pt-sk/ml_research_abs huggingface dataset:
Deep learning for distinguishing normal versus abnormal chest radiographs and generalization to two unseen diseases tuberculosis and COVID-19.
Authors: ZaidNabulsi, AndrewSellergren, ShaharJamshy, CharlesLau, EdwardSantos, Atilla PKiraly, WenxingYe, JieYang, RoryPilgrim, SaharKazemzadeh, JinYu, Sreenivasa RajuKalidindi, MozziyarEtemadi, FlorenciaGarcia-Vicente, DavidMelnick, Greg SCorrado, LilyPeng, KrishEswaran, DanielTse, NeeralBeladia, YunLiu, Po-Hsuan CameronChen, ShravyaShetty
Journal: Scientific reports

Chest radiography (CXR) is the most widely-used thoracic clinical imaging modality and is crucial for guiding the management of cardiothoracic conditions. The detection of specific CXR findings has been the main focus of several artificial intelligence (AI) systems. However, the wide range of possible CXR abnormalities makes it impractical to detect every possible condition by building multiple separate systems, each of which detects one or more pre-specified conditions. In this work, we developed and evaluated an AI system to classify CXRs as normal or abnormal. For training and tuning the system, we used a de-identified dataset of 248,445 patients from a multi-city hospital network in India. To assess generalizability, we evaluated our system using 6 international datasets from India, China, and the United States. Of these datasets, 4 focused on diseases that the AI was not trained to detect: 2 datasets with tuberculosis and 2 datasets with coronavirus disease 2019. Our results suggest that the AI system trained using a large dataset containing a diverse array of CXR abnormalities generalizes to new patient populations and unseen diseases. In a simulated workflow where the AI system prioritized abnormal cases, the turnaround time for abnormal cases reduced by 7-28%. These results represent an important step towards evaluating whether AI can be safely used to flag cases in a general setting where previously unseen abnormalities exist. Lastly, to facilitate the continued development of AI models for CXR, we release our collected labels for the publicly available dataset.
Auto informing COVID-19 detection result from x-ray/CT images based on deep learning.
Authors: Ahlam FadhilMahmood, Saja WaleedMahmood
Journal: The Review of scientific instruments

It is no secret to all that the corona pandemic has caused a decline in all aspects of the world. Therefore, offering an accurate automatic diagnostic system is very important. This paper proposed an accurate COVID-19 system by testing various deep learning models for x-ray/computed tomography (CT) medical images. A deep preprocessing procedure was done with two filters and segmentation to increase classification results. According to the results obtained, 99.94% of accuracy, 98.70% of sensitivity, and 100% of specificity scores were obtained by the Xception model in the x-ray dataset and the InceptionV3 model for CT scan images. The compared results have demonstrated that the proposed model is proven to be more successful than the deep learning algorithms in previous studies. Moreover, it has the ability to automatically notify the examination results to the patients, the health authority, and the community after taking any x-ray or CT images.
CORONA-Net: Diagnosing COVID-19 from X-ray Images Using Re-Initialization and Classification Networks.
Authors: SherifElbishlawi, Mohamed HAbdelpakey, Mohamed SShehata, Mostafa MMohamed
Journal: Journal of imaging

The COVID-19 pandemic has been deemed a global health pandemic. The early detection of COVID-19 is key to combating its outbreak and could help bring this pandemic to an end. One of the biggest challenges in combating COVID-19 is accurate testing for the disease. Utilizing the power of Convolutional Neural Networks (CNNs) to detect COVID-19 from chest X-ray images can help radiologists compare and validate their results with an automated system. In this paper, we propose a carefully designed network, dubbed CORONA-Net, that can accurately detect COVID-19 from chest X-ray images. CORONA-Net is divided into two phases: (1) The reinitialization phase and (2) the classification phase. In the reinitialization phase, the network consists of encoder and decoder networks. The objective of this phase is to train and initialize the encoder and decoder networks by a distribution that comes out of medical images. In the classification phase, the decoder network is removed from CORONA-Net, and the encoder network acts as a backbone network to fine-tune the classification phase based on the learned weights from the reinitialization phase. Extensive experiments were performed on a publicly available dataset, COVIDx, and the results show that CORONA-Net significantly outperforms the current state-of-the-art networks with an overall accuracy of 95.84%.
Research on Classification of COVID-19 Chest X-Ray Image Modal Feature Fusion Based on Deep Learning.
Authors: DongshengJi, ZhujunZhang, YanzhongZhao, QianchuanZhao
Journal: Journal of healthcare engineering

Most detection methods of coronavirus disease 2019 (COVID-19) use classic image classification models, which have problems of low recognition accuracy and inaccurate capture of modal features when detecting chest X-rays of COVID-19. This study proposes a COVID-19 detection method based on image modal feature fusion. This method first performs small-sample enhancement processing on chest X-rays, such as rotation, translation, and random transformation. Five classic pretraining models are used when extracting modal features. A global average pooling layer reduces training parameters and prevents overfitting. The model is trained and fine-tuned, the machine learning evaluation standard is used to evaluate the model, and the receiver operating characteristic (ROC) curve is drawn. Experiments show that compared with the classic model, the classification method in this study can more effectively detect COVID-19 image modal information, and it achieves the expected effect of accurately detecting cases.
ANFIS-Net for automatic detection of COVID-19.
Authors: AfnanAl-Ali, OmarElharrouss, UvaisQidwai, SomayaAl-Maaddeed
Journal: Scientific reports

Among the most leading causes of mortality across the globe are infectious diseases which have cost tremendous lives with the latest being coronavirus (COVID-19) that has become the most recent challenging issue. The extreme nature of this infectious virus and its ability to spread without control has made it mandatory to find an efficient auto-diagnosis system to assist the people who work in touch with the patients. As fuzzy logic is considered a powerful technique for modeling vagueness in medical practice, an Adaptive Neuro-Fuzzy Inference System (ANFIS) was proposed in this paper as a key rule for automatic COVID-19 detection from chest X-ray images based on the characteristics derived by texture analysis using gray level co-occurrence matrix (GLCM) technique. Unlike the proposed method, especially deep learning-based approaches, the proposed ANFIS-based method can work on small datasets. The results were promising performance accuracy, and compared with the other state-of-the-art techniques, the proposed method gives the same performance as the deep learning with complex architectures using many backbone.
Pulmonary COVID-19: Learning Spatiotemporal Features Combining CNN and LSTM Networks for Lung Ultrasound Video Classification.
Authors: BrunoBarros, PauloLacerda, CélioAlbuquerque, AuraConci
Journal: Sensors (Basel, Switzerland)

Deep Learning is a very active and important area for building Computer-Aided Diagnosis (CAD) applications. This work aims to present a hybrid model to classify lung ultrasound (LUS) videos captured by convex transducers to diagnose COVID-19. A Convolutional Neural Network (CNN) performed the extraction of spatial features, and the temporal dependence was learned using a Long Short-Term Memory (LSTM). Different types of convolutional architectures were used for feature extraction. The hybrid model (CNN-LSTM) hyperparameters were optimized using the Optuna framework. The best hybrid model was composed of an Xception pre-trained on ImageNet and an LSTM containing 512 units, configured with a dropout rate of 0.4, two fully connected layers containing 1024 neurons each, and a sequence of 20 frames in the input layer (20×2018). The model presented an average accuracy of 93% and sensitivity of 97% for COVID-19, outperforming models based purely on spatial approaches. Furthermore, feature extraction using transfer learning with models pre-trained on ImageNet provided comparable results to models pre-trained on LUS images. The results corroborate with other studies showing that this model for LUS classification can be an important tool in the fight against COVID-19 and other lung diseases.
Precise Segmentation of COVID-19 Infected Lung from CT Images Based on Adaptive First-Order Appearance Model with Morphological/Anatomical Constraints.
Authors: AhmedSharafeldeen, MohamedElsharkawy, Norah SalehAlghamdi, AhmedSoliman, AymanEl-Baz
Journal: Sensors (Basel, Switzerland)

A new segmentation technique is introduced for delineating the lung region in 3D computed tomography (CT) images. To accurately model the distribution of Hounsfield scale values within both chest and lung regions, a new probabilistic model is developed that depends on a linear combination of Gaussian (LCG). Moreover, we modified the conventional expectation-maximization (EM) algorithm to be run in a sequential way to estimate both the dominant Gaussian components (one for the lung region and one for the chest region) and the subdominant Gaussian components, which are used to refine the final estimated joint density. To estimate the marginal density from the mixed density, a modified k-means clustering approach is employed to classify the Gaussian subdominant components to determine which components belong properly to a lung and which components belong to a chest. The initial segmentation, based on the LCG-model, is then refined by the imposition of 3D morphological constraints based on a 3D Markov-Gibbs random field (MGRF) with analytically estimated potentials. The proposed approach was tested on CT data from 32 coronavirus disease 2019 (COVID-19) patients. Segmentation quality was quantitatively evaluated using four metrics:
The Applications of Artificial Intelligence in Chest Imaging of COVID-19 Patients: A Literature Review.
Authors: Maria ElenaLaino, AngelaAmmirabile, AlessandroPosa, PierandreaCancian, SherifShalaby, VictorSavevski, EmanueleNeri
Journal: Diagnostics (Basel, Switzerland)

Diagnostic imaging is regarded as fundamental in the clinical work-up of patients with a suspected or confirmed COVID-19 infection. Recent progress has been made in diagnostic imaging with the integration of artificial intelligence (AI) and machine learning (ML) algorisms leading to an increase in the accuracy of exam interpretation and to the extraction of prognostic information useful in the decision-making process. Considering the ever expanding imaging data generated amid this pandemic, COVID-19 has catalyzed the rapid expansion in the application of AI to combat disease. In this context, many recent studies have explored the role of AI in each of the presumed applications for COVID-19 infection chest imaging, suggesting that implementing AI applications for chest imaging can be a great asset for fast and precise disease screening, identification and characterization. However, various biases should be overcome in the development of further ML-based algorithms to give them sufficient robustness and reproducibility for their integration into clinical practice. As a result, in this literature review, we will focus on the application of AI in chest imaging, in particular, deep learning, radiomics and advanced imaging as quantitative CT.
Microscopic segmentation and classification of COVID-19 infection with ensemble convolutional neural network.
Authors: JaveriaAmin, Muhammad AlmasAnjum, MuhammadSharif, AmjadRehman, TanzilaSaba, RidaZahra
Journal: Microscopy research and technique

The detection of biological RNA from sputum has a comparatively poor positive rate in the initial/early stages of discovering COVID-19, as per the World Health Organization. It has a different morphological structure as compared to healthy images, manifested by computer tomography (CT). COVID-19 diagnosis at an early stage can aid in the timely cure of patients, lowering the mortality rate. In this reported research, three-phase model is proposed for COVID-19 detection. In Phase I, noise is removed from CT images using a denoise convolutional neural network (DnCNN). In the Phase II, the actual lesion region is segmented from the enhanced CT images by using deeplabv3 and ResNet-18. In Phase III, segmented images are passed to the stack sparse autoencoder (SSAE) deep learning model having two stack auto-encoders (SAE) with the selected hidden layers. The designed SSAE model is based on both SAE and softmax layers for COVID19 classification. The proposed method is evaluated on actual patient data of Pakistan Ordinance Factories and other public benchmark data sets with different scanners/mediums. The proposed method achieved global segmentation accuracy of 0.96 and 0.97 for classification.
Application of deep learning to identify COVID-19 infection in posteroanterior chest X-rays.
Authors: JenishMaharjan, JacobCalvert, EmilyPellegrini, AbigailGreen-Saxena, JanaHoffman, AndreaMcCoy, QingqingMao, RitankarDas
Journal: Clinical imaging

The objective of this study was to assess seven configurations of six convolutional deep neural network architectures for classification of chest X-rays (CXRs) as COVID-19 positive or negative.
The primary dataset consisted of 294 COVID-19 positive and 294 COVID-19 negative CXRs, the latter comprising roughly equally many pneumonia, emphysema, fibrosis, and healthy images. We used six common convolutional neural network architectures, VGG16, DenseNet121, DenseNet201, MobileNet, NasNetMobile and InceptionV3. We studied six models (one for each architecture) which were pre-trained on a vast repository of generic (non-CXR) images, as well as a seventh DenseNet121 model, which was pre-trained on a repository of CXR images. For each model, we replaced the output layers with custom fully connected layers for the task of binary classification of images as COVID-19 positive or negative. Performance metrics were calculated on a hold-out test set with CXRs from patients who were not included in the training/validation set.
When pre-trained on generic images, the VGG16, DenseNet121, DenseNet201, MobileNet, NasNetMobile, and InceptionV3 architectures respectively produced hold-out test set areas under the receiver operating characteristic (AUROCs) of 0.98, 0.95, 0.97, 0.95, 0.99, and 0.96 for the COVID-19 classification of CXRs. The X-ray pre-trained DenseNet121 model, in comparison, had a test set AUROC of 0.87.
Common convolutional neural network architectures with parameters pre-trained on generic images yield high-performance and well-calibrated COVID-19 CXR classification.
COVID-19 lung infection segmentation with a novel two-stage cross-domain transfer learning framework.
Authors: JiannanLiu, BoDong, ShuaiWang, HuiCui, Deng-PingFan, JiquanMa, GengChen
Journal: Medical image analysis

With the global outbreak of COVID-19 in early 2020, rapid diagnosis of COVID-19 has become the urgent need to control the spread of the epidemic. In clinical settings, lung infection segmentation from computed tomography (CT) images can provide vital information for the quantification and diagnosis of COVID-19. However, accurate infection segmentation is a challenging task due to (i) the low boundary contrast between infections and the surroundings, (ii) large variations of infection regions, and, most importantly, (iii) the shortage of large-scale annotated data. To address these issues, we propose a novel two-stage cross-domain transfer learning framework for the accurate segmentation of COVID-19 lung infections from CT images. Our framework consists of two major technical innovations, including an effective infection segmentation deep learning model, called nCoVSegNet, and a novel two-stage transfer learning strategy. Specifically, our nCoVSegNet conducts effective infection segmentation by taking advantage of attention-aware feature fusion and large receptive fields, aiming to resolve the issues related to low boundary contrast and large infection variations. To alleviate the shortage of the data, the nCoVSegNet is pre-trained using a two-stage cross-domain transfer learning strategy, which makes full use of the knowledge from natural images (i.e., ImageNet) and medical images (i.e., LIDC-IDRI) to boost the final training on CT images with COVID-19 infections. Extensive experiments demonstrate that our framework achieves superior segmentation accuracy and outperforms the cutting-edge models, both quantitatively and qualitatively.
Deep transfer learning for COVID-19 detection and infection localization with superpixel based segmentation.
Authors: N BPrakash, MMurugappan, G RHemalakshmi, MJayalakshmi, MuftiMahmud
Journal: Sustainable cities and society

The evolution the novel corona virus disease (COVID-19) as a pandemic has inflicted several thousand deaths per day endangering the lives of millions of people across the globe. In addition to thermal scanning mechanisms, chest imaging examinations provide valuable insights to the detection of this virus, diagnosis and prognosis of the infections. Though Chest CT and Chest X-ray imaging are common in the clinical protocols of COVID-19 management, the latter is highly preferred, attributed to its simple image acquisition procedure and mobility of the imaging mechanism. However, Chest X-ray images are found to be less sensitive compared to Chest CT images in detecting infections in the early stages. In this paper, we propose a deep learning based framework to enhance the diagnostic values of these images for improved clinical outcomes. It is realized as a variant of the conventional SqueezeNet classifier with segmentation capabilities, which is trained with deep features extracted from the Chest X-ray images of a standard dataset for binary and multi class classification. The binary classifier achieves an accuracy of 99.53% in the discrimination of COVID-19 and Non COVID-19 images. Similarly, the multi class classifier performs classification of COVID-19, Viral Pneumonia and Normal cases with an accuracy of 99.79%. This model called the COVID-19 Super pixel SqueezNet (COVID-SSNet) performs super pixel segmentation of the activation maps to extract the regions of interest which carry perceptual image features and constructs an overlay of the Chest X-ray images with these regions. The proposed classifier model adds significant value to the Chest X-rays for an integral examination of the image features and the image regions influencing the classifier decisions to expedite the COVID-19 treatment regimen.
Exploiting Shared Knowledge From Non-COVID Lesions for Annotation-Efficient COVID-19 CT Lung Infection Segmentation.
Authors: YichiZhang, QingchengLiao, LinYuan, HeZhu, JiezhenXing, JicongZhang
Journal: IEEE journal of biomedical and health informatics

The novel Coronavirus disease (COVID-19) is a highly contagious virus and has spread all over the world, posing an extremely serious threat to all countries. Automatic lung infection segmentation from computed tomography (CT) plays an important role in the quantitative analysis of COVID-19. However, the major challenge lies in the inadequacy of annotated COVID-19 datasets. Currently, there are several public non-COVID lung lesion segmentation datasets, providing the potential for generalizing useful information to the related COVID-19 segmentation task. In this paper, we propose a novel relation-driven collaborative learning model to exploit shared knowledge from non-COVID lesions for annotation-efficient COVID-19 CT lung infection segmentation. The model consists of a general encoder to capture general lung lesion features based on multiple non-COVID lesions, and a target encoder to focus on task-specific features based on COVID-19 infections. We develop a collaborative learning scheme to regularize feature-level relation consistency of given input and encourage the model to learn more general and discriminative representation of COVID-19 infections. Extensive experiments demonstrate that trained with limited COVID-19 data, exploiting shared knowledge from non-COVID lesions can further improve state-of-the-art performance with up to 3.0% in dice similarity coefficient and 4.2% in normalized surface dice. In addition, experimental results on large scale 2D dataset with CT slices show that our method significantly outperforms cutting-edge segmentation methods metrics. Our method promotes new insights into annotation-efficient deep learning and illustrates strong potential for real-world applications in the global fight against COVID-19 in the absence of sufficient high-quality annotations.
An explainable AI system for automated COVID-19 assessment and lesion categorization from CT-scans.
Authors: MatteoPennisi, IsaakKavasidis, ConcettoSpampinato, VincenzoSchinina, SimonePalazzo, Federica ProiettoSalanitri, GiovanniBellitto, FrancescoRundo, MarcoAldinucci, MassimoCristofaro, PaoloCampioni, ElisaPianura, FedericaDi Stefano, AdaPetrone, FabrizioAlbarello, GiuseppeIppolito, SalvatoreCuzzocrea, SabrinaConoci
Journal: Artificial intelligence in medicine

COVID-19 infection caused by SARS-CoV-2 pathogen has been a catastrophic pandemic outbreak all over the world, with exponential increasing of confirmed cases and, unfortunately, deaths. In this work we propose an AI-powered pipeline, based on the deep-learning paradigm, for automated COVID-19 detection and lesion categorization from CT scans. We first propose a new segmentation module aimed at automatically identifying lung parenchyma and lobes. Next, we combine the segmentation network with classification networks for COVID-19 identification and lesion categorization. We compare the model's classification results with those obtained by three expert radiologists on a dataset of 166 CT scans. Results showed a sensitivity of 90.3% and a specificity of 93.5% for COVID-19 detection, at least on par with those yielded by the expert radiologists, and an average lesion categorization accuracy of about 84%. Moreover, a significant role is played by prior lung and lobe segmentation, that allowed us to enhance classification performance by over 6 percent points. The interpretation of the trained AI models reveals that the most significant areas for supporting the decision on COVID-19 identification are consistent with the lesions clinically associated to the virus, i.e., crazy paving, consolidation and ground glass. This means that the artificial models are able to discriminate a positive patient from a negative one (both controls and patients with interstitial pneumonia tested negative to COVID) by evaluating the presence of those lesions into CT scans. Finally, the AI models are integrated into a user-friendly GUI to support AI explainability for radiologists, which is publicly available at http://perceivelab.com/covid-ai. The whole AI system is unique since, to the best of our knowledge, it is the first AI-based software, publicly available, that attempts to explain to radiologists what information is used by AI methods for making decisions and that proactively involves them in the decision loop to further improve the COVID-19 understanding.