization, but multi-slice analysis faces two coupled difficulties: large non-rigid deformations across slices and inter-slice batch effects when alignment…

Computer Vision and Pattern Recognition · Computer Science 2026-04-15 Bonian Han , Cong Qi , Przemyslaw Musialski , Zhi Wei

The integration of AI in digital pathology, particularly in whole slide image (WSI) and spatial transcriptomics (ST) analysis, holds immense potential for enhancing our understanding of diseases. Despite challenges such as training pattern…

Quantitative Methods · Quantitative Biology 2024-11-18 Chao-Hui Huang , Sara Lichtarge , Diane Fernandez

X-ray Photoelectron Spectroscopy (XPS) is a crucial technique for material surface analysis, yet interpreting its spectra is often challenging for both human analysts and automated methods due to the prevalence of variable spectral shifts…

Materials Science · Physics 2026-03-06 Issa Saddiq , Yuxin Fan , Robert G. Palgrave , Mark A. Isaacs , David Morgan , Keith T. Butler

In the visual spatial understanding (VSU) area, spatial image-to-text (SI2T) and spatial text-to-image (ST2I) are two fundamental tasks that appear in dual form. Existing methods for standalone SI2T or ST2I perform imperfectly in spatial…

Computer Vision and Pattern Recognition · Computer Science 2025-09-03 Yu Zhao , Hao Fei , Xiangtai Li , Libo Qin , Jiayi Ji , Hongyuan Zhu , Meishan Zhang , Min Zhang , Jianguo Wei

$\textbf{This is the conference version of our paper: Spatiotemporal Implicit Neural Representation as a Generalized Traffic Data Learner}$. Spatiotemporal Traffic Data (STTD) measures the complex dynamical behaviors of the multiscale…

Machine Learning · Computer Science 2024-06-14 Tong Nie , Guoyang Qin , Wei Ma , Jian Sun

Conventional hematoxylin-eosin (H&E) staining is limited to revealing cell morphology and distribution, whereas immunohistochemical (IHC) staining provides precise and specific visualization of protein activation at the molecular level.…

Image and Video Processing · Electrical Eng. & Systems 2024-07-30 Fuqiang Chen , Ranran Zhang , Boyun Zheng , Yiwen Sun , Jiahui He , Wenjian Qin

Deep neural networks face several challenges in hyperspectral image classification, including high-dimensional data, sparse distribution of ground objects, and spectral redundancy, which often lead to classification overfitting and limited…

Computer Vision and Pattern Recognition · Computer Science 2025-06-12 Guandong Li , Mengxia Ye

The advent of next-generation sequencing-based spatially resolved transcriptomics (SRT) techniques has reshaped genomic studies by enabling high-throughput gene expression profiling while preserving spatial and morphological context.…

Applications · Statistics 2025-02-20 Bencong Zhu , Alberto Cassese , Marina Vannucci , Michele Guindani , Qiwei Li

A saliency guided hierarchical visual tracking (SHT) algorithm containing global and local search phases is proposed in this paper. In global search, a top-down saliency model is novelly developed to handle abrupt motion and appearance…

Computer Vision and Pattern Recognition · Computer Science 2018-12-24 Fangwen Tu , Shuzhi Sam Ge , Yazhe Tang , Chang Chieh Hang