Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Article Citation - WoS: 13Citation - Scopus: 20IGPRED: Combination of Convolutional Neural and Graph Convolutional Networks for Protein Secondary Structure Prediction(Wiley, 2021-05-25) Gormez, Yasin; Sabzekar, Mostafa; Aydin, ZaferThere is a close relationship between the tertiary structure and the function of a protein. One of the important steps to determine the tertiary structure is protein secondary structure prediction (PSSP). For this reason, predicting secondary structure with higher accuracy will give valuable information about the tertiary structure. Recently, deep learning techniques have obtained promising improvements in several machine learning applications including PSSP. In this article, a novel deep learning model, based on convolutional neural network and graph convolutional network is proposed. PSIBLAST PSSM, HHMAKE PSSM, physico-chemical properties of amino acids are combined with structural profiles to generate a rich feature set. Furthermore, the hyper-parameters of the proposed network are optimized using Bayesian optimization. The proposed model IGPRED obtained 89.19%, 86.34%, 87.87%, 85.76%, and 86.54% Q3 accuracies for CullPDB, EVAset, CASP10, CASP11, and CASP12 datasets, respectively.Article Citation - Scopus: 8Building a Challenging Medical Dataset for Comparative Evaluation of Classifier Capabilities(Elsevier Ltd, 2024-08) Bozkurt, Berat; Coskun, Kerem; Bakal, GokhanSince the 2000s, digitalization has been a crucial transformation in our lives. Nevertheless, digitalization brings a bulk of unstructured textual data to be processed, including articles, clinical records, web pages, and shared social media posts. As a critical analysis, the classification task classifies the given textual entities into correct categories. Categorizing documents from different domains is straightforward since the instances are unlikely to contain similar contexts. However, document classification in a single domain is more complicated due to sharing the same context. Thus, we aim to classify medical articles about four common cancer types (Leukemia, Non-Hodgkin Lymphoma, Bladder Cancer, and Thyroid Cancer) by constructing machine learning and deep learning models. We used 383,914 medical articles about four common cancer types collected by the PubMed API. To build classification models, we split the dataset into 70% as training, 20% as testing, and 10% as validation. We built widely used machine-learning (Logistic Regression, XGBoost, CatBoost, and Random Forest Classifiers) and modern deep-learning (convolutional neural networks - CNN, long short-term memory - LSTM, and gated recurrent unit - GRU) models. We computed the average classification performances (precision, recall, F-score) to evaluate the models over ten distinct dataset splits. The best-performing deep learning model(s) yielded a superior F1 score of 98%. However, traditional machine learning models also achieved reasonably high F1 scores, 95% for the worst-performing case. Ultimately, we constructed multiple models to classify articles, which compose a hard-to-classify dataset in the medical domain. © 2024 Elsevier B.V., All rights reserved.Conference Object Benchmarking CNN Architectures for Eye Disease Detection With Transfer Learning Techniques(Institute of Electrical and Electronics Engineers Inc., 2025-06-27) Keles, Tolgahan; Aykanat, Muhammet Ali; Kurban, RifatIn this study, convolutional neural networks (CNN)-based approaches were compared to classify eye diseases using transfer learning techniques. A series of data augmentation strategies, including random rotation, shifting, shearing, zooming, and horizontal flipping, were applied to increase the training data's robustness and diversity. Several state-of-the-art CNNs, including ResNet50, VGG19, EfficientNetB0, Xception, InceptionV3, DenseNet121, MobileNetV2, NASNetMobile, and ConvNeXtBase, were fine-tuned through transfer learning. During training, models were evaluated based on their accuracy, training time, and validation performance, while early stopping mechanisms were employed to prevent overfitting. Experimental results demonstrated that DenseNet121 achieved the highest validation accuracy (72%) during the training phase and the best test set performance with an accuracy of 68% and an AUC-ROC of 0.93. MobileNetV2, on the other hand, provided a strong balance between classification accuracy (65%) and low inference time (7.28 ms), making it appropriate for real-time uses. The findings highlight the importance of selecting appropriate architectures by considering both predictive performance and computational efficiency, particularly in the context of medical imaging, where real-world deployment constraints are critical. © 2025 Elsevier B.V., All rights reserved.Conference Object Citation - Scopus: 1A Federated Learning Framework for Classifying the Images in Ultrasonic Nondestructive Testing(Institute of Electrical and Electronics Engineers Inc., 2024-10-26) Gulsen, Abdulkadir; Hacilar, Hilal; Kolukisa, Burak; Bakir-Güngör, BurcuUltrasonic inspection is a critical technique in non-destructive testing that ensures the safety and integrity of the material by detecting internal defects. Defect classification within this context is vital for preventing failures and extending the lifespan of materials. However, the advancement of ultrasonic testing technology is hindered by a scarcity of publicly available, realistic datasets, which are essential for developing accurate models. To address these challenges, this paper introduces a Federated Learning (FL) framework employing a Convolutional Neural Network (CNN) model for defect classification using ultrasonic inspection images. This innovative approach allows for the decentralized training of models on private datasets without the need for data exchange, thus preserving data privacy. Our comparative analysis demonstrates that the FL achieves performance comparable to traditional methods while maintaining the confidentiality of sensitive information. The framework also proves to be robust and scalable with an increase in the number of participating clients. This pioneering study highlights the potential of FL in transforming ultrasonic defect classification and suggests possibilities for its application in other areas of non-destructive testing where publicly available datasets are scarce. These findings would encourage researchers to develop a federated platform for enhanced collaboration and explore advanced CNN architectures to improve training efficiency. © 2025 Elsevier B.V., All rights reserved.