Publications

Journal Papers

Enhancing resolution and contrast in fibre bundle‐based fluorescence microscopy using generative adversarial network, Ketabchi, A. M., Morova, B., Uysalli, Y., Musa Aydin, Eren, F., Bavili, N., … & Kiraz, A “Enhancing resolution and contrast in fibre bundle‐based fluorescence microscopy using generative adversarial network.” Journal of Microscopy (2024)(Code).

Retina Damar Segmentasyonunda Sinir Mimarisi Arama için Farklı Kodlama Yöntemlerinin Karşılaştırılması, Zeki Kuş, & Berna Kiraz. Retina Damar Segmentasyonunda Sinir Mimarisi Arama için Farklı Kodlama Yöntemlerinin Karşılaştırılması. International Journal of Advances in Engineering and Pure Sciences (2023), 35(4), 447-459.

Evolutionary Architecture Optimization for Retinal Vessel Segmentation, Zeki Kuş and Berna Kiraz, “Evolutionary Architecture Optimization for Retinal Vessel Segmentation,” in IEEE Journal of Biomedical and Health Informatics, 2023. doi: 10.1109/JBHI.2023.3314981.(Code)

Differential evolution-based neural architecture search for brain vessel segmentation, Zeki Kuş, Berna Kiraz, Tuğçe Koçak Göksu, Musa Aydın, E. Özkan, A. Vural, A. Kiraz, B. Can. “Differential evolution-based neural architecture search for brain vessel segmentation”, In Engineering Science and Technology, an International Journal, Volume 46, 2023. doi: 10.1016/j.jestch.2023.101502 (Code)

Low-cost VIS/NIR range hand-held and portable photospectrometer and evaluation of machine learning algorithms for classification performance, S. Heydarov, Musa Aydin, C. Faydaci, S. Tuna, S. Ozturk, “Low-cost VIS/NIR range hand-held and portable photospectrometer and evaluation of machine learning algorithms for classification performance”, Engineering Science and Technology, an International Journal, Volume 37, 2023, doi: 10.1016/j.jestch.2022.101302.

An LED-Based structured illumination microscope using a digital micromirror device and GPU accelerated image reconstruction, Musa Aydin, Y. Uysallı, E. Özgönül, B. Morova, F. Tiryaki, E.N. Firat-Karalar, B. Doğan, A. Kiraz, “An LED-Based structured illumination microscope using a digital micromirror device and GPU accelerated image reconstruction”, PLoS One, 2022, 17(9):e0273990, doi: 10.1371/journal.pone.0273990. PMID: 36084054.

DeepCAN: A Modular Deep Learning System for Automated Cell Counting and Viability Analysis, F. Eren, M. Aslan, D. Kanarya, Y. Uysalli, Musa Aydin, Berna Kiraz, O. Aydin, A. Kiraz. “DeepCAN: A Modular Deep Learning System for Automated Cell Counting and Viability Analysis”, IEEE Journal of Biomedical and Health Informatics, vol. 26, no. 11, pp. 5575-5583, Nov. 2022, doi: 10.1109/JBHI.2022.3203893.

Experimental evaluation of meta-heuristics for multi-objective capacitated multiple allocation hub location problem, İ. Demir, Berna Kiraz, F. Corut Ergin, “Experimental evaluation of meta-heuristics for multi-objective capacitated multiple allocation hub location problem”, Engineering Science and Technology, an International Journal, Volume 29, 2022.

Recommending healthy meal plans by optimising nature-inspired many-objective diet problem, C. Turkmenoglu, A.Ş. Etaner-Uyar, Berna Kiraz, “Recommending healthy meal plans by optimising nature-inspired many-objective diet problem”, Health Informatics Journal, vol. 27, no. 1, 2021, doi:10.1177/1460458220976719.

A New Model for the Multi-Objective Multiple Allocation Hub Network Design and Routing Problem İ. Demır, F. Corut Ergin, Berna Kıraz, “A New Model for the Multi-Objective Multiple Allocation Hub Network Design and Routing Problem”, IEEE Access, vol. 7, pp. 90678-90689, 2019, doi: 10.1109/ACCESS.2019.2927418.

Conference Papers

Machine Learning Approaches for Cell Viability Zeliha Kaya, Zeki Kuş, Berna Kiraz and Gönül Uludağ, “Machine Learning Approaches for Cell Viability,” 2023 31st Signal Processing and Communications Applications Conference (SIU), Istanbul, Turkiye, 2023, pp. 1-4, doi: 10.1109/SIU59756.2023.10223821.

BaDENAS: Bayesian Based Neural Architecture Search for Retinal Vessel Segmentation, Zeki Kuş and Berna Kiraz, “BaDENAS: Bayesian Based Neural Architecture Search for Retinal Vessel Segmentation,” 2023 31st Signal Processing and Communications Applications Conference (SIU), Istanbul, Turkiye, 2023, pp. 1-4, doi: 10.1109/SIU59756.2023.10223862. (Code)

Neural Architecture Search Using Metaheuristics for Automated Cell Segmentation, Kuş, Z., Aydın, M., Kiraz, B., Can, B. (2023). Neural Architecture Search Using Metaheuristics for Automated Cell Segmentation. In: Di Gaspero, L., Festa, P., Nakib, A., Pavone, M. (eds) Metaheuristics. MIC 2022. Lecture Notes in Computer Science, vol 13838. Springer, Cham. https://doi.org/10.1007/978-3-031-26504-4_12{:target=”_blank”}

Removal of Gaussian Distributed Noise in Images with Deep Neural Network Models, Zeki Kuş and Musa Aydin, “Removal of Gaussian Distributed Noise in Images with Deep Neural Network Models,” 2022 30th Signal Processing and Communications Applications Conference (SIU), 2022, pp. 1-4, doi: 10.1109/SIU55565.2022.9864913 (Code)

A Deep Learning Model for Automated Segmentation of Fluorescence Cell images, Musa Aydın, Berna Kiraz, F. Eren, Y. Uysallı, B. Morova, S. C. Özcan, C. Açılan, A. Kiraz. (2022, February). “A Deep Learning Model for Automated Segmentation of Fluorescence Cell images”, In Journal of Physics: Conference Series (Vol. 2191, No. 1, p. 012003). IOP Publishing.

Beyin Damar Bölütlemesinde Derin Sinir Ağlarının Deneysel Karşılaştırılması, Tuğçe Koçak, Musa Aydın, Berna Kiraz, “Beyin Damar Bölütlemesinde Derin Sinir Ağlarının Deneysel Karşılaştırılması”, 2021 6th International Conference on Computer Science and Engineering UBMK 2021, 2021.

Thesis

Kuş, Zeki. Hyper-parameter optimization of deep neural networks for cell-vessel segmentation. Doctoral thesis (YOK Thesis ID: 824767), Fatih Sultan Mehmet Vakıf University, 2023.