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Lesion appearance is a crucial clue for medical providers to distinguish referable diabetic retinopathy (rDR) from non-referable DR. Most existing large-scale DR datasets contain only image-level labels rather than pixel-based annotations. This motivates us to develop algorithms to classify rDR and segment lesions via image-level labels. This paper leverages self-supervised equivariant learning and attention-based multi-instance learning (MIL) to tackle this problem. MIL is an effective strategy to differentiate positive and negative instances, helping us discard background regions (negative instances) while localizing lesion regions (positive ones). However, MIL only provides coarse lesion localization and cannot distinguish lesions located across adjacent patches. Conversely, a self-supervised equivariant attention mechanism (SEAM) generates a segmentation-level class activation map (CAM) that can guide patch extraction of lesions more accurately. Our work aims at integrating both methods to improve rDR classification accuracy. We conduct extensive validation experiments on the Eyepacs dataset, achieving an area under the receiver operating characteristic curve (AU ROC) of 0.958, outperforming current state-of-the-art algorithms.
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http://dx.doi.org/10.1117/12.2669772 | DOI Listing |
Bioinformatics
June 2025
Department of Biomedical Engineering and Informatics, Indiana University Indianapolis, Indianapolis, IN 46202, United States.
Motivation: Chronic kidney disease (CKD) and acute kidney injury (AKI) are prominent public health concerns affecting more than 15% of the global population. The ongoing development of spatially resolved transcriptomics (SRT) technologies presents a promising approach for discovering the spatial distribution patterns of gene expression within diseased tissues. However, existing computational tools are predominantly calibrated and designed on the ribbon-like structure of the brain cortex, presenting considerable computational obstacles in discerning highly heterogeneous mosaic-like tissue architectures in the kidney.
View Article and Find Full Text PDFJ Chem Phys
January 2025
Department of Chemistry and James Franck Institute, University of Chicago, Chicago, Illinois 60637, USA.
Identifying informative low-dimensional features that characterize dynamics in molecular simulations remains a challenge, often requiring extensive manual tuning and system-specific knowledge. Here, we introduce geom2vec, in which pretrained graph neural networks (GNNs) are used as universal geometric featurizers. By pretraining equivariant GNNs on a large dataset of molecular conformations with a self-supervised denoising objective, we obtain transferable structural representations that are useful for learning conformational dynamics without further fine-tuning.
View Article and Find Full Text PDFArXiv
December 2024
Department of Chemistry and James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States.
Identifying informative low-dimensional features that characterize dynamics in molecular simulations remains a challenge, often requiring extensive manual tuning and system-specific knowledge. Here, we introduce geom2vec, in which pretrained graph neural networks (GNNs) are used as universal geometric featurizers. By pretraining equivariant GNNs on a large dataset of molecular conformations with a self-supervised denoising objective, we obtain transferable structural representations that are useful for learning conformational dynamics without further fine-tuning.
View Article and Find Full Text PDFJ Imaging Inform Med
June 2025
School of Artificial Intelligence and Big Data, Henan University of Technology, Zhengzhou, 450001, China.
Med Image Anal
January 2025
School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei Anhui, 230026, China; Center for Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE), Suzhou Institute for Advanced Research, USTC, Suzhou Jiangsu, 215
Optical coherence tomography (OCT) is a noninvasive technology that enables real-time imaging of tissue microanatomies. The axial resolution of OCT is intrinsically constrained by the spectral bandwidth of the employed light source while maintaining a fixed center wavelength for a specific application. Physically extending this bandwidth faces strong limitations and requires a substantial cost.
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