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    Automated Segmentation of Lung Lesions Using Deep Learning: A Study on a Multi-Class CT Dataset
    (Institute of Electrical and Electronics Engineers Inc., 2025) Kiliç, Murat; Yelman, Abdulkadir; Üzen, Hüseyin; Firat, Hüseyin; Biyikli, Merve; Balikçi Çyçek, Ipek; Şengür, Abdulkadir
    Lung cancer is the leading cause of cancer-related deaths worldwide, making early diagnosis from CT images critically important for patient outcomes. In this study, a unique dataset was collected at Inönü University Turgut Özal Medical Center, consisting of 3526 CT slices from 210 patients manually annotated by expert physicians. The lesions, classified into benign, malignant, and cystic categories, were segmented using seven different deep learning architectures: U-Net, VGG16UNet, EFF-UNet, UNet++, FPNet, PSPNet, and EFF-PSPNet. The models were evaluated based on metrics such as Dice, Jaccard, precision, recall, and FPS. The most successful results were achieved by the EFF-UNet (Dice: 92.14%) and U-Net (Dice: 92.25%) models. While cystic lesions were detected with high accuracy, benign lesions presented the lowest results due to their morphological variability. Visual analyses indicated that some models exhibited uncertainty in class differentiation, and the quality of annotations was found to directly influence model performance. This study demonstrates the potential of deep learning-based segmentation for clinical decision support systems and contributes to the field with its original dataset. © 2025 IEEE.
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    Deep Learning-Assisted Detection and Classification of Thymoma Tumors in CT Scans
    (Mdpi, 2025) Kilic, Murat; Biyikli, Merve; Ozcelik, Salih Taha Alperen; Uzen, Huseyin; Firat, Huseyin
    Background/Objectives: Thymoma is a rare epithelial neoplasm originating from the thymus gland, and its accurate detection and classification using computed tomography (CT) images remain diagnostically challenging due to subtle morphological similarities with other mediastinal pathologies. This study presents a deep learning (DL)-based model designed to improve diagnostic accuracy for both thymoma detection and subtype classification (benign vs. malignant). Methods: The proposed approach integrates a pre-trained VGG16 network for efficient feature extraction-capitalizing on its capacity to capture hierarchical spatial features-and an MLP-Mixer-based feature enhancement module, which effectively models both local and global feature dependencies without relying on conventional convolutional mechanisms. Additionally, customized preprocessing and post-processing methods are employed to enhance image quality and suppress redundant data. The model's performance was evaluated on two classification tasks: distinguishing thymoma from healthy cases and discriminating between benign and malignant thymoma. Comparative analysis was conducted against state-of-the-art DL models including ResNet50, ResNet34, SEResNeXt50, InceptionResNetV2, MobileNetV2, VGG16, InceptionV3, and DenseNet121 using metrics such as F1 score, accuracy, recall, and precision. Results: The model proposed in this study obtained its best performance in thymoma vs. healthy classification, with an accuracy of 97.15% and F1 score of 80.99%. In the benign vs. malignant task, it attained an accuracy of 79.20% and an F1 score of 78.51%, outperforming all baseline methods. Conclusions: The integration of VGG16's robust spatial feature extraction and the MLP-Mixer's effective feature mixing demonstrates superior and balanced performance, highlighting the model's potential for clinical decision support in thymoma diagnosis.
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    Grad-CAM Enhanced Explainable Deep Learning for Multi-Class Lung Cancer Classification Using DE-SAMNet Model
    (Mdpi, 2026) Kilic, Murat; Biyikli, Merve; Yelman, Abdulkadir; Firat, Huseyin; Uzen, Huseyin; Cicek, Ipek Balikci; Sengur, Abdulkadir
    Background/Objectives: Lung cancer (LC) is the leading cause of cancer-related mortality worldwide, making early and accurate diagnosis crucial for improving patient outcomes. Although chest computed tomography (CT) enables detailed assessment of lung abnormalities, manual interpretation is time-consuming, requires expert expertise, and is prone to diagnostic variability. To address these challenges, this study proposes DE-SAMNet, a hybrid deep learning framework for automated multi-class LC classification from CT scans. Methods: The model integrates two pre-trained convolutional neural networks-DenseNet121 and EfficientNetB0-operating in parallel to extract complementary multi-scale features. A Spatial Attention Module (SAM) is applied to each feature stream to emphasize clinically important regions. Final classification is performed through a compact fusion mechanism involving global average pooling, batch normalization, and a fully connected layer. DE-SAMNet was evaluated on two datasets: a public dataset (IQ-OTH/NCCD) with benign, malignant, and normal cases, and a private clinical dataset including benign, malignant, cystic, and healthy cases. Results: On the public dataset, the model achieved a 99.00% F1-score, 98.41% recall, 99.64% precision, and 99.54% accuracy. On the private dataset, it obtained 95.96% accuracy, 95.99% precision, 96.04% F1-score, and 96.21% recall, outperforming existing approaches. To enhance reliability, explainable AI (XAI) techniques such as Grad-CAM were used to visualize the model's decision rationale. The resulting heatmaps effectively highlight lesion-specific regions, offering transparency and supporting clinical interpretability. Conclusions: This explainability strengthens trust in automated predictions and demonstrates the clinical potential of the proposed system. Overall, DE-SAMNet delivers a highly accurate and interpretable solution for early LC detection.