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Yayın Retinal disease diagnosis in OCT scans using a foundational model(Springer Science and Business Media Deutschland GmbH, 2025) Nazlı, Muhammet Serdar; Turkan, Yasemin; Tek, Faik Boray; Toslak, Devrim; Bulut, Mehmet; Arpacı, Fatih; Öcal, Mevlüt CelalThis study examines the feasibility and performance of using single OCT slices from the OCTA-500 dataset to classify DR (Diabetic Retinopathy) and AMD (Age-Related Macular Degeneration) with a pre-trained transformer-based model (RETFound). The experiments revealed the effective adaptation capability of the pretrained model to the retinal disease classification problem. We further explored the impact of using different slices from the OCT volume, assessing the sensitivity of the results to the choice of a single slice (e.g., “middle slice”) and whether analyzing both horizontal and vertical cross-sectional slices could improve outcomes. However, deep neural networks are complex systems that do not indicate directly whether they have learned and generalized the disease appearance as human experts do. The original dataset lacked disease localization annotations. Therefore, we collected new disease classification and localization annotations from independent experts for a subset of OCTA-500 images. We compared RETFound’s explainability-based localization outputs with these newly collected annotations and found that the region attributions aligned well with the expert annotations. Additionally, we assessed the agreement and variability between experts and RETFound in classifying disease conditions. The Kappa values, ranging from 0.35 to 0.69, indicated moderate agreement among experts and between the experts and the model. The transformer-based RETFound model using single or multiple OCT slices, is an efficient approach to diagnosing AMD and DR.Yayın Retinal disease classification from bimodal OCT and OCTA using a CNN-ViT hybrid architecture(Institute of Electrical and Electronics Engineers Inc., 2025-09-21) Aydın, Ömer Faruk; Tek, Faik Boray; Turkan, YaseminRetinal diseases are the leading cause of vision impairment and blindness worldwide. Early and accurate diagnosis is critical for effective treatment, and recent advances in imaging technologies such as Optical Coherence Tomography (OCT) and OCT Angiography (OCTA), have enabled detailed visualization of the retinal structure and vasculature. By leveraging these modalities, this study proposes an advanced deep learning architecture called MultiModalNet for automated multi-class retinal disease classification. MultiModalNet employs a dual-branch design, where OCTA projection maps are processed through a ResNet101 encoder, and cross-sectional slices from the OCT volume (B-scans) are analyzed using a Vision Transformer (ViT-Large). The extracted features from both branches were fused and passed through the fully connected layers for the final classification. Evaluated on the 3-class OCTA-500 dataset, which includes Age-related Macular Degeneration (AMD), Diabetic Retinopathy (DR), and Normal cases, the proposed model achieved state-of-the-art classification accuracy of 94.59 percent, significantly o utperforming single-modality baselines. This result highlights the effectiveness of integrating vascular and structural information to improve the diagnostic performance. The findings suggest that hybrid multi-modal deep learning approaches can play a transformative role in computer-aided ophthalmology, enhancing both clinical decision-making and screening workflows.Yayın Self-supervised learning of 3D structure from 2D OCT slices for retinal disease diagnosis on UK biobank scans(Institute of Electrical and Electronics Engineers Inc., 2025-09-21) Nazlı, Muhammet Serdar; Turkan, Yasemin; Tek, Faik BorayThis study presents a self-supervised learning framework for retinal disease classification using Optical Coherence Tomography (OCT) scans. To balance the contextual richness of 3D volumes with the computational efficiency of 2D architectures, we introduce a quasi-3D input generation strategy. Each input is constructed by stacking three OCT slices, sampled from channel-specific Gaussian distributions centered on the volume midplane, and arranged in a standard three-channel 2D format compatible with existing pre-trained models. These quasi-3D images are used to pre-train a Vision Transformer (ViT-Base) via a Masked Autoencoder (MAE) with a shared masking pattern, encouraging the model to reconstruct masked regions by encoding anatomical continuity across slices. Pre-training is conducted on 10,000 unlabeled OCT volumes from the UK Biobank. The encoder is then fine-tuned on the OCTA-500 dataset for three-class and four-class retinal disease classification tasks, including macular degeneration and diabetic retinopathy. The model achieves 92.57% accuracy on the three-class task, matching the performance of RETFound while using over 150 times less pre-training data and a smaller backbone.
