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Indexed at: search.filters.indexed.ScopusSubject: search.filters.subject.Deep learning

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    PublicationMetadata only
    A deep learning model for automated segmentation of fluorescence cell images
    (IOP Publishing Ltd, 2022) Aydın, Musa; Kiraz, Berna; Eren, Furkan; N/A; Department of Physics; N/A; N/A; N/A; Ayhan, Ceyda Açılan; Kiraz, Alper; Uysallı, Yiğit; Morova, Berna; Özcan, Selahattin Can; Faculty Member; Faculty Member; PhD Student; Researcher; Researcher; Department of Physics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; College of Sciences; Graduate School of Sciences and Engineering; N/A; N/A; 219658; 22542; N/A; N/A; N/A
    Deep learning techniques bring together key advantages in biomedical image segmentation. They speed up the process, increase the reproducibility, and reduce the workload in segmentation and classifcation. Deep learning techniques can be used for analysing cell concentration, cell viability, as well as the size and form of each cell. In this study, we develop a deep learning model for automated segmentation of fuorescence cell images, and apply it to fuorescence images recorded with a home-built epi-fuorescence microscope. A deep neural network model based on U-Net architecture was built using a publicly available dataset of cell nuclei images [1]. A model accuracy of 97.3% was reached at the end of model training. Fluorescence cell images acquired with our home-built microscope were then segmented using the developed model. 141 of 151 cells in 5 images were successfully segmented, revealing a segmentation success rate of 93.4%. This deep learning model can be extended to the analysis of diferent cell types and cell viability. © 2021 Published under licence by IOP Publishing Ltd.
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    PublicationOpen Access
    Computerized counting of individuals in Ottoman population registers with deep learning
    (Springer, 2020) Department of History; Can, Yekta Said; Kabadayı, Mustafa Erdem; Faculty Member; Department of History; College of Social Sciences and Humanities; N/A; 33267
    The digitalization of historical documents continues to gain pace for further processing and extract meanings from these documents. Page segmentation and layout analysis are crucial for historical document analysis systems. Errors in these steps will create difficulties in the information retrieval processes. Degradation of documents, digitization errors and varying layout styles complicate the segmentation of historical documents. The properties of Arabic scripts such as connected letters, ligatures, diacritics and different writing styles make it even more challenging to process Arabic historical documents. In this study, we developed an automatic system for counting registered individuals and assigning them to populated places by using a CNN-based architecture. To evaluate the performance of our system, we created a labeled dataset of registers obtained from the first wave of population registers of the Ottoman Empire held between the 1840s–1860s. We achieved promising results for classifying different types of objects and counting the individuals and assigning them to populated places.
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    PublicationOpen Access
    Self-organized residual blocks for image super-resolution
    (Institute of Electrical and Electronics Engineers (IEEE), 2021) Malik, J.; Kıranyaz, S.; Department of Electrical and Electronics Engineering; Tekalp, Ahmet Murat; Keleş, Onur; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and Engineering; 26207; N/A
    It has become a standard practice to use the convolutional networks (ConvNet) with RELU non-linearity in image restoration and super-resolution (SR). Although the universal approximation theorem states that a multi-layer neural network can approximate any non-linear function with the desired precision, it does not reveal the best network architecture to do so. Recently, operational neural networks (ONNs) that choose the best non-linearity from a set of alternatives, and their “self-organized” variants (Self-ONN) that approximate any non-linearity via Taylor series have been proposed to address the well-known limitations and drawbacks of conventional ConvNets such as network homogeneity using only the McCulloch-Pitts neuron model. In this paper, we propose the concept of self-organized operational residual (SOR) blocks, and present hybrid network architectures combining regular residual and SOR blocks to strike a balance between the benefits of stronger non-linearity and the overall number of parameters. The experimental results demonstrate that the proposed architectures yield performance improvements in both PSNR and perceptual metrics.
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    PublicationOpen Access
    Self-organized variational autoencoders (self-vae) for learned image compression
    (Institute of Electrical and Electronics Engineers (IEEE), 2021) Malik, J.; Kıranyaz S.; Department of Electrical and Electronics Engineering; Tekalp, Ahmet Murat; Keleş, Onur; Yılmaz, Mustafa Akın; Güven, Hilal; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and Engineering; 26207; N/A; N/A; N/A
    In end-to-end optimized learned image compression, it is standard practice to use a convolutional variational autoencoder with generalized divisive normalization (GDN) to transform images into a latent space. Recently, Operational Neural Networks (ONNs) that learn the best non-linearity from a set of alternatives, and their “self-organized” variants, Self-ONNs, that approximate any non-linearity via Taylor series have been proposed to address the limitations of convolutional layers and a fixed nonlinear activation. In this paper, we propose to replace the convolutional and GDN layers in the variational autoencoder with self-organized operational layers, and propose a novel self-organized variational autoencoder (Self-VAE) architecture that benefits from stronger non-linearity. The experimental results demonstrate that the proposed Self-VAE yields improvements in both rate-distortion performance and perceptual image quality.