zurlog/subset_wlabels huggingface dataset:
Title: bias field poses a threat to dnn-based x-ray recognition
Published: 2021-05-03 (Preprint, arXiv)
Condition: COVID-19;Lung Diseases
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: The chest X-ray plays a key role in screening and diagnosis of many lung diseases including the COVID-19. More recently, many works construct deep neural networks (DNNs) for chest X-ray images to realize automated and efficient diagnosis of lung diseases. However, bias field caused by the improper medical image acquisition process widely exists in the chest X-ray images while the robustness of DNNs to the bias field is rarely explored, which definitely poses a threat to the X-ray-based automated diagnosis system. In this paper, we study this problem based on the recent adversarial attack and propose a brand new attack, i.e., the adversarial bias field attack where the bias field instead of the additive noise works as the adversarial perturbations for fooling the DNNs. This novel attack posts a key problem: how to locally tune the bias field to realize high attack success rate while maintaining its spatial smoothness to guarantee high realisticity. These two goals contradict each other and thus has made the attack significantly challenging. To overcome this challenge, we propose the adversarial-smooth bias field attack that can locally tune the bias field with joint smooth and adversarial constraints. As a result, the adversarial X-ray images can not only fool the DNNs effectively but also retain very high level of realisticity. We validate our method on real chest X-ray datasets with powerful DNNs, e.g., ResNet50, DenseNet121, and MobileNet, and show different properties to the state-of-the-art attacks in both image realisticity and attack transferability. Our method reveals the potential threat to the DNN-based X-ray automated diagnosis and can definitely benefit the development of bias-field-robust automated diagnosis system.
Title: chest x-ray image phase features for improved diagnosis of covid-19 using convolutional neural network
Published: 2021-04-14 (Preprint, arXiv)
Condition: COVID-19;COVID-19 Pandemic;Pneumonia
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: Recently, the outbreak of the novel Coronavirus disease 2019 (COVID-19) pandemic has seriously endangered human health and life. Due to limited availability of test kits, the need for auxiliary diagnostic approach has increased. Recent research has shown radiography of COVID-19 patient, such as CT and X-ray, contains salient information about the COVID-19 virus and could be used as an alternative diagnosis method. Chest X-ray (CXR) due to its faster imaging time, wide availability, low cost and portability gains much attention and becomes very promising. Computational methods with high accuracy and robustness are required for rapid triaging of patients and aiding radiologist in the interpretation of the collected data. In this study, we design a novel multi-feature convolutional neural network (CNN) architecture for multi-class improved classification of COVID-19 from CXR images. CXR images are enhanced using a local phase-based image enhancement method. The enhanced images, together with the original CXR data, are used as an input to our proposed CNN architecture. Using ablation studies, we show the effectiveness of the enhanced images in improving the diagnostic accuracy. We provide quantitative evaluation on two datasets and qualitative results for visual inspection. Quantitative evaluation is performed on data consisting of 8,851 normal (healthy), 6,045 pneumonia, and 3,323 Covid-19 CXR scans. In Dataset-1, our model achieves 95.57\% average accuracy for a three classes classification, 99\% precision, recall, and F1-scores for COVID-19 cases. For Dataset-2, we have obtained 94.44\% average accuracy, and 95\% precision, recall, and F1-scores for detection of COVID-19. Our proposed multi-feature guided CNN achieves improved results compared to single-feature CNN proving the importance of the local phase-based CXR image enhancement (GitHub).
Title: convolutional sparse support estimator-based covid-19 recognition from x-ray images
Journal: IEEE Trans Neural Netw Learn Syst
Published: 2021-04-20 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19;Pneumonia, Bacterial;Pneumonia, Viral
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: Coronavirus disease (COVID-19) has been the main agenda of the whole world ever since it came into sight. X-ray imaging is a common and easily accessible tool that has great potential for COVID-19 diagnosis and prognosis. Deep learning techniques can generally provide state-of-the-art performance in many classification tasks when trained properly over large data sets. However, data scarcity can be a crucial obstacle when using them for COVID-19 detection. Alternative approaches such as representation-based classification might provide satisfactory performance with limited size data sets, but they generally fall short in performance or speed compared to the neural network (NN)-based methods. To address this deficiency, convolution support estimation network (CSEN) has recently been proposed as a bridge between representation-based and NN approaches by providing a noniterative real-time mapping from query sample to ideally SR coefficient support, which is critical information for class decision in representation-based techniques. The main premises of this study can be summarized as follows: 1) A benchmark X-ray data set, namely QaTa-Cov19, containing over 6200 X-ray images is created. The data set covering 462 X-ray images from COVID-19 patients along with three other classes; bacterial pneumonia, viral pneumonia, and normal. 2) The proposed CSEN-based classification scheme equipped with feature extraction from state-of-the-art deep NN solution for X-ray images, CheXNet, achieves over 98% sensitivity and over 95% specificity for COVID-19 recognition directly from raw X-ray images when the average performance of 5-fold cross validation over QaTa-Cov19 data set is calculated. 3) Having such an elegant COVID-19 assistive diagnosis performance, this study further provides evidence that COVID-19 induces a unique pattern in X-rays that can be discriminated with high accuracy.
Title: covxnet: a multi-dilation convolutional neural network for automatic covid-19 and other pneumonia detection from chest x-ray images with transferable multi-receptive feature optimization
Journal: Comput Biol Med
Published: 2020-07-14 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19;COVID-19 Pandemic;Pneumonia;Pneumonia, Bacterial;Pneumonia, Viral
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: With the recent outbreak of COVID-19, fast diagnostic testing has become one of the major challenges due to the critical shortage of test kit. Pneumonia, a major effect of COVID-19, needs to be urgently diagnosed along with its underlying reasons. In this paper, deep learning aided automated COVID-19 and other pneumonia detection schemes are proposed utilizing a small amount of COVID-19 chest X-rays. A deep convolutional neural network (CNN) based architecture, named as CovXNet, is proposed that utilizes depthwise convolution with varying dilation rates for efficiently extracting diversified features from chest X-rays. Since the chest X-ray images corresponding to COVID-19 caused pneumonia and other traditional pneumonias have significant similarities, at first, a large number of chest X-rays corresponding to normal and (viral/bacterial) pneumonia patients are used to train the proposed CovXNet. Learning of this initial training phase is transferred with some additional fine-tuning layers that are further trained with a smaller number of chest X-rays corresponding to COVID-19 and other pneumonia patients. In the proposed method, different forms of CovXNets are designed and trained with X-ray images of various resolutions and for further optimization of their predictions, a stacking algorithm is employed. Finally, a gradient-based discriminative localization is integrated to distinguish the abnormal regions of X-ray images referring to different types of pneumonia. Extensive experimentations using two different datasets provide very satisfactory detection performance with accuracy of 97.4% for COVID/Normal, 96.9% for COVID/Viral pneumonia, 94.7% for COVID/Bacterial pneumonia, and 90.2% for multiclass COVID/normal/Viral/Bacterial pneumonias. Hence, the proposed schemes can serve as an efficient tool in the current state of COVID-19 pandemic. All the architectures are made publicly available at: GitHub
Title: toward data-efficient learning: a benchmark for covid-19 ct lung and infection segmentation
Journal: Med Phys
Published: 2020-12-24 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19;Infections
Task: Segmentation-only | Modality: CT

Abstract: Accurate segmentation of lung and infection in COVID-19 computed tomography (CT) scans plays an important role in the quantitative management of patients. Most of the existing studies are based on large and private annotated datasets that are impractical to obtain from a single institution, especially when radiologists are busy fighting the coronavirus disease. Furthermore, it is hard to compare current COVID-19 CT segmentation methods as they are developed on different datasets, trained in different settings, and evaluated with different metrics. To promote the development of data-efficient deep learning methods, in this paper, we built three benchmarks for lung and infection segmentation based on 70 annotated COVID-19 cases, which contain current active research areas, for example, few-shot learning, domain generalization, and knowledge transfer. For a fair comparison among different segmentation methods, we also provide standard training, validation and testing splits, evaluation metrics and, the corresponding code. Based on the state-of-the-art network, we provide more than 40 pretrained baseline models, which not only serve as out-of-the-box segmentation tools but also save computational time for researchers who are interested in COVID-19 lung and infection segmentation. We achieve average dice similarity coefficient (DSC) scores of 97.3%, 97.7%, and 67.3% and average normalized surface dice (NSD) scores of 90.6%, 91.4%, and 70.0% for left lung, right lung, and infection, respectively. To the best of our knowledge, this work presents the first data-efficient learning benchmark for medical image segmentation, and the largest number of pretrained models up to now. All these resources are publicly available, and our work lays the foundation for promoting the development of deep learning methods for efficient COVID-19 CT segmentation with limited data.
Title: a deep learning system to screen novel coronavirus disease 2019 pneumonia
Journal: Engineering (Beijing)
Published: 2020-08-25 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19;Infections;Influenza, Human;Pneumonia;Pneumonia, Viral
Task: 2. Detection/Diagnosis | Modality: CT

Abstract: The real-time reverse transcription-polymerase chain reaction (RT-PCR) detection of viral RNA from sputum or nasopharyngeal swab had a relatively low positive rate in the early stage of coronavirus disease 2019 (COVID-19). Meanwhile, the manifestations of COVID-19 as seen through computed tomography (CT) imaging show individual characteristics that differ from those of other types of viral pneumonia such as influenza-A viral pneumonia (IAVP). This study aimed to establish an early screening model to distinguish COVID-19 from IAVP and healthy cases through pulmonary CT images using deep learning techniques. A total of 618 CT samples were collected: 219 samples from 110 patients with COVID-19 (mean age 50 years; 63 male patients); 224 samples from 224 patients with IAVP (mean age 61 years; 156 male patients); and 175 samples from 175 healthy cases (mean age 39 years; 97 male patients). All CT samples were contributed from three COVID-19-designated hospitals in Zhejiang Province, China. First, the candidate infection regions were segmented out from the pulmonary CT image set using a 3D deep learning model. These separated images were then categorized into the COVID-19, IAVP, and irrelevant to infection (ITI) groups, together with the corresponding confidence scores, using a location-attention classification model. Finally, the infection type and overall confidence score for each CT case were calculated using the Noisy-OR Bayesian function. The experimental result of the benchmark dataset showed that the overall accuracy rate was 86.7% in terms of all the CT cases taken together. The deep learning models established in this study were effective for the early screening of COVID-19 patients and were demonstrated to be a promising supplementary diagnostic method for frontline clinical doctors.
Title: severity assessment of coronavirus disease 2019 (covid-19) using quantitative features from chest ct images
Published: 2020-03-26 (Preprint, arXiv)
Condition: COVID-19;Infections
Task: 2. Detection/Diagnosis | Modality: CT

Abstract: Chest computed tomography (CT) is recognized as an important tool for COVID-19 severity assessment. As the number of affected patients increase rapidly, manual severity assessment becomes a labor-intensive task, and may lead to delayed treatment. Using machine learning method to realize automatic severity assessment (non-severe or severe) of COVID-19 based on chest CT images, and to explore the severity-related features from the resulting assessment model. Materials and Chest CT images of 176 patients (age 45.3 years, 96 male and 80 female) with confirmed COVID-19 are used, from which 63 quantitative features, e.g., the infection volume/ratio of the whole lung and the volume of ground-glass opacity (GGO) regions, are calculated. A random forest (RF) model is trained to assess the severity (non-severe or severe) based on quantitative features. Importance of each quantitative feature, which reflects the correlation to the severity of COVID-19, is calculated from the RF model. Using three-fold cross validation, the RF model shows promising results, i.e., 0.933 of true positive rate, 0.745 of true negative rate, 0.875 of accuracy, and 0.91 of area under receiver operating characteristic curve (AUC). The resulting importance of quantitative features shows that the volume and its ratio (with respect to the whole lung volume) of ground glass opacity (GGO) regions are highly related to the severity of COVID-19, and the quantitative features calculated from the right lung are more related to the severity assessment than those of the left lung. The RF based model can achieve automatic severity assessment (non-severe or severe) of COVID-19 infection, and the performance is promising. Several quantitative features, which have the potential to reflect the severity of COVID-19, were revealed.
Title: ensemble-cvdnet: a deep learning based end-to-end classification framework for covid-19 detection using ensembles of networks
Published: 2020-12-24 (Preprint, arXiv)
Condition: COVID-19;Pneumonia;Pneumonia, Viral
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: The new type of coronavirus disease (COVID-19), which started in Wuhan, China in December 2019, continues to spread rapidly affecting the whole world. It is essential to have a highly sensitive diagnostic screening tool to detect the disease as early as possible. Currently, chest CT imaging is preferred as the primary screening tool for evaluating the COVID-19 pneumonia by radiological imaging. However, CT imaging requires larger radiation doses, longer exposure time, higher cost, and may suffer from patient movements. X-Ray imaging is a fast, cheap, more patient-friendly and available in almost every healthcare facility. Therefore, we have focused on X-Ray images and developed an end-to-end deep learning model, i.e. Ensemble-CVDNet, to distinguish COVID-19 pneumonia from non-COVID pneumonia and healthy cases in this work. The proposed model is based on a combination of three lightweight pre-trained models SqueezeNet, ShuffleNet, and EfficientNet-B0 at different depths, and combines feature maps in different abstraction levels. In the proposed end to-end model, networks are used as feature extractors in parallel after fine-tuning, and some additional layers are used at the top of them. The proposed model is evaluated in the COVID-19 Radiography Database, a public data set consisting of 219 COVID-19, 1341 Healthy, and 1345 Viral Pneumonia chest X-Ray images. Experimental results show that our lightweight Ensemble-CVDNet model provides 98.30% accuracy, 97.78% sensitivity, and 97.61% F1 score using only 5.62M parameters. Moreover, it takes about 10ms to process and predict an X-Ray image using the proposed method using a mid level GPU. We believe that the method proposed in this study can be a helpful diagnostic screening tool for radiologists in the early diagnosis of the disease.
Title: curbing the ai-induced enthusiasm in diagnosing covid-19 on chest x-rays: the present and the near-future
Published: 2020-05-01 (Preprint, medRxiv)
Condition: Bronchopneumonia;COVID-19;COVID-19 Pandemic
Task: Review | Modality: X-Ray

Abstract: In the current context of COVID-19 pandemic, a rapid and accessible screening tool based on image processing of chest X-rays (CXRs) using machine learning (ML) approaches would be much needed. Initially, we intended to create and validate an ML software solution able to discriminate on the basis of the CXR between SARS-CoV-2-induced bronchopneumonia and other bronchopneumonia etiologies. A systematic search of PubMed, Scopus and arXiv databases using the following search terms , AND AND found 14 recent studies. Most of them declared to be able to confidently identify COVID-19 based on CXRs using deep neural networks. Firstly, weaknesses of artificial intelligence (AI) solutions were analyzed, tackling the issues with datasets (from both medical and technical points of view) and the vulnerability of used algorithms. Then, arguments were provided for why our study design is stronger and more realistic than the previously quoted papers, balancing the possible false expectations with facts. The authors consider that the potential of AI use in COVID-19 diagnosis on CXR is real. However, scientific community should be careful in interpreting statements, results and conclusions regarding AI use in imaging. It is therefore necessary to adopt standards for research and publication of data, because it seems that in the recent months scientific reality suffered manipulations and distortions. Also, a call for responsible approaches to the imaging methods in COVID-19 is raised. It seems mandatory to follow some rigorous approaches in order to provide with adequate results in daily routine. In addition, the authors intended to raise public awareness about the quality of AI protocols and algorithms and to encourage public sharing of as many CXR images with common quality standards.
Title: data science and the role of artificial intelligence in achieving the fast diagnosis of covid-19
Journal: Chaos Solitons Fractals
Published: 2020-08-25 (Journal Article, Peer reviewed (PubMed))
Condition: COVID-19
Task: Review | Modality: Multimodal

Abstract: The rapid spread of novel coronavirus (namely Covid-19) worldwide has alarmed a pandemic since its outbreak in the city of Wuhan, China in December 2019. While the world still tries to wrap its head around as to how to contain the rapid spread of the novel coronavirus, the pandemic has already claimed several thousand lives throughout the world. Yet, the diagnosis of virus spread in humans has proven complexity. A blend of computed tomography imaging, entire genome sequencing, and electron microscopy have been at first adapted to screen and distinguish SARS-CoV-2, the viral etiology of Covid-19. There are a less number of Covid-19 test kits accessible in hospitals because of the expanding cases every day. Accordingly, it is required to utensil a self-exposure framework as a fast substitute analysis to contain Covid-19 spreading among individuals considering the world at large. In the present work, we have elaborated a prudent methodology that helps identify Covid-19 infected people among the normal individuals by utilizing CT scan and chest x-ray images using Artificial Intelligence (AI). The strategy works with a dataset of Covid-19 and normal chest x-ray images. The image diagnosis tool utilizes decision tree classifier for finding novel corona virus infected person. The percentage accuracy of an image is analyzed in terms of precision, recall score and F1 score. The outcome depends on the information accessible in the store of Kaggle and Open-I according to their approved chest X-ray and CT scan images. Interestingly, the test methodology demonstrates that the intended algorithm is robust, accurate and precise. Our technique accomplishes the exactness focused on the AI innovation which provides faster results during both training and inference.
Title: cov-elm classifier: an extreme learning machine based identification of covid-19 using chest x-ray images
Published: 2021-09-28 (Preprint, arXiv)
Condition: COVID-19;Pneumonia
Task: 2. Detection/Diagnosis | Modality: X-Ray

Abstract: Coronaviruses constitute a family of viruses that gives rise to respiratory diseases. As COVID-19 is highly contagious, early diagnosis of COVID-19 is crucial for an effective treatment strategy. However, the RT-PCR test which is considered to be a gold standard in the diagnosis of COVID-19 suffers from a high false-negative rate. Chest X-ray (CXR) image analysis has emerged as a feasible and effective diagnostic technique towards this objective. In this work, we propose the COVID-19 classification problem as a three-class classification problem to distinguish between COVID-19, normal, and pneumonia classes. We propose a three-stage framework, named COV-ELM. Stage one deals with preprocessing and transformation while stage two deals with feature extraction. These extracted features are passed as an input to the ELM at the third stage, resulting in the identification of COVID-19. The choice of ELM in this work has been motivated by its faster convergence, better generalization capability, and shorter training time in comparison to the conventional gradient-based learning algorithms. As bigger and diverse datasets become available, ELM can be quickly retrained as compared to its gradient-based competitor models. The proposed model achieved a macro average F1-score of 0.95 and the overall sensitivity of 0.94 at a 95% confidence interval. When compared to state-of-the-art machine learning algorithms, the COV-ELM is found to outperform its competitors in this three-class classification scenario. Further, LIME has been integrated with the proposed COV-ELM model to generate annotated CXR images. The annotations are based on the superpixels that have contributed to distinguish between the different classes. It was observed that the superpixels correspond to the regions of the human lungs that are clinically observed in COVID-19 and Pneumonia cases.