Aysen Degerli

Mete Ahishali, Aysen Degerli, Serkan Kiranyaz et al.

Restoration of poor quality images with a blended set of artifacts plays a vital role for a reliable diagnosis. Existing studies have focused on specific restoration problems such as image deblurring, denoising, and exposure correction where there is usually a strong assumption on the artifact type and severity. As a pioneer study in blind X-ray restoration, we propose a joint model for generic image restoration and classification: Restore-to-Classify Generative Adversarial Networks (R2C-GANs). Such a jointly optimized model keeps any disease intact after the restoration. Therefore, this will naturally lead to a higher diagnosis performance thanks to the improved X-ray image quality. To accomplish this crucial objective, we define the restoration task as an Image-to-Image translation problem from poor quality having noisy, blurry, or over/under-exposed images to high quality image domain. The proposed R2C-GAN model is able to learn forward and inverse transforms between the two domains using unpaired training samples. Simultaneously, the joint classification preserves the disease label during restoration. Moreover, the R2C-GANs are equipped with operational layers/neurons reducing the network depth and further boosting both restoration and classification performances. The proposed joint model is extensively evaluated over the QaTa-COV19 dataset for Coronavirus Disease 2019 (COVID-19) classification. The proposed restoration approach achieves over 90% F1-Score which is significantly higher than the performance of any deep model. Moreover, in the qualitative analysis, the restoration performance of R2C-GANs is approved by a group of medical doctors. We share the software implementation at https://github.com/meteahishali/R2C-GAN.

Mete Ahishali, Aysen Degerli, Mehmet Yamac et al.

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.

Aysen Degerli, Fahad Sohrab, Serkan Kiranyaz et al.

Myocardial infarction (MI) is the leading cause of mortality and morbidity in the world. Early therapeutics of MI can ensure the prevention of further myocardial necrosis. Echocardiography is the fundamental imaging technique that can reveal the earliest sign of MI. However, the scarcity of echocardiographic datasets for the MI detection is the major issue for training data-driven classification algorithms. In this study, we propose a framework for early detection of MI over multi-view echocardiography that leverages one-class classification (OCC) techniques. The OCC techniques are used to train a model for detecting a specific target class using instances from that particular category only. We investigated the usage of uni-modal and multi-modal one-class classification techniques in the proposed framework using the HMC-QU dataset that includes apical 4-chamber (A4C) and apical 2-chamber (A2C) views in a total of 260 echocardiography recordings. Experimental results show that the multi-modal approach achieves a sensitivity level of 85.23% and F1-Score of 80.21%.

Ilke Adalioglu, Mete Ahishali, Aysen Degerli et al.

Myocardial infarction (MI) is a severe case of coronary artery disease (CAD) and ultimately, its detection is substantial to prevent progressive damage to the myocardium. In this study, we propose a novel view-fusion model named self-attention fusion network (SAF-Net) to detect MI from multi-view echocardiography recordings. The proposed framework utilizes apical 2-chamber (A2C) and apical 4-chamber (A4C) view echocardiography recordings for classification. Three reference frames are extracted from each recording of both views and deployed pre-trained deep networks to extract highly representative features. The SAF-Net model utilizes a self-attention mechanism to learn dependencies in extracted feature vectors. The proposed model is computationally efficient thanks to its compact architecture having three main parts: a feature embedding to reduce dimensionality, self-attention for view-pooling, and dense layers for the classification. Experimental evaluation is performed using the HMC-QU-TAU dataset which consists of 160 patients with A2C and A4C view echocardiography recordings. The proposed SAF-Net model achieves a high-performance level with 88.26% precision, 77.64% sensitivity, and 78.13% accuracy. The results demonstrate that the SAF-Net model achieves the most accurate MI detection over multi-view echocardiography recordings.

Aysen Degerli, Pekka Jakala, Juha Pajula et al.

Stroke is a major cause of mortality and disability worldwide from which one in four people are in danger of incurring in their lifetime. The pre-hospital stroke assessment plays a vital role in identifying stroke patients accurately to accelerate further examination and treatment in hospitals. Accordingly, the National Institutes of Health Stroke Scale (NIHSS), Cincinnati Pre-hospital Stroke Scale (CPSS) and Face Arm Speed Time (F.A.S.T.) are globally known tests for stroke assessment. However, the validity of these tests is skeptical in the absence of neurologists and access to healthcare may be limited. Therefore, in this study, we propose a motion-aware and multi-attention fusion network (MAMAF-Net) that can detect stroke from multimodal examination videos. Contrary to other studies on stroke detection from video analysis, our study for the first time proposes an end-to-end solution from multiple video recordings of each subject with a dataset encapsulating stroke, transient ischemic attack (TIA), and healthy controls. The proposed MAMAF-Net consists of motion-aware modules to sense the mobility of patients, attention modules to fuse the multi-input video data, and 3D convolutional layers to perform diagnosis from the attention-based extracted features. Experimental results over the collected Stroke-data dataset show that the proposed MAMAF-Net achieves a successful detection of stroke with 93.62% sensitivity and 95.33% AUC score.

Aysen Degerli, Serkan Kiranyaz, Tahir Hamid et al.

Myocardial infarction (MI) is the leading cause of mortality in the world that occurs due to a blockage of the coronary arteries feeding the myocardium. An early diagnosis of MI and its localization can mitigate the extent of myocardial damage by facilitating early therapeutic interventions. Following the blockage of a coronary artery, the regional wall motion abnormality (RWMA) of the ischemic myocardial segments is the earliest change to set in. Echocardiography is the fundamental tool to assess any RWMA. Assessing the motion of the left ventricle (LV) wall only from a single echocardiography view may lead to missing the diagnosis of MI as the RWMA may not be visible on that specific view. Therefore, in this study, we propose to fuse apical 4-chamber (A4C) and apical 2-chamber (A2C) views in which a total of 12 myocardial segments can be analyzed for MI detection. The proposed method first estimates the motion of the LV wall by Active Polynomials (APs), which extract and track the endocardial boundary to compute myocardial segment displacements. The features are extracted from the A4C and A2C view displacements, which are concatenated and fed into the classifiers to detect MI. The main contributions of this study are 1) creation of a new benchmark dataset by including both A4C and A2C views in a total of 260 echocardiography recordings, which is publicly shared with the research community, 2) improving the performance of the prior work of threshold-based APs by a Machine Learning based approach, and 3) a pioneer MI detection approach via multi-view echocardiography by fusing the information of A4C and A2C views. Experimental results show that the proposed method achieves 90.91% sensitivity and 86.36% precision for MI detection over multi-view echocardiography. The software implementation is shared at https://github.com/degerliaysen/MultiEchoAI.

Mete Ahishali, Anis Ur Rahman, Einari Heinaro et al.

Mapping standing dead trees is crucial for acquiring information on the effects of climate change on forests and forest biodiversity. However, leveraging high-quality aerial imagery for dead tree segmentation poses challenges due to limitations in sensor availability and the scarcity of annotated data. In this study, we propose a generic blind super-resolution framework that incorporates Attention-Guided Domain Adaptation Networks (ADA-Nets) to learn the mapping from low-resolution to high-resolution multispectral image domains. Our approach operates solely on unpaired samples, mimicking real-world conditions, i.e., low-resolution images are not synthetically obtained by downsampling the high-resolution images. Moreover, the proposed method serves as a general-purpose restorer addressing several image degradation types, including saturation, noise, and low contrast that typically occur in low-resolution images acquired by low-end sensors. To the best of our knowledge, this is the first study to perform real-world and generic super-resolution for multispectral data in the scope of standing dead tree segmentation. Experimental evaluations demonstrate segmentation performances of 54% and 64% in Dice scores. Notably, the first result is obtained without using any high-resolution annotations; the segmentation network is trained on super-resolved low-resolution images, while evaluation is performed on the high-resolution data. We publicly share the aerial multispectral dataset with manually annotated labels at https://www.kaggle.com/datasets/meteahishali/aerial-imagery-for-dead-tree-segmentation-poland.

Muhammad Uzair Zahid, Aysen Degerli, Fahad Sohrab et al.

Early detection of myocardial infarction (MI), a critical condition arising from coronary artery disease (CAD), is vital to prevent further myocardial damage. This study introduces a novel method for early MI detection using a one-class classification (OCC) algorithm in echocardiography. Our study overcomes the challenge of limited echocardiography data availability by adopting a novel approach based on Multi-modal Subspace Support Vector Data Description. The proposed technique involves a specialized MI detection framework employing multi-view echocardiography incorporating a composite kernel in the non-linear projection trick, fusing Gaussian and Laplacian sigmoid functions. Additionally, we enhance the update strategy of the projection matrices by adapting maximization for both or one of the modalities in the optimization process. Our method boosts MI detection capability by efficiently transforming features extracted from echocardiography data into an optimized lower-dimensional subspace. The OCC model trained specifically on target class instances from the comprehensive HMC-QU dataset that includes multiple echocardiography views indicates a marked improvement in MI detection accuracy. Our findings reveal that our proposed multi-view approach achieves a geometric mean of 71.24%, signifying a substantial advancement in echocardiography-based MI diagnosis and offering more precise and efficient diagnostic tools.

Aysen Degerli, Mika Hilvo, Juha Pajula et al.

Stroke is globally a major cause of mortality and morbidity, and hence accurate and rapid diagnosis of stroke is valuable. Retinal fundus imaging reveals the known markers of elevated stroke risk in the eyes, which are retinal venular widening, arteriolar narrowing, and increased tortuosity. In contrast to other imaging techniques used for stroke diagnosis, the acquisition of fundus images is easy, non-invasive, fast, and inexpensive. Therefore, in this study, we propose a multi-view stroke network (MVS-Net) to detect stroke and transient ischemic attack (TIA) using retinal fundus images. Contrary to existing studies, our study proposes for the first time a solution to discriminate stroke and TIA with deep multi-view learning by proposing an end-to-end deep network, consisting of multi-view inputs of fundus images captured from both right and left eyes. Accordingly, the proposed MVS-Net defines representative features from fundus images of both eyes and determines the relation within their macula-centered and optic nerve head-centered views. Experiments performed on a dataset collected from stroke and TIA patients, in addition to healthy controls, show that the proposed framework achieves an AUC score of 0.84 for stroke and TIA detection.

Ilke Adalioglu, Serkan Kiranyaz, Mete Ahishali et al.

Echocardiography is the most widely used imaging to monitor cardiac functions, serving as the first line in early detection of myocardial ischemia and infarction. However, echocardiography often suffers from several artifacts including sensor noise, lack of contrast, severe saturation, and missing myocardial segments which severely limit its usage in clinical diagnosis. In recent years, several machine learning methods have been proposed to improve echocardiography views. Yet, these methods usually address only a specific problem (e.g. denoising) and thus cannot provide a robust and reliable restoration in general. On the other hand, cardiac MRI provides a clean view of the heart without suffering such severe issues. However, due to its significantly higher cost, it is often only afforded by a few major hospitals, hence hindering its use and accessibility. In this pilot study, we propose a novel approach to transform echocardiography into the cardiac MRI view. For this purpose, Echo2MRI dataset, consisting of echocardiography and real cardiac MRI image pairs, is composed and will be shared publicly. A dedicated Cycle-consistent Generative Adversarial Network (Cycle-GAN) is trained to learn the transformation from echocardiography frames to cardiac MRI views. An extensive set of qualitative evaluations shows that the proposed transformer can synthesize high-quality artifact-free synthetic cardiac MRI views from a given sequence of echocardiography frames. Medical evaluations performed by a group of cardiologists further demonstrate that synthetic MRI views are indistinguishable from their original counterparts and are preferred over their initial sequence of echocardiography frames for diagnosis in 78.9% of the cases.

Aysen Degerli, Serkan Kiranyaz, Muhammad E. H. Chowdhury et al.

Coronavirus disease 2019 (COVID-19) has been diagnosed automatically using Machine Learning algorithms over chest X-ray (CXR) images. However, most of the earlier studies used Deep Learning models over scarce datasets bearing the risk of overfitting. Additionally, previous studies have revealed the fact that deep networks are not reliable for classification since their decisions may originate from irrelevant areas on the CXRs. Therefore, in this study, we propose Operational Segmentation Network (OSegNet) that performs detection by segmenting COVID-19 pneumonia for a reliable diagnosis. To address the data scarcity encountered in training and especially in evaluation, this study extends the largest COVID-19 CXR dataset: QaTa-COV19 with 121,378 CXRs including 9258 COVID-19 samples with their corresponding ground-truth segmentation masks that are publicly shared with the research community. Consequently, OSegNet has achieved a detection performance with the highest accuracy of 99.65% among the state-of-the-art deep models with 98.09% precision.

Aysen Degerli, Mete Ahishali, Serkan Kiranyaz et al.

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.

Aysen Degerli, Morteza Zabihi, Serkan Kiranyaz et al.

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

Aysen Degerli, Mete Ahishali, Mehmet Yamac et al.

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.

Serkan Kiranyaz, Aysen Degerli, Tahir Hamid et al.

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.

Mete Ahishali, Aysen Degerli, Mehmet Yamac et al.

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.

Mehmet Yamac, Mete Ahishali, Aysen Degerli et al.

Coronavirus disease (Covid-19) has been the main agenda of the whole world since it came in sight in December 2019. It has already caused thousands of causalities and infected several millions worldwide. Any technological tool that can be provided to healthcare practitioners to save time, effort, and possibly lives has crucial importance. The main tools practitioners currently use to diagnose Covid-19 are Reverse Transcription-Polymerase Chain reaction (RT-PCR) and Computed Tomography (CT), which require significant time, resources and acknowledged experts. X-ray imaging is a common and easily accessible tool that has great potential for Covid-19 diagnosis. In this study, we propose a novel approach for Covid-19 recognition from chest X-ray images. Despite the importance of the problem, recent studies in this domain produced not so satisfactory results due to the limited datasets available for training. Recall that Deep Learning techniques can generally provide state-of-the-art performance in many classification tasks when trained properly over large datasets, such data scarcity can be a crucial obstacle when using them for Covid-19 detection. Alternative approaches such as representation-based classification (collaborative or sparse representation) might provide satisfactory performance with limited size datasets, but they generally fall short in performance or speed compared to Machine Learning methods. To address this deficiency, Convolution Support Estimation Network (CSEN) has recently been proposed as a bridge between model-based and Deep Learning approaches by providing a non-iterative real-time mapping from query sample to ideally sparse representation coefficient' support, which is critical information for class decision in representation based techniques.

Dat Thanh Tran, Mehmet Yamac, Aysen Degerli et al.

Compressive Learning is an emerging topic that combines signal acquisition via compressive sensing and machine learning to perform inference tasks directly on a small number of measurements. Many data modalities naturally have a multi-dimensional or tensorial format, with each dimension or tensor mode representing different features such as the spatial and temporal information in video sequences or the spatial and spectral information in hyperspectral images. However, in existing compressive learning frameworks, the compressive sensing component utilizes either random or learned linear projection on the vectorized signal to perform signal acquisition, thus discarding the multi-dimensional structure of the signals. In this paper, we propose Multilinear Compressive Learning, a framework that takes into account the tensorial nature of multi-dimensional signals in the acquisition step and builds the subsequent inference model on the structurally sensed measurements. Our theoretical complexity analysis shows that the proposed framework is more efficient compared to its vector-based counterpart in both memory and computation requirement. With extensive experiments, we also empirically show that our Multilinear Compressive Learning framework outperforms the vector-based framework in object classification and face recognition tasks, and scales favorably when the dimensionalities of the original signals increase, making it highly efficient for high-dimensional multi-dimensional signals.

Aysen Degerli, Sinem Aslan, Mehmet Yamac et al.

Compressive Sensing (CS) theory asserts that sparse signal reconstruction is possible from a small number of linear measurements. Although CS enables low-cost linear sampling, it requires non-linear and costly reconstruction. Recent literature works show that compressive image classification is possible in CS domain without reconstruction of the signal. In this work, we introduce a DCT base method that extracts binary discriminative features directly from CS measurements. These CS measurements can be obtained by using (i) a random or a pseudo-random measurement matrix, or (ii) a measurement matrix whose elements are learned from the training data to optimize the given classification task. We further introduce feature fusion by concatenating Bag of Words (BoW) representation of our binary features with one of the two state-of-the-art CNN-based feature vectors. We show that our fused feature outperforms the state-of-the-art in both cases.