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Yayın Çizge evrişim ağı kullanarak patojen-konak ağlarında protein etkileşim tahmini(IEEE, 2021-06-09) Koca, Mehmet Burak; Karadeniz, İlknur; Nourani, Esmaeil; Sevilgen, Fatih ErdoğanProteinler yaşamsal faaliyetlerin gerçekleşmesinde kritik rol oynayan biyolojik moleküllerdir. Konak canlı proteinleri ile patojen proteinleri arasındaki etkileşimler patojenkonak etkileşim (PHI) ağlarını oluşturmaktadır. Bu iki parçalı etkileşim ağları patojenin hangi yaşamsal faaliyetleri etkilediğini belirlemede ve dolayısıyla sebep olabileceği hastalıkların tespitinde büyük öneme sahiptir. Proteinler arası etkileşimlerin laboratuvar ortamında tespiti hem zaman alıcı hem de maliyetlidir. Deneysel olarak saptanabilen etkileşim sayısının kısıtlı olması ve bazı etkileşimlerin gözden kaçması hesaplamalı tahmin yöntemlerinin geliştirilmesine önayak olmaktadır. Bu çalışmada PHI ağlarında protein etkileşim tahmini yapmayı sağlayan çizge evrişim ağı (GCN) tabanlı bir yöntem sunulmaktadır. Gözetimsiz olarak eğitilen GCN modeli (GraphSAGE) topolojik bilginin yanı sıra temel öznitelik olarak amino asit dizilimlerini kullanmaktadır. Bu çalışma bildiğimiz kadarıyla PHI ağlarında GCN tabanlı etkileşim tahmini sağlayan ilk çalışmadır. Deneysel sonuçlar geliştirilen modelin kıyaslama için kullanılan PHI veri seti üzerinde yüksek performanslı algoritmalardan %10 daha iyi performans göstererek %96 oranında doğrulukla etkileşim tahmini yaptığını göstermektedir.Yayın Unsupervised textile defect detection using convolutional neural networks(Elsevier Ltd, 2021-12) Koulali, Imane; Eskil, Mustafa TanerIn this study, we propose a novel motif-based approach for unsupervised textile anomaly detection that combines the benefits of traditional convolutional neural networks with those of an unsupervised learning paradigm. It consists of five main steps: preprocessing, automatic pattern period extraction, patch extraction, features selection and anomaly detection. This proposed approach uses a new dynamic and heuristic method for feature selection which avoids the drawbacks of initialization of the number of filters (neurons) and their weights, and those of the backpropagation mechanism such as the vanishing gradients, which are common practice in the state-of-the-art methods. The design and training of the network are performed in a dynamic and input domain-based manner and, thus, no ad-hoc configurations are required. Before building the model, only the number of layers and the stride are defined. We do not initialize the weights randomly nor do we define the filter size or number of filters as conventionally done in CNN-based approaches. This reduces effort and time spent on hyper-parameter initialization and fine-tuning. Only one defect-free sample is required for training and no further labeled data is needed. The trained network is then used to detect anomalies on defective fabric samples. We demonstrate the effectiveness of our approach on the Patterned Fabrics benchmark dataset. Our algorithm yields reliable and competitive results (on recall, precision, accuracy and f1-measure) compared to state-of-the-art unsupervised approaches, in less time, with efficient training in a single epoch and a lower computational cost.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 Adaptive convolution kernel for artificial neural networks(Academic Press Inc., 2021-02) Tek, Faik Boray; Çam, İlker; Karlı, DenizMany deep neural networks are built by using stacked convolutional layers of fixed and single size (often 3 × 3) kernels. This paper describes a method for learning the size of convolutional kernels to provide varying size kernels in a single layer. The method utilizes a differentiable, and therefore backpropagation-trainable Gaussian envelope which can grow or shrink in a base grid. Our experiments compared the proposed adaptive layers to ordinary convolution layers in a simple two-layer network, a deeper residual network, and a U-Net architecture. The results in the popular image classification datasets such as MNIST, MNIST-CLUTTERED, CIFAR-10, Fashion, and ‘‘Faces in the Wild’’ showed that the adaptive kernels can provide statistically significant improvements on ordinary convolution kernels. A segmentation experiment in the Oxford-Pets dataset demonstrated that replacing ordinary convolution layers in a U-shaped network with 7 × 7 adaptive layers can improve its learning performance and ability to generalize.Yayın Subset selection for tuning of hyper-parameters in artificial neural networks(IEEE, 2017) Aki, K.K.Emre; Erkoç, Tuğba; Eskil, Mustafa TanerHyper-parameters of a machine learning architecture define its design. Tuning of hyper-parameters is costly and for large data sets outright impractical, whether it is performed manually or algorithmically. In this study we propose a Neocognitron based method for reducing the training set to a fraction, while keeping the dynamics and complexity of the domain. Our approach does not require processing of the entire training set, making it feasible for larger data sets. In our experiments we could successfully reduce the MNIST training data set to less than 2.5% (1,489 images) by processing less than 10% of the 60K images. We showed that the reduced data set can be used for tuning of number of hidden neurons in a multi-layer perceptron.Yayın An adaptive locally connected neuron model: Focusing neuron(Elsevier B.V., 2021-01-02) Tek, Faik BorayThis paper presents a new artificial neuron model capable of learning its receptive field in the topological domain of inputs. The experiments include tests of focusing neuron networks of one or two hidden layers on synthetic and well-known image recognition data sets. The results demonstrated that the focusing neurons can move their receptive fields towards more informative inputs. In the simple two-hidden layer networks, the focusing layers outperformed the dense layers in the classification of the 2D spatial data sets. Moreover, the focusing networks performed better than the dense networks even when 70% of the weights were pruned. The tests on convolutional networks revealed that using focusing layers instead of dense layers for the classification of convolutional features may work better in some data sets.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).
