arXiv subjects

Serkan Kiranyaz

Publications and source records attributed to Serkan Kiranyaz.

At least 73 records · Page 4Linked to original sources

arXiv2021

Robust R-Peak Detection in Low-Quality Holter ECGs using 1D Convolutional Neural Network

Noise and low quality of ECG signals acquired from Holter or wearable devices deteriorate the accuracy and robustness of R-peak detection algorithms. This paper presents a generic and robust system for R-peak detection in Holter ECG signals. While many proposed algorithms have successfully addressed the problem of ECG R-peak detection, there is still a notable gap in the performance of these detectors on such low-quality ECG records. Therefore, in this study, a novel implementation of the 1D Convolutional Neural Network (CNN) is used integrated with a verification model to reduce the number of false alarms. This CNN architecture consists of an encoder block and a corresponding decoder block followed by a sample-wise classification layer to construct the 1D segmentation map of R- peaks from the input ECG signal. Once the proposed model has been trained, it can solely be used to detect R-peaks possibly in a single channel ECG data stream quickly and accurately, or alternatively, such a solution can be conveniently employed for real-time monitoring on a lightweight portable device. The model is tested on two open-access ECG databases: The China Physiological Signal Challenge (2020) database (CPSC-DB) with more than one million beats, and the commonly used MIT-BIH Arrhythmia Database (MIT-DB). Experimental results demonstrate that the proposed systematic approach achieves 99.30% F1-score, 99.69% recall, and 98.91% precision in CPSC-DB, which is the best R-peak detection performance ever achieved. Compared to all competing methods, the proposed approach can reduce the false-positives and false-negatives in Holter ECG signals by more than 54% and 82%, respectively. Results also demonstrate similar or better performance than most competing algorithms on MIT-DB with 99.83% F1-score, 99.85% recall, and 99.82% precision.

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arXiv2021

Deep Learning for Reliable Classification of COVID-19, MERS, and SARS from Chest X-Ray Images

Novel Coronavirus disease (COVID-19) is an extremely contagious and quickly spreading Coronavirus infestation. Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS), which outbreak in 2002 and 2011, and the current COVID-19 pandemic are all from the same family of coronavirus. This work aims to classify COVID-19, SARS, and MERS chest X-ray (CXR) images using deep Convolutional Neural Networks (CNNs). A unique database was created, so-called QU-COVID-family, consisting of 423 COVID-19, 144 MERS, and 134 SARS CXR images. Besides, a robust COVID-19 recognition system was proposed to identify lung regions using a CNN segmentation model (U-Net), and then classify the segmented lung images as COVID-19, MERS, or SARS using a pre-trained CNN classifier. Furthermore, the Score-CAM visualization method was utilized to visualize classification output and understand the reasoning behind the decision of deep CNNs. Several Deep Learning classifiers were trained and tested; four outperforming algorithms were reported. Original and preprocessed images were used individually and all together as the input(s) to the networks. Two recognition schemes were considered: plain CXR classification and segmented CXR classification. For plain CXRs, it was observed that InceptionV3 outperforms other networks with a 3-channel scheme and achieves sensitivities of 99.5%, 93.1%, and 97% for classifying COVID-19, MERS, and SARS images, respectively. In contrast, for segmented CXRs, InceptionV3 outperformed using the original CXR dataset and achieved sensitivities of 96.94%, 79.68%, and 90.26% for classifying COVID-19, MERS, and SARS images, respectively. All networks showed high COVID-19 detection sensitivity (>96%) with the segmented lung images. This indicates the unique radiographic signature of COVID-19 cases in the eyes of AI, which is often a challenging task for medical doctors.

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arXiv2021

Convolutional versus Self-Organized Operational Neural Networks for Real-World Blind Image Denoising

Real-world blind denoising poses a unique image restoration challenge due to the non-deterministic nature of the underlying noise distribution. Prevalent discriminative networks trained on synthetic noise models have been shown to generalize poorly to real-world noisy images. While curating real-world noisy images and improving ground truth estimation procedures remain key points of interest, a potential research direction is to explore extensions to the widely used convolutional neuron model to enable better generalization with fewer data and lower network complexity, as opposed to simply using deeper Convolutional Neural Networks (CNNs). Operational Neural Networks (ONNs) and their recent variant, Self-organized ONNs (Self-ONNs), propose to embed enhanced non-linearity into the neuron model and have been shown to outperform CNNs across a variety of regression tasks. However, all such comparisons have been made for compact networks and the efficacy of deploying operational layers as a drop-in replacement for convolutional layers in contemporary deep architectures remains to be seen. In this work, we tackle the real-world blind image denoising problem by employing, for the first time, a deep Self-ONN. Extensive quantitative and qualitative evaluations spanning multiple metrics and four high-resolution real-world noisy image datasets against the state-of-the-art deep CNN network, DnCNN, reveal that deep Self-ONNs consistently achieve superior results with performance gains of up to 1.76dB in PSNR. Furthermore, Self-ONNs with half and even quarter the number of layers that require only a fraction of computational resources as that of DnCNN can still achieve similar or better results compared to the state-of-the-art.

cs.CV↗

arXiv2021

Advance Warning Methodologies for COVID-19 using Chest X-Ray Images

Coronavirus disease 2019 (COVID-19) has rapidly become a global health concern after its first known detection in December 2019. As a result, accurate and reliable advance warning system for the early diagnosis of COVID-19 has now become a priority. The detection of COVID-19 in early stages is not a straightforward task from chest X-ray images according to expert medical doctors because the traces of the infection are visible only when the disease has progressed to a moderate or severe stage. In this study, our first aim is to evaluate the ability of recent \textit{state-of-the-art} Machine Learning techniques for the early detection of COVID-19 from chest X-ray images. Both compact classifiers and deep learning approaches are considered in this study. Furthermore, we propose a recent compact classifier, Convolutional Support Estimator Network (CSEN) approach for this purpose since it is well-suited for a scarce-data classification task. Finally, this study introduces a new benchmark dataset called Early-QaTa-COV19, which consists of 1065 early-stage COVID-19 pneumonia samples (very limited or no infection signs) labelled by the medical doctors and 12 544 samples for control (normal) class. A detailed set of experiments shows that the CSEN achieves the top (over 97%) sensitivity with over 95.5% specificity. Moreover, DenseNet-121 network produces the leading performance among other deep networks with 95% sensitivity and 99.74% specificity.

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arXiv2021

Early Detection of Myocardial Infarction in Low-Quality Echocardiography

Myocardial infarction (MI), or commonly known as heart attack, is a life-threatening health problem worldwide from which 32.4 million people suffer each year. Early diagnosis and treatment of MI are crucial to prevent further heart tissue damages or death. The earliest and most reliable sign of ischemia is regional wall motion abnormality (RWMA) of the affected part of the ventricular muscle. Echocardiography can easily, inexpensively, and non-invasively exhibit the RWMA. In this article, we introduce a three-phase approach for early MI detection in low-quality echocardiography: 1) segmentation of the entire left ventricle (LV) wall using a state-of-the-art deep learning model, 2) analysis of the segmented LV wall by feature engineering, and 3) early MI detection. The main contributions of this study are highly accurate segmentation of the LV wall from low-quality echocardiography, pseudo labeling approach for ground-truth formation of the unannotated LV wall, and the first public echocardiographic dataset (HMC-QU)* for MI detection. Furthermore, the outputs of the proposed approach can significantly help cardiologists for a better assessment of the LV wall characteristics. The proposed approach has achieved 95.72% sensitivity and 99.58% specificity for the LV wall segmentation, and 85.97% sensitivity, 74.03% specificity, and 86.85% precision for MI detection on the HMC-QU dataset. *The benchmark HMC-QU dataset is publicly shared at the repository https://www.kaggle.com/aysendegerli/hmcqu-dataset

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arXiv2021

COVID-19 Infection Localization and Severity Grading from Chest X-ray Images

Coronavirus disease 2019 (COVID-19) has been the main agenda of the whole world, since it came into sight in December 2019 as it has significantly affected the world economy and healthcare system. Given the effects of COVID-19 on pulmonary tissues, chest radiographic imaging has become a necessity for screening and monitoring the disease. Numerous studies have proposed Deep Learning approaches for the automatic diagnosis of COVID-19. Although these methods achieved astonishing performance in detection, they have used limited chest X-ray (CXR) repositories for evaluation, usually with a few hundred COVID-19 CXR images only. Thus, such data scarcity prevents reliable evaluation with the potential of overfitting. In addition, most studies showed no or limited capability in infection localization and severity grading of COVID-19 pneumonia. In this study, we address this urgent need by proposing a systematic and unified approach for lung segmentation and COVID-19 localization with infection quantification from CXR images. To accomplish this, we have constructed the largest benchmark dataset with 33,920 CXR images, including 11,956 COVID-19 samples, where the annotation of ground-truth lung segmentation masks is performed on CXRs by a novel human-machine collaborative approach. An extensive set of experiments was performed using the state-of-the-art segmentation networks, U-Net, U-Net++, and Feature Pyramid Networks (FPN). The developed network, after an extensive iterative process, reached a superior performance for lung region segmentation with Intersection over Union (IoU) of 96.11% and Dice Similarity Coefficient (DSC) of 97.99%. Furthermore, COVID-19 infections of various shapes and types were reliably localized with 83.05% IoU and 88.21% DSC. Finally, the proposed approach has achieved an outstanding COVID-19 detection performance with both sensitivity and specificity values above 99%.

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arXiv2021

BM3D vs 2-Layer ONN

Despite their recent success on image denoising, the need for deep and complex architectures still hinders the practical usage of CNNs. Older but computationally more efficient methods such as BM3D remain a popular choice, especially in resource-constrained scenarios. In this study, we aim to find out whether compact neural networks can learn to produce competitive results as compared to BM3D for AWGN image denoising. To this end, we configure networks with only two hidden layers and employ different neuron models and layer widths for comparing the performance with BM3D across different AWGN noise levels. Our results conclusively show that the recently proposed self-organized variant of operational neural networks based on a generative neuron model (Self-ONNs) is not only a better choice as compared to CNNs, but also provide competitive results as compared to BM3D and even significantly surpass it for high noise levels.

cs.CV↗

arXiv2021

Detection and severity classification of COVID-19 in CT images using deep learning

Since the breakout of coronavirus disease (COVID-19), the computer-aided diagnosis has become a necessity to prevent the spread of the virus. Detecting COVID-19 at an early stage is essential to reduce the mortality risk of the patients. In this study, a cascaded system is proposed to segment the lung, detect, localize, and quantify COVID-19 infections from computed tomography (CT) images Furthermore, the system classifies the severity of COVID-19 as mild, moderate, severe, or critical based on the percentage of infected lungs. An extensive set of experiments were performed using state-of-the-art deep Encoder-Decoder Convolutional Neural Networks (ED-CNNs), UNet, and Feature Pyramid Network (FPN), with different backbone (encoder) structures using the variants of DenseNet and ResNet. The conducted experiments showed the best performance for lung region segmentation with Dice Similarity Coefficient (DSC) of 97.19% and Intersection over Union (IoU) of 95.10% using U-Net model with the DenseNet 161 encoder. Furthermore, the proposed system achieved an elegant performance for COVID-19 infection segmentation with a DSC of 94.13% and IoU of 91.85% using the FPN model with the DenseNet201 encoder. The achieved performance is significantly superior to previous methods for COVID-19 lesion localization. Besides, the proposed system can reliably localize infection of various shapes and sizes, especially small infection regions, which are rarely considered in recent studies. Moreover, the proposed system achieved high COVID-19 detection performance with 99.64% sensitivity and 98.72% specificity. Finally, the system was able to discriminate between different severity levels of COVID-19 infection over a dataset of 1,110 subjects with sensitivity values of 98.3%, 71.2%, 77.8%, and 100% for mild, moderate, severe, and critical infections, respectively.

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arXiv2021

Speech Command Recognition in Computationally Constrained Environments with a Quadratic Self-organized Operational Layer

Automatic classification of speech commands has revolutionized human computer interactions in robotic applications. However, employed recognition models usually follow the methodology of deep learning with complicated networks which are memory and energy hungry. So, there is a need to either squeeze these complicated models or use more efficient light-weight models in order to be able to implement the resulting classifiers on embedded devices. In this paper, we pick the second approach and propose a network layer to enhance the speech command recognition capability of a lightweight network and demonstrate the result via experiments. The employed method borrows the ideas of Taylor expansion and quadratic forms to construct a better representation of features in both input and hidden layers. This richer representation results in recognition accuracy improvement as shown by extensive experiments on Google speech commands (GSC) and synthetic speech commands (SSC) datasets.

cs.SD↗

arXiv2021

Reliable COVID-19 Detection Using Chest X-ray Images

Coronavirus disease 2019 (COVID-19) has emerged the need for computer-aided diagnosis with automatic, accurate, and fast algorithms. Recent studies have applied Machine Learning algorithms for COVID-19 diagnosis over chest X-ray (CXR) images. However, the data scarcity in these studies prevents a reliable evaluation with the potential of overfitting and limits the performance of deep networks. Moreover, these networks can discriminate COVID-19 pneumonia usually from healthy subjects only or occasionally, from limited pneumonia types. Thus, there is a need for a robust and accurate COVID-19 detector evaluated over a large CXR dataset. To address this need, in this study, we propose a reliable COVID-19 detection network: ReCovNet, which can discriminate COVID-19 pneumonia from 14 different thoracic diseases and healthy subjects. To accomplish this, we have compiled the largest COVID-19 CXR dataset: QaTa-COV19 with 124,616 images including 4603 COVID-19 samples. The proposed ReCovNet achieved a detection performance with 98.57% sensitivity and 99.77% specificity.

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arXiv2021

COVID-19 Infection Map Generation and Detection from Chest X-Ray Images

Computer-aided diagnosis has become a necessity for accurate and immediate coronavirus disease 2019 (COVID-19) detection to aid treatment and prevent the spread of the virus. Numerous studies have proposed to use Deep Learning techniques for COVID-19 diagnosis. However, they have used very limited chest X-ray (CXR) image repositories for evaluation with a small number, a few hundreds, of COVID-19 samples. Moreover, these methods can neither localize nor grade the severity of COVID-19 infection. For this purpose, recent studies proposed to explore the activation maps of deep networks. However, they remain inaccurate for localizing the actual infestation making them unreliable for clinical use. This study proposes a novel method for the joint localization, severity grading, and detection of COVID-19 from CXR images by generating the so-called infection maps. To accomplish this, we have compiled the largest dataset with 119,316 CXR images including 2951 COVID-19 samples, where the annotation of the ground-truth segmentation masks is performed on CXRs by a novel collaborative human-machine approach. Furthermore, we publicly release the first CXR dataset with the ground-truth segmentation masks of the COVID-19 infected regions. A detailed set of experiments show that state-of-the-art segmentation networks can learn to localize COVID-19 infection with an F1-score of 83.20%, which is significantly superior to the activation maps created by the previous methods. Finally, the proposed approach achieved a COVID-19 detection performance with 94.96% sensitivity and 99.88% specificity.

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arXiv2020

Exploring the Effect of Image Enhancement Techniques on COVID-19 Detection using Chest X-rays Images

The use of computer-aided diagnosis in the reliable and fast detection of coronavirus disease (COVID-19) has become a necessity to prevent the spread of the virus during the pandemic to ease the burden on the medical infrastructure. Chest X-ray (CXR) imaging has several advantages over other imaging techniques as it is cheap, easily accessible, fast and portable. This paper explores the effect of various popular image enhancement techniques and states the effect of each of them on the detection performance. We have compiled the largest X-ray dataset called COVQU-20, consisting of 18,479 normal, non-COVID lung opacity and COVID-19 CXR images. To the best of our knowledge, this is the largest public COVID positive database. Ground glass opacity is the common symptom reported in COVID-19 pneumonia patients and so a mixture of 3616 COVID-19, 6012 non-COVID lung opacity, and 8851 normal chest X-ray images were used to create this dataset. Five different image enhancement techniques: histogram equalization, contrast limited adaptive histogram equalization, image complement, gamma correction, and Balance Contrast Enhancement Technique were used to improve COVID-19 detection accuracy. Six different Convolutional Neural Networks (CNNs) were investigated in this study. Gamma correction technique outperforms other enhancement techniques in detecting COVID-19 from standard and segmented lung CXR images. The accuracy, precision, sensitivity, f1-score, and specificity in the detection of COVID-19 with gamma correction on CXR images were 96.29%, 96.28%, 96.29%, 96.28% and 96.27% respectively. The accuracy, precision, sensitivity, F1-score, and specificity were 95.11 %, 94.55 %, 94.56 %, 94.53 % and 95.59 % respectively for segmented lung images. The proposed approach with very high and comparable performance will boost the fast and robust COVID-19 detection using chest X-ray images.

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arXiv2020

Classification of Polarimetric SAR Images Using Compact Convolutional Neural Networks

Classification of polarimetric synthetic aperture radar (PolSAR) images is an active research area with a major role in environmental applications. The traditional Machine Learning (ML) methods proposed in this domain generally focus on utilizing highly discriminative features to improve the classification performance, but this task is complicated by the well-known "curse of dimensionality" phenomena. Other approaches based on deep Convolutional Neural Networks (CNNs) have certain limitations and drawbacks, such as high computational complexity, an unfeasibly large training set with ground-truth labels, and special hardware requirements. In this work, to address the limitations of traditional ML and deep CNN based methods, a novel and systematic classification framework is proposed for the classification of PolSAR images, based on a compact and adaptive implementation of CNNs using a sliding-window classification approach. The proposed approach has three advantages. First, there is no requirement for an extensive feature extraction process. Second, it is computationally efficient due to utilized compact configurations. In particular, the proposed compact and adaptive CNN model is designed to achieve the maximum classification accuracy with minimum training and computational complexity. This is of considerable importance considering the high costs involved in labelling in PolSAR classification. Finally, the proposed approach can perform classification using smaller window sizes than deep CNNs. Experimental evaluations have been performed over the most commonly-used four benchmark PolSAR images: AIRSAR L-Band and RADARSAT-2 C-Band data of San Francisco Bay and Flevoland areas. Accordingly, the best obtained overall accuracies range between 92.33 - 99.39% for these benchmark study sites.

cs.CV↗

arXiv2020

Operational vs Convolutional Neural Networks for Image Denoising

Convolutional Neural Networks (CNNs) have recently become a favored technique for image denoising due to its adaptive learning ability, especially with a deep configuration. However, their efficacy is inherently limited owing to their homogenous network formation with the unique use of linear convolution. In this study, we propose a heterogeneous network model which allows greater flexibility for embedding additional non-linearity at the core of the data transformation. To this end, we propose the idea of an operational neuron or Operational Neural Networks (ONN), which enables a flexible non-linear and heterogeneous configuration employing both inter and intra-layer neuronal diversity. Furthermore, we propose a robust operator search strategy inspired by the Hebbian theory, called the Synaptic Plasticity Monitoring (SPM) which can make data-driven choices for non-linearities in any architecture. An extensive set of comparative evaluations of ONNs and CNNs over two severe image denoising problems yield conclusive evidence that ONNs enriched by non-linear operators can achieve a superior denoising performance against CNNs with both equivalent and well-known deep configurations.

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arXiv2020

Self-Organized Operational Neural Networks for Severe Image Restoration Problems

Discriminative learning based on convolutional neural networks (CNNs) aims to perform image restoration by learning from training examples of noisy-clean image pairs. It has become the go-to methodology for tackling image restoration and has outperformed the traditional non-local class of methods. However, the top-performing networks are generally composed of many convolutional layers and hundreds of neurons, with trainable parameters in excess of several millions. We claim that this is due to the inherent linear nature of convolution-based transformation, which is inadequate for handling severe restoration problems. Recently, a non-linear generalization of CNNs, called the operational neural networks (ONN), has been shown to outperform CNN on AWGN denoising. However, its formulation is burdened by a fixed collection of well-known nonlinear operators and an exhaustive search to find the best possible configuration for a given architecture, whose efficacy is further limited by a fixed output layer operator assignment. In this study, we leverage the Taylor series-based function approximation to propose a self-organizing variant of ONNs, Self-ONNs, for image restoration, which synthesizes novel nodal transformations onthe-fly as part of the learning process, thus eliminating the need for redundant training runs for operator search. In addition, it enables a finer level of operator heterogeneity by diversifying individual connections of the receptive fields and weights. We perform a series of extensive ablation experiments across three severe image restoration tasks. Even when a strict equivalence of learnable parameters is imposed, Self-ONNs surpass CNNs by a considerable margin across all problems, improving the generalization performance by up to 3 dB in terms of PSNR.

cs.CV↗

arXiv2020

Exploiting Heterogeneity in Operational Neural Networks by Synaptic Plasticity

The recently proposed network model, Operational Neural Networks (ONNs), can generalize the conventional Convolutional Neural Networks (CNNs) that are homogenous only with a linear neuron model. As a heterogenous network model, ONNs are based on a generalized neuron model that can encapsulate any set of non-linear operators to boost diversity and to learn highly complex and multi-modal functions or spaces with minimal network complexity and training data. However, the default search method to find optimal operators in ONNs, the so-called Greedy Iterative Search (GIS) method, usually takes several training sessions to find a single operator set per layer. This is not only computationally demanding, also the network heterogeneity is limited since the same set of operators will then be used for all neurons in each layer. To address this deficiency and exploit a superior level of heterogeneity, in this study the focus is drawn on searching the best-possible operator set(s) for the hidden neurons of the network based on the Synaptic Plasticity paradigm that poses the essential learning theory in biological neurons. During training, each operator set in the library can be evaluated by their synaptic plasticity level, ranked from the worst to the best, and an elite ONN can then be configured using the top ranked operator sets found at each hidden layer. Experimental results over highly challenging problems demonstrate that the elite ONNs even with few neurons and layers can achieve a superior learning performance than GIS-based ONNs and as a result the performance gap over the CNNs further widens.

cs.NE↗

arXiv2020

Left Ventricular Wall Motion Estimation by Active Polynomials for Acute Myocardial Infarction Detection

Echocardiogram (echo) is the earliest and the primary tool for identifying regional wall motion abnormalities (RWMA) in order to diagnose myocardial infarction (MI) or commonly known as heart attack. This paper proposes a novel approach, Active Polynomials, which can accurately and robustly estimate the global motion of the Left Ventricular (LV) wall from any echo in a robust and accurate way. The proposed algorithm quantifies the true wall motion occurring in LV wall segments so as to assist cardiologists diagnose early signs of an acute MI. It further enables medical experts to gain an enhanced visualization capability of echo images through color-coded segments along with their "maximum motion displacement" plots helping them to better assess wall motion and LV Ejection-Fraction (LVEF). The outputs of the method can further help echo-technicians to assess and improve the quality of the echocardiogram recording. A major contribution of this study is the first public echo database collection composed by physicians at the Hamad Medical Corporation Hospital in Qatar. The so-called HMC-QU database will serve as the benchmark for the forthcoming relevant studies. The results over the HMC-QU dataset show that the proposed approach can achieve high accuracy, sensitivity and precision in MI detection even though the echo quality is quite poor, and the temporal resolution is low.

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arXiv2020

FastONN -- Python based open-source GPU implementation for Operational Neural Networks

Operational Neural Networks (ONNs) have recently been proposed as a special class of artificial neural networks for grid structured data. They enable heterogenous non-linear operations to generalize the widely adopted convolution-based neuron model. This work introduces a fast GPU-enabled library for training operational neural networks, FastONN, which is based on a novel vectorized formulation of the operational neurons. Leveraging on automatic reverse-mode differentiation for backpropagation, FastONN enables increased flexibility with the incorporation of new operator sets and customized gradient flows. Additionally, bundled auxiliary modules offer interfaces for performance tracking and checkpointing across different data partitions and customized metrics.

cs.NE↗