Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Label-Free Retraining for Improved Ground Plane Segmentation(Springer, 2022) Uzyıldırım, Furkan Eren; Özuysal, MustafaDue to increased potential applications of unmanned aerial vehicles over urban areas, algorithms for the safe landing of these devices have become more critical. One way to ensure a safe landing is to locate the ground plane regions of images captured by the device camera that are free of obstacles by deep semantic segmentation networks. In this paper, we study the performance of semantic segmentation networks trained for this purpose at a particular altitude and location. We show that a variation in altitude and location significantly decreases network performance. We then propose an approach to retrain the network using only a new set of images and without marking the ground regions in this novel training set. Our experiments show that we can convert a network’s operating range from low to high altitudes and vice versa by label-free retraining.Article Citation - Scopus: 1Performance Analysis and Feature Selection for Network-Based Intrusion Detection With Deep Learning(Türkiye Klinikleri, 2022) Caner, Serhat; Erdoğmuş, Nesli; Erten, Yusuf MuratAn intrusion detection system is an automated monitoring tool that analyzes network traffic and detects malicious activities by looking out either for known patterns of attacks or for an anomaly. In this study, intrusion detection and classification performances of different deep learning based systems are examined. For this purpose, 24 deep neural networks with four different architectures are trained and evaluated on CICIDS2017 dataset. Furthermore, the best performing model is utilized to inspect raw network traffic features and rank them with respect to their contributions to success rates. By selecting features with respect to their ranks, sets of varying size from 3 to 77 are assessed in terms of classification accuracy and time efficiency. The results show that recurrent neural networks with a certain level of complexity can achieve comparable success rates with state-of-the-art systems using a small feature set of size 9; while the average time required to classify a test sample is halved compared to the complete set.Conference Object Citation - WoS: 3Citation - Scopus: 4Deep Learning Based Segmentation Pipeline for Label-Free Phase-Contrast Microscopy Images(IEEE, 2020) Ayanzadeh, Aydın; Yalçın Özuysal, Özden; Okvur, Devrim Pesen; Önal, Sevgi; Töreyin, Behçet Uğur; Ünay, DevrimThe segmentation of cells is necessary for biologists in the morphological statistics for quantitative and qualitative analysis in Phase-contrast Microscopy (PCM) images. In this paper, we address the cell segmentation problem in PCM images. Deep Neural Networks (DNNs) commonly is initialized with weights from a network pre-trained on a large annotated data set like ImageNet have superior performance than those trained from scratch on a small dataset. Here, we demonstrate how encoder-decoder type architectures such as U-Net and Feature Pyramid Network (FPN) can be improved by an alternative encoder which pre-trained on the ImageNet dataset. In particular, our experimental results confirm that the image descriptors from ResNet-18 are highly effective in accurate prediction of the cell boundary and have higher Intersection over Union (IoU) in comparison to the classical U-Net and require fewer training epochs.Conference Object Citation - Scopus: 2Yara İyileşmesi Mikroskopi Görüntü Serilerinin Otomatik Analizi - Bir Ön-çalışma(IEEE, 2020) Mayalı, Berkay; Şaylığ, Orkun; Yalçın Özuysal, Özden; Pesen Okvur, Devrim; Töreyin, Behçet Uğur; Ünay, DevrimCollective cell analysis from microscopy image series is important for wound healing research. Computer-based automation of such analyses may help in rapid acquisition of reliable and reproducible results. In this study phase -contrast optical microscopy image series of an in-vitro wound healing essay is manually delineated by two experts and its analysis is realized, traditional image processing and deep learning based approaches for automated segmentation of wound area are developed and their perlOrmance comparisons are carried out.Conference Object Citation - Scopus: 1A Preliminary Study on Cell Motility Analysis From Phase-Contrast Microscopy Image Series(IEEE, 2020) Kayan, Emre; Kavuşan, Tarık; Önal, Sevgi; Pesen Okvur, Devrim; Yalçın Özuysal, Özden; Töreyin, Behçet Uğur; Ünay, DevrimAnalyses of morphology, polarity, and motility of cells is important for cell biology research such as metastatic and invasive capacity of cells, wound healing, and embryonic development. Automation of such analyses using image series of phase-contrast optical microscopy, which allows label-free imaging of live cells in their living environment, is a need. With this purpose, in this study image series of a cell motility experiment is manually annotated, and an automation algorithm realizing motion and shape analyses of cells using the annotated data is developed. In addition, due to the low number of annotated data at hand, a U-Net based solution is devised for automated segmentation of the cells and its performance is evaluated.Conference Object Citation - WoS: 2Citation - Scopus: 3Impact of Variations in Synthetic Training Data on Fingerprint Classification(IEEE, 2019) İrtem, Pelin; İrtem, Emre; Erdoğmuş, NesliCreating and labeling data can be extremely time consuming and labor intensive. For this reason, lack of sufficiently large datasets for training deep structures is often noted as a major obstacle and instead, synthetic data generation is proposed. With their high acquisition and labeling complexity, this also applies to fingerprints. In the literature, a number of synthetic fingerprint generation systems have been proposed, but mostly for algorithm evaluation purposes. In this paper, we aim to analyze the use of synthetic fingerprint data with different levels of degradation for training deep neural networks. Fingerprint classification problem is selected as a case-study and the experiments are conducted on a public domain database, NIST SD4. A positive correlation between the synthetic data variation and the classification rate is observed while achieving state-of-the-art results.Article Citation - WoS: 2Citation - Scopus: 2Improving Outdoor Plane Estimation Without Manual Supervision(Springer, 2022) Uzyıldırım, Furkan Eren; Özuysal, MustafaRecently, great progress has been made in the automatic detection and segmentation of planar regions from monocular images of indoor scenes. This has been achieved thanks to the development of convolutional neural network architectures for the task and the availability of large amounts of training data usually obtained with the help of active depth sensors. Unfortunately, it is much harder to obtain large image sets outdoors partly due to limited range of active sensors. Therefore, there is a need to develop techniques that transfer features learned from the indoor dataset to segmentation of outdoor images. We propose such an approach that does not require manual annotations on the outdoor datasets. Instead, we exploit a network trained on indoor images and an automatically reconstructed point cloud to estimate the training ground truth on the outdoor images in an energy minimization framework. We show that the resulting ground truth estimate is good enough to improve the network weights. Moreover, the process can be repeated multiple times to further improve plane detection and segmentation accuracy on monocular images of outdoor scenes.Article Citation - WoS: 55Citation - Scopus: 56Evaluation of an Artificial Intelligence System for Diagnosing Scaphoid Fracture on Direct Radiography(Springer Verlag, 2020) Özkaya, Emre; Topal, Fatih Esad; Bulut, Tuğrul; Gürsoy, Merve; Özuysal, Mustafa; Karakaya, ZeynepPurpose The aim of this study is to determine the diagnostic performance of artificial intelligence with the use of convolutional neural networks (CNN) for detecting scaphoid fractures on anteroposterior wrist radiographs. The performance of the deep learning algorithm was also compared with that of the emergency department (ED) physician and two orthopaedic specialists (less experienced and experienced in the hand surgery). Methods A total 390 patients with AP wrist radiographs were included in the study. The presence/absence of the fracture on radiographs was confirmed via CT. The diagnostic performance of the CNN, ED physician and two orthopaedic specialists (less experienced and experienced) as measured by AUC, sensitivity, specificity, F-Score and Youden index, to detect scaphoid fractures was evaluated and compared between the groups. Results The CNN had 76% sensitivity and 92% specificity, 0.840 AUC, 0.680 Youden index and 0.826Fscore values in identifying scaphoid fractures. The experienced orthopaedic specialist had the best diagnostic performance according to AUC. While CNN's performance was similar to a less experienced orthopaedic specialist, it was better than the ED physician. Conclusion The deep learning algorithm has the potential to be used for diagnosing scaphoid fractures on radiographs. Artificial intelligence can be useful for scaphoid fracture diagnosis particularly in the absence of an experienced orthopedist or hand surgeon.Conference Object Citation - WoS: 7Citation - Scopus: 11Cell Segmentation of 2d Phase-Contrast Microscopy Images With Deep Learning Method(Institute of Electrical and Electronics Engineers Inc., 2019) Ayanzadeh, Aydın; Yağar, Hüseyin Onur; Yalçın Özuysal, Özden; Pesen Okvur, Devrim; Töreyin, Behçet Uğur; Unay, Devrim; Önal, SevgiThe quantitative and qualitative ascertainment of cell culture is integral to the robust determination of the cell structure analysis. Microscopy cell analysis and the epithet structures of cells in cell cultures are momentous in the fields of the biological research process. In this paper, we addressed the problem of phase-contrast microscopy under cell segmentation application. In our proposed method, we utilized the state-of-the-art deep learning models trained on our proposed dataset. Due to the low number of annotated images, we propose a multi-resolution network which is based on the U-Net architecture. Moreover, we applied multi-combination augmentation to our dataset which has increased the performance of segmentation accuracy significantly. Experimental results suggest that the proposed model provides superior performance in comparison to traditional state-of-the-art segmentation algorithms.Article Citation - WoS: 3Citation - Scopus: 3Elimination of Useless Images From Raw Camera-Trap Data(Türkiye Klinikleri Journal of Medical Sciences, 2019) Tekeli, Ulaş; Baştanlar, YalınCamera-traps are motion triggered cameras that are used to observe animals in nature. The number of images collected from camera-traps has increased significantly with the widening use of camera-traps thanks to advances in digital technology. A great workload is required for wild-life researchers to group and label these images. We propose a system to decrease the amount of time spent by the researchers by eliminating useless images from raw camera-trap data. These images are too bright, too dark, blurred, or they contain no animals To eliminate bright, dark, and blurred images we employ techniques based on image histograms and fast Fourier transform. To eliminate the images without animals, we propose a system combining convolutional neural networks and background subtraction. We experimentally show that the proposed approach keeps 99% of photos with animals while eliminating more than 50% of photos without animals. We also present a software prototype that employs developed algorithms to eliminate useless images.