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Yayın Convolutional attention network for MRI-based Alzheimer's disease classification and its interpretability analysis(IEEE, 2021-09-17) Türkan, Yasemin; Tek, Faik BorayNeuroimaging techniques, such as Magnetic Resonance Imaging (MRI) and Positron Emission Tomography (PET), help to identify Alzheimer's disease (AD). These techniques generate large-scale, high-dimensional, multimodal neuroimaging data, which is time-consuming and difficult to interpret and classify. Therefore, interest in deep learning approaches for the classification of 3D structural MRI brain scans has grown rapidly. In this research study, we improved the 3D VGG model proposed by Korolev et al. [2]. We increased the filters in the 3D convolutional layers and then added an attention mechanism for better classification. We compared the performance of the proposed approaches for the classification of Alzheimer's disease versus mild cognitive impairments and normal cohorts on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset. We observed that both the accuracy and area under curve results improved with the proposed models. However, deep neural networks are black boxes that produce predictions that require further explanation for medical usage. We compared the 3D-data interpretation capabilities of the proposed models using four different interpretability methods: Occlusion, 3D Ultrametric Contour Map, 3D Gradient-Weighted Class Activation Mapping, and SHapley Additive explanations (SHAP). We observed that explanation results differed in different network models and data classes.Yayın Convolutional neural network (CNN) algorithm based facial emotion recognition (FER) system for FER-2013 dataset(IEEE, 2022-11-18) Ezerceli, Özay; Eskil, Mustafa TanerFacial expression recognition (FER) is the key to understanding human emotions and feelings. It is an active area of research since human thoughts can be collected, processed, and used in customer satisfaction, politics, and medical domains. Automated FER systems had been developed and have been used to recognize humans’ emotions but it has been a quite challenging problem in machine learning due to the high intra-class variation. The first models were using known methods such as Support Vector Machines (SVM), Bayes classifier, Fuzzy Techniques, Feature Selection, Artificial Neural Networks (ANN) in their models but still, some limitations affect the accuracy critically such as subjectivity, occlusion, pose, low resolution, scale, illumination variation, etc. The ability of CNN boosts FER accuracy. Deep learning algorithms have emerged as the greatest way to produce the best results in FER in recent years. Various datasets were used to train, test, and validate the models. FER2013, CK+, JAFFE and FERG are some of the most popular datasets. To improve the accuracy of FER models, one dataset or a mix of datasets has been employed. Every dataset includes limitations and issues that have an impact on the model that is trained for it. As a solution to this problem, our state-of-the-art model based on deep learning architectures, particularly convolutional neural network architectures (CNN) with supportive techniques has been implemented. The proposed model achieved 93.7% accuracy with the combination of FER2013 and CK+ datasets for FER2013.Yayın Automatic propbank generation for Turkish(Incoma Ltd, 2019-09) Ak, Koray; Yıldız, Olcay TanerSemantic role labeling (SRL) is an important task for understanding natural languages, where the objective is to analyse propositions expressed by the verb and to identify each word that bears a semantic role. It provides an extensive dataset to enhance NLP applications such as information retrieval, machine translation, information extraction, and question answering. However, creating SRL models are difficult. Even in some languages, it is infeasible to create SRL models that have predicate-argument structure due to lack of linguistic resources. In this paper, we present our method to create an automatic Turkish PropBank by exploiting parallel data from the translated sentences of English PropBank. Experiments show that our method gives promising results. © 2019 Association for Computational Linguistics (ACL).Yayın Malaria parasite detection with deep transfer learning(IEEE, 2018-12-06) Var, Esra; Tek, Faik BorayThis study aims to automatically detect malaria parasites (Plasmodium sp) on images taken from Giemsa stained blood smears. Deep learning methods provide limited performance when sample size is low. In transfer learning, visual features are learned from large general data sets, and problem-specific classification problem can be solved successfully in restricted problem specific data sets. In this study, we apply transfer learning method to detect and classify malaria parasites. We use a popular pre-trained CNN model VGG19. We trained the model for 20 epoch on 1428 P Vivax, 1425 P Ovule, 1446 E Falciparum, 1450 P Malariae and 1440 non-parasite samples. The transfer learning model achieves %80, %83, %86, %75 precision and 83%, 86%, 86%, 79% f-measure on 19 test images.Yayın Unreasonable effectiveness of last hidden layer activations for adversarial robustness(Institute of Electrical and Electronics Engineers Inc., 2022) Tuna, Ömer Faruk; Çatak, Ferhat Özgür; Eskil, Mustafa TanerIn standard Deep Neural Network (DNN) based classifiers, the general convention is to omit the activation function in the last (output) layer and directly apply the softmax function on the logits to get the probability scores of each class. In this type of architectures, the loss value of the classifier against any output class is directly proportional to the difference between the final probability score and the label value of the associated class. Standard White-box adversarial evasion attacks, whether targeted or untargeted, mainly try to exploit the gradient of the model loss function to craft adversarial samples and fool the model. In this study, we show both mathematically and experimentally that using some widely known activation functions in the output layer of the model with high temperature values has the effect of zeroing out the gradients for both targeted and untargeted attack cases, preventing attackers from exploiting the model's loss function to craft adversarial samples. We've experimentally verified the efficacy of our approach on MNIST (Digit), CIFAR10 datasets. Detailed experiments confirmed that our approach substantially improves robustness against gradient-based targeted and untargeted attack threats. And, we showed that the increased non-linearity at the output layer has some ad-ditional benefits against some other attack methods like Deepfool attack.Yayın An open, extendible, and fast Turkish morphological analyzer(Incoma Ltd, 2019-09) Yıldız, Olcay Taner; Avar, Begüm; Ercan, GökhanIn this paper, we present a two-level morphological analyzer for Turkish which consists of five main components: finite state transducer, rule engine for suffixation, lexicon, trie data structure, and LRU cache. We use Java language to implement finite state machine logic and rule engine, Xml language to describe the finite state transducer rules of the Turkish language, which makes the morphological analyzer both easily extendible and easily applicable to other languages. Empowered with a comprehensive lexicon of 54,000 bare-forms including 19,000 proper nouns, our morphological analyzer is amongst the most reliable analyzers produced so far. The analyzer is compared with Turkish morphological analyzers in the literature. By using LRU cache and a trie data structure, the system can analyze 100,000 words per second, which enables users to analyze huge corpora in a few hours.Yayın Animal sound classification using a convolutional neural network(IEEE, 2018-12-06) Şaşmaz, Emre; Tek, Faik BorayIn this paper, we investigate the problem of animal sound classification using deep learning and propose a system based on convolutional neural network architecture. As the input to the network, sound files were preprocessed to extract Mel Frequency Cepstral Coefficients (MFCC) using LibROSA library. To train and test the system we have collected 875 animal sound samples from an online sound source site for 10 different animal types. We report classification confusion matrices and the results obtained by different gradient descent optimizers. The best accuracy of 75% was obtained by Nesterov-accelerated Adaptive Moment Estimation (Nadam).Yayın BOUN-ISIK participation: an unsupervised approach for the named entity normalization and relation extraction of Bacteria Biotopes(Association for Computational Linguistics (ACL), 2019-11-04) Karadeniz, İlknur; Tuna, Ömer Faruk; Özgu, ArzucanThis paper presents our participation at the Bacteria Biotope Task of the BioNLP Shared Task 2019. Our participation includes two systems for the two subtasks of the Bacteria Biotope Task: the normalization of entities (BB-norm) and the identification of the relations between the entities given a biomedical text (BB-rel). For the normalization of entities, we utilized word embeddings and syntactic re-ranking. For the relation extraction task, pre-defined rules are used. Although both approaches are unsupervised, in the sense that they do not need any labeled data, they achieved promising results. Especially, for the BB-norm task, the results have shown that the proposed method performs as good as deep learning based methods, which require labeled data.Yayın Analysis of single image super resolution models(IEEE, 2022-11-18) Köprülü, Mertali; Eskil, Mustafa TanerImage Super-Resolution (SR) is a set of image processing techniques which improve the resolution of images and videos. Deep learning approaches have made remarkable improvement in image super-resolution in recent years. This article aims and seeks to provide a comprehensive analysis on recent advances of models which has been used in image superresolution. This study has been investigated over other essential topics of current model problems, such as publicly accessible benchmark data-sets and performance evaluation measures. Finally, The study concluded these analysis by highlighting several weaknesses of existing base models as their feeding strategy and approved that the training technique which is Blind Feeding, which led several model to achieve state-of-the art.Yayın Segmentation based classification of retinal diseases in OCT images(Institute of Electrical and Electronics Engineers Inc., 2024) Eren, Öykü; Tek, Faik Boray; Turkan, YaseminVolumetric optical coherence tomography (OCT) scans offer detailed visualization of the retinal layers, where any deformation can indicate potential abnormalities. This study introduced a method for classifying ocular diseases in OCT images through transfer learning. Applying transfer learning from natural images to Optical Coherence Tomography (OCT) scans present challenges, particularly when target domain examples are limited. Our approach aimed to enhance OCT-based retinal disease classification by leveraging transfer learning more effectively. We hypothesize that providing an explicit layer structure can improve classification accuracy. Using the OCTA-500 dataset, we explored various configurations by segmenting the retinal layers and integrating these segmentations with OCT scans. By combining horizontal and vertical cross-sectional middle slices and their blendings with segmentation outputs, we achieved a classification a ccuracy of 91.47% and an Area Under the Curve (AUC) of 0.96, significantly outperforming the classification of OCT slice images.
