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Keywords = slice-wise data split

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18 pages, 2234 KB  
Article
A Gated Attention-Based Multiple Instance Learning and Test-Time Augmentation Approach for Diagnosing Active Sacroiliitis in Sacroiliac Joint MRI Scans
by Zeynep Keskin, Onur İnan, Ömer Özberk, Reyhan Bilici, Sema Servi, Selma Özlem Çelikdelen and Mehmet Yıldırım
J. Clin. Med. 2026, 15(6), 2101; https://doi.org/10.3390/jcm15062101 - 10 Mar 2026
Cited by 1 | Viewed by 873
Abstract
Background and Objective: Axial spondyloarthritis (axSpA) is a group of chronic inflammatory diseases that primarily affect the sacroiliac joints. Early diagnosis is crucial for preventing irreversible structural damage. Magnetic Resonance Imaging (MRI) is the gold standard for detecting early inflammatory changes such as [...] Read more.
Background and Objective: Axial spondyloarthritis (axSpA) is a group of chronic inflammatory diseases that primarily affect the sacroiliac joints. Early diagnosis is crucial for preventing irreversible structural damage. Magnetic Resonance Imaging (MRI) is the gold standard for detecting early inflammatory changes such as sacroiliitis. However, conventional MRI interpretation is inherently subjective and susceptible to both intra- and inter-observer variability. Therefore, artificial intelligence (AI)-driven diagnostic solutions are increasingly being explored. Among them, the Gated Attention Multiple Instance Learning (MIL) framework holds strong potential in modeling heterogeneous inflammatory distributions, thanks to its slice-level attention mechanism. This study aims to evaluate the diagnostic performance of a deep learning model based on Gated Attention MIL for automated sacroiliitis detection. Furthermore, its results are compared with a baseline deep learning architecture (standard ResNet-18), and its consistency with radiologist annotations is analyzed. Materials and Methods: The dataset included 554 subjects, comprising 276 patients diagnosed with axSpA and 278 healthy controls. All MRI data were derived from axial T2-weighted fat-suppressed (T2_TSE_TRA_FS) sequences. Patient-wise data splitting was employed to construct training, validation, and independent test sets. The proposed model architecture integrates ResNet-18-based feature extraction, a gated attention mechanism for instance-level weighting, and bag-level classification. Additionally, Test-Time Augmentation (TTA) was implemented to enhance robustness during inference. Results: On the independent test set, the model achieved an accuracy of 85.88%, sensitivity of 92.86%, specificity of 79.07%, and an F1-score of 86.67%. Attention heatmaps generated by the MIL module showed strong spatial overlap with bone marrow edema regions annotated by expert radiologists. Implementation of TTA led to an approximate 10% improvement in overall classification accuracy. Conclusions: The Gated Attention MIL framework demonstrated high diagnostic performance for sacroiliitis detection, indicating its value as a reliable decision support tool for early axSpA diagnosis. Validation on larger, multi-center datasets is warranted to ensure generalizability and to support clinical integration in routine radiology workflows. Full article
(This article belongs to the Topic Machine Learning and Deep Learning in Medical Imaging)
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21 pages, 2169 KB  
Article
Enhancing Early Detection of Alzheimer’s Disease via Vision Transformer Machine Learning Architecture Using MRI Images
by Wided Hechkel, Marco Leo, Pierluigi Carcagnì, Marco Del-Coco and Abdelhamid Helali
Information 2026, 17(2), 163; https://doi.org/10.3390/info17020163 - 6 Feb 2026
Cited by 2 | Viewed by 2475
Abstract
Computer-aided diagnosis (CAD) systems based on deep learning have shown significant potential for Alzheimer’s disease (AD) stage classification from Magnetic Resonance Imaging (MRI). Nevertheless, challenges such as class imbalance, small sample sizes, and the presence of multiple slices per subject may lead to [...] Read more.
Computer-aided diagnosis (CAD) systems based on deep learning have shown significant potential for Alzheimer’s disease (AD) stage classification from Magnetic Resonance Imaging (MRI). Nevertheless, challenges such as class imbalance, small sample sizes, and the presence of multiple slices per subject may lead to biased evaluation and statistically unreliable performance, particularly for minority classes. In this study, a Vision Transformer (ViT)-based framework is proposed for multi-class AD classification using a Kaggle dataset containing 6400 MRI slices across four cognitive stages. A subject-wise data-splitting strategy is employed to prevent information leakage between the training and testing sets, and the statistical unreliability of near-perfect scores in underrepresented classes is critically examined. An ablation study is conducted to assess the contribution of key architectural components, demonstrating the effectiveness of self-attention and patch embedding in capturing discriminative features. Furthermore, attention-based visualization maps are incorporated to highlight brain regions influencing the model’s decisions and to illustrate subtle anatomical differences between MildDemented and VeryMildDemented cases. The proposed approach achieves a test accuracy of 97.98%, outperforming existing methods on the same dataset while providing improved interpretability. It supports early and accurate AD stage identification. Full article
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12 pages, 1925 KB  
Article
Explainable Precision Medicine in Breast MRI: A Combined Radiomics and Deep Learning Approach for the Classification of Contrast Agent Uptake
by Sylwia Nowakowska, Karol Borkowski, Carlotta Ruppert, Patryk Hejduk, Alexander Ciritsis, Anna Landsmann, Magda Marcon, Nicole Berger, Andreas Boss and Cristina Rossi
Bioengineering 2024, 11(6), 556; https://doi.org/10.3390/bioengineering11060556 - 31 May 2024
Cited by 6 | Viewed by 2322
Abstract
In DCE-MRI, the degree of contrast uptake in normal fibroglandular tissue, i.e., background parenchymal enhancement (BPE), is a crucial biomarker linked to breast cancer risk and treatment outcome. In accordance with the Breast Imaging Reporting & Data System (BI-RADS), it should be visually [...] Read more.
In DCE-MRI, the degree of contrast uptake in normal fibroglandular tissue, i.e., background parenchymal enhancement (BPE), is a crucial biomarker linked to breast cancer risk and treatment outcome. In accordance with the Breast Imaging Reporting & Data System (BI-RADS), it should be visually classified into four classes. The susceptibility of such an assessment to inter-reader variability highlights the urgent need for a standardized classification algorithm. In this retrospective study, the first post-contrast subtraction images for 27 healthy female subjects were included. The BPE was classified slice-wise by two expert radiologists. The extraction of radiomic features from segmented BPE was followed by dataset splitting and dimensionality reduction. The latent representations were then utilized as inputs to a deep neural network classifying BPE into BI-RADS classes. The network’s predictions were elucidated at the radiomic feature level with Shapley values. The deep neural network achieved a BPE classification accuracy of 84 ± 2% (p-value < 0.00001). Most of the misclassifications involved adjacent classes. Different radiomic features were decisive for the prediction of each BPE class underlying the complexity of the decision boundaries. A highly precise and explainable pipeline for BPE classification was achieved without user- or algorithm-dependent radiomic feature selection. Full article
(This article belongs to the Special Issue Advances in Breast Cancer Imaging)
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14 pages, 3582 KB  
Article
Biased Deep Learning Methods in Detection of COVID-19 Using CT Images: A Challenge Mounted by Subject-Wise-Split ISFCT Dataset
by Shiva Parsarad, Narges Saeedizadeh, Ghazaleh Jamalipour Soufi, Shamim Shafieyoon, Farzaneh Hekmatnia, Andrew Parviz Zarei, Samira Soleimany, Amir Yousefi, Hengameh Nazari, Pegah Torabi, Abbas S. Milani, Seyed Ali Madani Tonekaboni, Hossein Rabbani, Ali Hekmatnia and Rahele Kafieh
J. Imaging 2023, 9(8), 159; https://doi.org/10.3390/jimaging9080159 - 8 Aug 2023
Cited by 3 | Viewed by 3005
Abstract
Accurate detection of respiratory system damage including COVID-19 is considered one of the crucial applications of deep learning (DL) models using CT images. However, the main shortcoming of the published works has been unreliable reported accuracy and the lack of repeatability with new [...] Read more.
Accurate detection of respiratory system damage including COVID-19 is considered one of the crucial applications of deep learning (DL) models using CT images. However, the main shortcoming of the published works has been unreliable reported accuracy and the lack of repeatability with new datasets, mainly due to slice-wise splits of the data, creating dependency between training and test sets due to shared data across the sets. We introduce a new dataset of CT images (ISFCT Dataset) with labels indicating the subject-wise split to train and test our DL algorithms in an unbiased manner. We also use this dataset to validate the real performance of the published works in a subject-wise data split. Another key feature provides more specific labels (eight characteristic lung features) rather than being limited to COVID-19 and healthy labels. We show that the reported high accuracy of the existing models on current slice-wise splits is not repeatable for subject-wise splits, and distribution differences between data splits are demonstrated using t-distribution stochastic neighbor embedding. We indicate that, by examining subject-wise data splitting, less complicated models show competitive results compared to the exiting complicated models, demonstrating that complex models do not necessarily generate accurate and repeatable results. Full article
(This article belongs to the Section Medical Imaging)
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