Browsing by Subject "Transfer learning"
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Item Open Access Artificial intelligence-based hybrid anomaly detection and clinical decision support techniques for automated detection of cardiovascular diseases and Covid-19(Bilkent University, 2023-10) Terzi, Merve BegümCoronary artery diseases are the leading cause of death worldwide, and early diagnosis is crucial for timely treatment. To address this, we present a novel automated arti cial intelligence-based hybrid anomaly detection technique com posed of various signal processing, feature extraction, supervised, and unsuper vised machine learning methods. By jointly and simultaneously analyzing 12-lead electrocardiogram (ECG) and cardiac sympathetic nerve activity (CSNA) data, the automated arti cial intelligence-based hybrid anomaly detection technique performs fast, early, and accurate diagnosis of coronary artery diseases. To develop and evaluate the proposed automated arti cial intelligence-based hybrid anomaly detection technique, we utilized the fully labeled STAFF III and PTBD databases, which contain 12-lead wideband raw recordings non invasively acquired from 260 subjects. Using the wideband raw recordings in these databases, we developed a signal processing technique that simultaneously detects the 12-lead ECG and CSNA signals of all subjects. Subsequently, using the pre-processed 12-lead ECG and CSNA signals, we developed a time-domain feature extraction technique that extracts the statistical CSNA and ECG features critical for the reliable diagnosis of coronary artery diseases. Using the extracted discriminative features, we developed a supervised classi cation technique based on arti cial neural networks that simultaneously detects anomalies in the 12-lead ECG and CSNA data. Furthermore, we developed an unsupervised clustering technique based on the Gaussian mixture model and Neyman-Pearson criterion that performs robust detection of the outliers corresponding to coronary artery diseases. By using the automated arti cial intelligence-based hybrid anomaly detection technique, we have demonstrated a signi cant association between the increase in the amplitude of CSNA signal and anomalies in ECG signal during coronary artery diseases. The automated arti cial intelligence-based hybrid anomaly de tection technique performed highly reliable detection of coronary artery diseases with a sensitivity of 98.48%, speci city of 97.73%, accuracy of 98.11%, positive predictive value (PPV) of 97.74%, negative predictive value (NPV) of 98.47%, and F1-score of 98.11%. Hence, the arti cial intelligence-based hybrid anomaly detection technique has superior performance compared to the gold standard diagnostic test ECG in diagnosing coronary artery diseases. Additionally, it out performed other techniques developed in this study that separately utilize either only CSNA data or only ECG data. Therefore, it signi cantly increases the detec tion performance of coronary artery diseases by taking advantage of the diversity in di erent data types and leveraging their strengths. Furthermore, its perfor mance is comparatively better than that of most previously proposed machine and deep learning methods that exclusively used ECG data to diagnose or clas sify coronary artery diseases. It also has a very short implementation time, which is highly desirable for real-time detection of coronary artery diseases in clinical practice. The proposed automated arti cial intelligence-based hybrid anomaly detection technique may serve as an e cient decision-support system to increase physicians' success in achieving fast, early, and accurate diagnosis of coronary artery diseases. It may be highly bene cial and valuable, particularly for asymptomatic coronary artery disease patients, for whom the diagnostic information provided by ECG alone is not su cient to reliably diagnose the disease. Hence, it may signi cantly improve patient outcomes, enable timely treatments, and reduce the mortality associated with cardiovascular diseases. Secondly, we propose a new automated arti cial intelligence-based hybrid clinical decision support technique that jointly analyzes reverse transcriptase polymerase chain reaction (RT-PCR) curves, thorax computed tomography im ages, and laboratory data to perform fast and accurate diagnosis of Coronavirus disease 2019 (COVID-19). For this purpose, we retrospectively created the fully labeled Ankara University Faculty of Medicine COVID-19 (AUFM-CoV) database, which contains a wide variety of medical data, including RT-PCR curves, thorax computed tomogra phy images, and laboratory data. The AUFM-CoV is the most comprehensive database that includes thorax computed tomography images of COVID-19 pneu monia (CVP), other viral and bacterial pneumonias (VBP), and parenchymal lung diseases (PLD), all of which present signi cant challenges for di erential diagnosis. We developed a new automated arti cial intelligence-based hybrid clinical de cision support technique, which is an ensemble learning technique consisting of two preprocessing methods, long short-term memory network-based deep learning method, convolutional neural network-based deep learning method, and arti cial neural network-based machine learning method. By jointly analyzing RT-PCR curves, thorax computed tomography images, and laboratory data, the proposed automated arti cial intelligence-based hybrid clinical decision support technique bene ts from the diversity in di erent data types that are critical for the reliable detection of COVID-19 and leverages their strengths. The multi-class classi cation performance results of the proposed convolu tional neural network-based deep learning method on the AUFM-CoV database showed that it achieved highly reliable detection of COVID-19 with a sensitivity of 91.9%, speci city of 92.5%, precision of 80.4%, and F1-score of 86%. There fore, it outperformed thorax computed tomography in terms of the speci city of COVID-19 diagnosis. Moreover, the convolutional neural network-based deep learning method has been shown to very successfully distinguish COVID-19 pneumonia (CVP) from other viral and bacterial pneumonias (VBP) and parenchymal lung diseases (PLD), which exhibit very similar radiological ndings. Therefore, it has great potential to be successfully used in the di erential diagnosis of pulmonary dis eases containing ground-glass opacities. The binary classi cation performance results of the proposed convolutional neural network-based deep learning method showed that it achieved a sensitivity of 91.5%, speci city of 94.8%, precision of 85.6%, and F1-score of 88.4% in diagnosing COVID-19. Hence, it has compara ble sensitivity to thorax computed tomography in diagnosing COVID-19. Additionally, the binary classi cation performance results of the proposed long short-term memory network-based deep learning method on the AUFM-CoV database showed that it performed highly reliable detection of COVID-19 with a sensitivity of 96.6%, speci city of 99.2%, precision of 98.1%, and F1-score of 97.3%. Thus, it outperformed the gold standard RT-PCR test in terms of the sensitivity of COVID-19 diagnosis Furthermore, the multi-class classi cation performance results of the proposed automated arti cial intelligence-based hybrid clinical decision support technique on the AUFM-CoV database showed that it diagnosed COVID-19 with a sen sitivity of 66.3%, speci city of 94.9%, precision of 80%, and F1-score of 73%. Hence, it has been shown to very successfully perform the di erential diagnosis of COVID-19 pneumonia (CVP) and other pneumonias. The binary classi cation performance results of the automated arti cial intelligence-based hybrid clinical decision support technique revealed that it diagnosed COVID-19 with a sensi tivity of 90%, speci city of 92.8%, precision of 91.8%, and F1-score of 90.9%. Therefore, it exhibits superior sensitivity and speci city compared to laboratory data in COVID-19 diagnosis. The performance results of the proposed automated arti cial intelligence-based hybrid clinical decision support technique on the AUFM-CoV database demon strate its ability to provide highly reliable diagnosis of COVID-19 by jointly ana lyzing RT-PCR data, thorax computed tomography images, and laboratory data. Consequently, it may signi cantly increase the success of physicians in diagnosing COVID-19, assist them in rapidly isolating and treating COVID-19 patients, and reduce their workload in daily clinical practice.Item Open Access Assessment of Parkinson's disease severity from videos using deep architecture(IEEE, 2021-07-26) Yin, Z.; Geraedts, V. J.; Wang, Z.; Contarino, M. F.; Dibeklioğlu, Hamdi; Gemert, J. V.Parkinson's disease (PD) diagnosis is based on clinical criteria, i.e., bradykinesia, rest tremor, rigidity, etc. Assessment of the severity of PD symptoms with clinical rating scales, however, is subject to inter-rater variability. In this paper, we propose a deep learning based automatic PD diagnosis method using videos to assist the diagnosis in clinical practices. We deploy a 3D Convolutional Neural Network (CNN) as the baseline approach for the PD severity classification and show the effectiveness. Due to the lack of data in clinical field, we explore the possibility of transfer learning from non-medical dataset and show that PD severity classification can benefit from it. To bridge the domain discrepancy between medical and non-medical datasets, we let the network focus more on the subtle temporal visual cues, i.e., the frequency of tremors, by designing a Temporal Self-Attention (TSA) mechanism. Seven tasks from the Movement Disorders Society - Unified PD rating scale (MDS-UPDRS) part III are investigated, which reveal the symptoms of bradykinesia and postural tremors. Furthermore, we propose a multi-domain learning method to predict the patient-level PD severity through task-assembling. We show the effectiveness of TSA and task-assembling method on our PD video dataset empirically. We achieve the best MCC of 0.55 on binary task-level and 0.39 on three-class patient-level classification.Item Open Access Deep learning based unsupervised tissue segmentation in histopathological images(Bilkent University, 2017-11) Köylü, Troya ÇağılIn the current practice of medicine, histopathological examination of tissues is essential for cancer diagnosis. However, this task is both subject to observer variability and time consuming for pathologists. Thus, it is important to develop automated objective tools, the first step of which usually comprises image segmentation. According to this need, in this thesis, we propose a novel approach for the segmentation of histopathological tissue images. Our proposed method, called deepSeg, is a two-tier method. The first tier transfers the knowledge from AlexNet, which is a convolutional neural network (CNN) trained for the non-medical domain of ImageNet, to the medical domain of histopathological tissue image characterization. The second tier uses this characterization in a seed-controlled region growing algorithm, for the unsupervised segmentation of heterogeneous tissue images into their homogeneous regions. To test the effectiveness of the segmentation, we conduct experiments on microscopic colon tissue images. Quantitative results reveal that the proposed method improves the performance of the previous methods that work on the same dataset. This study both illustrates one of the first successful demonstrations of using deep learning for tissue image segmentation, and shows the power of using deep learning features instead of handcrafted ones in the domain of histopathological image analysis.Item Open Access Deep learning for accelerated MR imaging(Bilkent University, 2021-02) Dar, Salman Ul HassanMagnetic resonance imaging is a non-invasive imaging modality that enables multi-contrast acquisition of an underlying anatomy, thereby supplementing mul-titude of information for diagnosis. However, prolonged scan duration may pro-hibit its practical use. Two mainstream frameworks for accelerating MR image acquisitions are reconstruction and synthesis. In reconstruction, acquisitions are accelerated by undersampling in k-space, followed by reconstruction algorithms. Lately deep neural networks have offered significant improvements over tradi-tional methods in MR image reconstruction. However, deep neural networks rely heavily on availability of large datasets which might not be readily available for some applications. Furthermore, a caveat of the reconstruction framework in general is that the performance naturally starts degrading towards higher accel-eration factors where fewer data samples are acquired. In the alternative syn-thesis framework, acquisitions are accelerated by acquiring a subset of desired contrasts, and recovering the missing ones from the acquired ones. Current syn-thesis methods are primarily based on deep neural networks, which are trained to minimize mean square or absolute loss functions. This can bring about loss of intermediate-to-high spatial frequency content in the recovered images. Fur-thermore, the synthesis performance in general relies on similarity in relaxation parameters between source and target contrasts, and large dissimilarities can lead to artifactual synthesis or loss of features. Here, we tackle issues associated with reconstruction and synthesis approaches. In reconstruction, the data scarcity is-sue is addressed by pre-training a network on large readily available datasets, and fine-tuning on just a few samples from target datasets. In synthesis, the loss of intermediate-to-high spatial frequency is catered for by adding adversarial and high-level perceptual losses on top of traditional mean absolute error. Fi-nally, a joint reconstruction and synthesis approach is proposed to mitigate the issues associated with both reconstruction and synthesis approaches in general. Demonstrations on MRI brain datasets of healthy subjects and patients indicate superior performance of the proposed techniques over the current state-of-the art ones.Item Open Access Early diagnosis of breakdown through transfer learning(Bilkent University, 2019-05) Özbek, SerenBreakdown prediction of equipment is an essential task considering the management of resources and maintenance operations. Early diagnosis systems allow creating alerts on time for taking precautions on production. A significant challenge for diagnosis is to have an insufficient size of data, yet, transfer learning approaches can alleviate such an issue when there is a constrained supply of training data. We intend to improve the reliability of breakdown prediction when there is a limited quantity of training data. We recommend similarity correlation on Remaining Useful Life of these equipment. To do this, we offer learning a common feature space between the target and the source equipment, where we acquire prior knowledge from the source that has different measurements than the target. Within the learned joint feature matrices, we train our model on the vast amount of data of different equipment and finetune it using the data of our target equipment. In this way, we aim to obtain an accurate and reliable model for early breakdown prediction.Item Open Access Improving image synthesis quality in multi-contrast MRI using transfer learning via autoencoders(IEEE, 2022-08-29) Selçuk, Şahan Yoruç; Dalmaz, Onat; Ul Hassan Dar, Salman; Çukur, TolgaThe capacity of magnetic resonance imaging (MRI) to capture several contrasts within a session enables it to obtain increased diagnostic information. However, such multi-contrast MRI tests take a long time to scan, resulting in acquiring just a part of the essential contrasts. Synthetic multi-contrast MRI has the potential to improve radiological observations and consequent image analysis activities. Because of its ability to generate realistic results, generative adversarial networks (GAN) have recently been the most popular choice for medical imaging synthesis. This paper proposes a novel generative adversarial framework to improve the image synthesis quality in multi-contrast MRI. Our method uses transfer learning to adapt pre-trained autoencoder networks to the synthesis task and enhances the image synthesis quality by initializing the training process with more optimal network parameters. We demonstrate that the proposed method outperforms competing synthesis models by 0.95 dB on average on a well-known multi-contrast MRI dataset.Item Open Access Indoor localization with transfer learning(IEEE, 2022-08-29) Korkmaz, İlter Onat; Özateş, Tuna; Koç, Enes; Aydın, Ege; Kor, Ege; Dilek, Doğaç; Güngen, Murat Alp; Köse, İdil Gökalp; Akman, ÇağlarIndoor positioning methods aim to estimate positions of transmitters where the GPS signals are unavailable. These systems usually employ algorithms explicitly trained for a single location such as fingerprinting method. For that reason, they can only be used in a particular location. This restriction prevents the use of the fingerprint method in tasks such as search and rescue operations where there is no prior knowledge of the place. A fingerprinting system using a trained algorithm with data collected from many places can work in multiple places. This paper proposes an indoor positioning system that uses the parameters of a pre-trained neural network trained with the data obtained from finite difference time domain simulations with transfer learning without collecting large amounts of data. The initial parameters for the model to be trained with the received signal strength (RSS) data collected from real places are used as be the parameters of the artificial neural network trained with the aforementioned simulation data. Performance results of the trained model are comparable to the results of the works in which fingerprinting method is employed in a single environment.Item Embargo A memory efficient novel deep learning architecture enabling diverse feature extraction on wearable motion sensor data(Bilkent University, 2022-09) Koşar, EnesExtracting representative features to recognize human activities through the use of wearables is an area of on-going research. We propose a novel hybrid net-work architecture to recognize human activities through the use of wearable motion sensors and deep learning techniques. The long short-term memory (LSTM) and the 2D convolutional neural network (CNN) branches of the model that run in parallel receive the raw signals and their spectrograms, respectively. We compare the classification performance of the proposed network with five commonly used network architectures: 1D CNN, 2D CNN, LSTM, standard 1D CNN-LSTM, and an alternative 1D CNN-LSTM model. We tune the hyper-parameters of all six models using Bayesian optimization and test the models on two publicly available datasets. The proposed 2D CNN-LSTM architecture achieves the highest aver-age accuracies of 95.66% and 92.95% on the two datasets, which are, respectively, 2.45% and 3.18% above those of the 2D CNN model that ranks the second. User identification is another problem that we have addressed in this thesis. Firstly, we use binary classifier models to detect activity signals that are useful for the user identity recognition task. Useful signals are transmitted to the next module and used by the proposed deep learning model for user identity recognition. Moreover, we investigate feature transfer between the human activity and user identity recognition tasks which enables shortening the training processes by 8.7 to 17 times without a significant degradation in classification accuracies. Finally, we elaborate on reducing the model sizes of the proposed models for human activity and user identity recognition problems. By using transfer learning, pooling layers, and eight-bit weight quantization methods, we have reduced the model sizes by 17–116 times without a significant degradation in classification accuracies.Item Open Access Real-time detection, tracking and classification of multiple moving objects in UAV videos(IEEE, 2017-11) Baykara, Hüseyin Can; Bıyık, Erdem; Gül, Gamze; Onural, Deniz; Öztürk, Ahmet Safa; Yıldız, İlkayUnnamed Aerial Vehicles (UAVs) are becoming increasingly popular and widely used for surveillance and reconnaissance. There are some recent studies regarding moving object detection, tracking, and classification from UAV videos. A unifying study, which also extends the application scope of such previous works and provides real-Time results, is absent from the literature. This paper aims to fill this gap by presenting a framework that can robustly detect, track and classify multiple moving objects in real-Time, using commercially available UAV systems and a common laptop computer. The framework can additionally deliver practical information about the detected objects, such as their coordinates and velocities. The performance of the proposed framework, which surpasses human capabilities for moving object detection, is reported and discussed.Item Open Access Text mining analysis of translation, social communication and literary writing for Turkish(Bilkent University, 2020-12) Çalışkan, SevilText mining is an important research area considering the increase in text generation and the need for analysis. Text mining in Turkish is still not a wellinvested research area, compared to the other languages. In this thesis, we analyze different types of Turkish text from different points of views, having an overall review on text mining in Turkish at the end. First, we analyze the translation quality of a Turkish novel, My Names is Red novel, to English, French, and Spanish with the features generated for each chapter. With the proposed method, translation loyalties to the original text can be quantified without any parallel comparisons. Then, we analyze the Turkish spoken texts of 98 people in different age groups in terms of gender and age attributes of the speakers. We also analyze the difference between written and spoken texts in Turkish. Results show that it is possible to predict the attributes of the speaker from the spoken text and written and spoken texts are significantly different in terms of stylometric measures. Later on, we make an assessment on cross-lingual transferring performances of multilingual networks from English to Turkish. We see that transferring is possible; however zero-shot cross-lingual transferring still has its way to be competitive with monolingual networks for Turkish. Lastly, we conduct a time-based stylometric analysis of Ahmet Hamdi Tanpınar’s works. We see that Ahmet Hamdi Tanpınar shows some differences compared to his contemporaries.Item Open Access A transfer-learning approach for accelerated MRI using deep neural networks(Wiley, 2020) Dar, Salman Ul Hassan; Özbey, Muzaffer; Çatlı, Ahmet Burak; Çukur, TolgaPurpose: Neural networks have received recent interest for reconstruction of undersampled MR acquisitions. Ideally, network performance should be optimized by drawing the training and testing data from the same domain. In practice, however, large datasets comprising hundreds of subjects scanned under a common protocol are rare. The goal of this study is to introduce a transfer‐learning approach to address the problem of data scarcity in training deep networks for accelerated MRI. Methods: Neural networks were trained on thousands (upto 4 thousand) of samples from public datasets of either natural images or brain MR images. The networks were then fine‐tuned using only tens of brain MR images in a distinct testing domain. Domain‐transferred networks were compared to networks trained directly in the testing domain. Network performance was evaluated for varying acceleration factors (4‐10), number of training samples (0.5‐4k), and number of fine‐tuning samples (0‐100). Results: The proposed approach achieves successful domain transfer between MR images acquired with different contrasts (T1‐ and T2‐weighted images) and between natural and MR images (ImageNet and T1‐ or T2‐weighted images). Networks obtained via transfer learning using only tens of images in the testing domain achieve nearly identical performance to networks trained directly in the testing domain using thousands (upto 4 thousand) of images. Conclusion: The proposed approach might facilitate the use of neural networks for MRI reconstruction without the need for collection of extensive imaging datasets.