pt-sk/ml_research_abs huggingface dataset:
Multi-texture features and optimized DeepNet for COVID-19 detection using chest x-ray images.
Authors: AnandbabuGopatoti, VijayalakshmiP
Journal: Concurrency and computation : practice & experience

The corona virus disease 2019 (COVID-19) pandemic has a severe influence on population health all over the world. Various methods are developed for detecting the COVID-19, but the process of diagnosing this problem from radiology and radiography images is one of the effective procedures for diagnosing the affected patients. Therefore, a robust and effective multi-local texture features (MLTF)-based feature extraction approach and Improved Weed Sea-based DeepNet (IWS-based DeepNet) approach is proposed for detecting the COVID-19 at an earlier stage. The developed IWS-based DeepNet is developed for detecting COVID-19to optimize the structure of the Deep Convolutional Neural Network (Deep CNN). The IWS is devised by incorporating the Improved Invasive Weed Optimization (IIWO) and Sea Lion Optimization (SLnO), respectively. The noises present in the input chest x-ray (CXR) image are discarded using Region of Interest (RoI) extraction by adaptive thresholding technique. For feature extraction, the proposed MLFT is newly developed by considering various texture features for extracting the best features. Finally, the COVID-19 detection is performed using the proposed IWS-based DeepNet. Furthermore, the proposed technique achieved effective performance in terms of True Positive Rate (TPR), True Negative Rate (TNR), and accuracy with the maximum values of 0.933%, 0.890%, and 0.919%.
Computer-aided diagnostic for classifying chest X-ray images using deep ensemble learning.
Authors: LaraVisuña, DandiYang, JavierGarcia-Blas, JesusCarretero
Journal: BMC medical imaging

Nowadays doctors and radiologists are overwhelmed with a huge amount of work. This led to the effort to design different Computer-Aided Diagnosis systems (CAD system), with the aim of accomplishing a faster and more accurate diagnosis. The current development of deep learning is a big opportunity for the development of new CADs. In this paper, we propose a novel architecture for a convolutional neural network (CNN) ensemble for classifying chest X-ray (CRX) images into four classes: viral Pneumonia, Tuberculosis, COVID-19, and Healthy. Although Computed tomography (CT) is the best way to detect and diagnoses pulmonary issues, CT is more expensive than CRX. Furthermore, CRX is commonly the first step in the diagnosis, so it's very important to be accurate in the early stages of diagnosis and treatment.
We applied the transfer learning technique and data augmentation to all CNNs for obtaining better performance. We have designed and evaluated two different CNN-ensembles: Stacking and Voting. This system is ready to be applied in a CAD system to automated diagnosis such a second or previous opinion before the doctors or radiology's. Our results show a great improvement, 99% accuracy of the Stacking Ensemble and 98% of accuracy for the the Voting Ensemble.
To minimize missclassifications, we included six different base CNN models in our architecture (VGG16, VGG19, InceptionV3, ResNet101V2, DenseNet121 and CheXnet) and it could be extended to any number as well as we expect extend the number of diseases to detected. The proposed method has been validated using a large dataset created by mixing several public datasets with different image sizes and quality. As we demonstrate in the evaluation carried out, we reach better results and generalization compared with previous works. In addition, we make a first approach to explainable deep learning with the objective of providing professionals more information that may be valuable when evaluating CRXs.
Deep learning of longitudinal chest X-ray and clinical variables predicts duration on ventilator and mortality in COVID-19 patients.
Authors: HongyiDuanmu, ThomasRen, HaifangLi, NeilMehta, Adam JSinger, Jeffrey MLevsky, Michael LLipton, Tim QDuong
Journal: Biomedical engineering online

To use deep learning of serial portable chest X-ray (pCXR) and clinical variables to predict mortality and duration on invasive mechanical ventilation (IMV) for Coronavirus disease 2019 (COVID-19) patients.
This is a retrospective study. Serial pCXR and serial clinical variables were analyzed for data from day 1, day 5, day 1-3, day 3-5, or day 1-5 on IMV (110 IMV survivors and 76 IMV non-survivors). The outcome variables were duration on IMV and mortality. With fivefold cross-validation, the performance of the proposed deep learning system was evaluated by receiver operating characteristic (ROC) analysis and correlation analysis.
Predictive models using 5-consecutive-day data outperformed those using 3-consecutive-day and 1-day data. Prediction using data closer to the outcome was generally better (i.e., day 5 data performed better than day 1 data, and day 3-5 data performed better than day 1-3 data). Prediction performance was generally better for the combined pCXR and non-imaging clinical data than either alone. The combined pCXR and non-imaging data of 5 consecutive days predicted mortality with an accuracy of 85 ± 3.5% (95% confidence interval (CI)) and an area under the curve (AUC) of 0.87 ± 0.05 (95% CI) and predicted the duration needed to be on IMV to within 2.56 ± 0.21 (95% CI) days on the validation dataset.
Deep learning of longitudinal pCXR and clinical data have the potential to accurately predict mortality and duration on IMV in COVID-19 patients. Longitudinal pCXR could have prognostic value if these findings can be validated in a large, multi-institutional cohort.
A novel abnormality annotation database for COVID-19 affected frontal lung X-rays.
Authors: SurbhiMittal, Vasantha KumarVenugopal, Vikash KumarAgarwal, ManuMalhotra, Jagneet SinghChatha, SavinayKapur, AnkurGupta, VikasBatra, PuspitaMajumdar, AakarshMalhotra, KartikThakral, SahebChhabra, MayankVatsa, RichaSingh, SantanuChaudhury
Journal: PloS one

Consistent clinical observations of characteristic findings of COVID-19 pneumonia on chest X-rays have attracted the research community to strive to provide a fast and reliable method for screening suspected patients. Several machine learning algorithms have been proposed to find the abnormalities in the lungs using chest X-rays specific to COVID-19 pneumonia and distinguish them from other etiologies of pneumonia. However, despite the enormous magnitude of the pandemic, there are very few instances of public databases of COVID-19 pneumonia, and to the best of our knowledge, there is no database with annotation of abnormalities on the chest X-rays of COVID-19 affected patients. Annotated databases of X-rays can be of significant value in the design and development of algorithms for disease prediction. Further, explainability analysis for the performance of existing or new deep learning algorithms will be enhanced significantly with access to ground-truth abnormality annotations. The proposed COVID Abnormality Annotation for X-Rays (CAAXR) database is built upon the BIMCV-COVID19+ database which is a large-scale dataset containing COVID-19+ chest X-rays. The primary contribution of this study is the annotation of the abnormalities in over 1700 frontal chest X-rays. Further, we define protocols for semantic segmentation as well as classification for robust evaluation of algorithms. We provide benchmark results on the defined protocols using popular deep learning models such as DenseNet, ResNet, MobileNet, and VGG for classification, and UNet, SegNet, and Mask-RCNN for semantic segmentation. The classwise accuracy, sensitivity, and AUC-ROC scores are reported for the classification models, and the IoU and DICE scores are reported for the segmentation models.
An Intelligent Sensor Based Decision Support System for Diagnosing Pulmonary Ailment through Standardized Chest X-ray Scans.
Authors: ShivaniBatra, HarshSharma, WadiiBoulila, VaishaliArya, PrakashSrivastava, Mohammad ZubairKhan, MoezKrichen
Journal: Sensors (Basel, Switzerland)

Academics and the health community are paying much attention to developing smart remote patient monitoring, sensors, and healthcare technology. For the analysis of medical scans, various studies integrate sophisticated deep learning strategies. A smart monitoring system is needed as a proactive diagnostic solution that may be employed in an epidemiological scenario such as COVID-19. Consequently, this work offers an intelligent medicare system that is an IoT-empowered, deep learning-based decision support system (DSS) for the automated detection and categorization of infectious diseases (COVID-19 and pneumothorax). The proposed DSS system was evaluated using three independent standard-based chest X-ray scans. The suggested DSS predictor has been used to identify and classify areas on whole X-ray scans with abnormalities thought to be attributable to COVID-19, reaching an identification and classification accuracy rate of 89.58% for normal images and 89.13% for COVID-19 and pneumothorax. With the suggested DSS system, a judgment depending on individual chest X-ray scans may be made in approximately 0.01 s. As a result, the DSS system described in this study can forecast at a pace of 95 frames per second (FPS) for both models, which is near to real-time.
Two-step machine learning to diagnose and predict involvement of lungs in COVID-19 and pneumonia using CT radiomics.
Authors: PegahMoradi Khaniabadi, YassineBouchareb, HumoudAl-Dhuhli, IsaacShiri, FaizaAl-Kindi, BitaMoradi Khaniabadi, HabibZaidi, ArmanRahmim
Journal: Computers in biology and medicine

To develop a two-step machine learning (ML) based model to diagnose and predict involvement of lungs in COVID-19 and non COVID-19 pneumonia patients using CT chest radiomic features.
Three hundred CT scans (3-classes: 100 COVID-19, 100 pneumonia, and 100 healthy subjects) were enrolled in this study. Diagnostic task included 3-class classification. Severity prediction score for COVID-19 and pneumonia was considered as mild (0-25%), moderate (26-50%), and severe (>50%). Whole lungs were segmented utilizing deep learning-based segmentation. Altogether, 107 features including shape, first-order histogram, second and high order texture features were extracted. Pearson correlation coefficient (PCC≥90%) followed by different features selection algorithms were employed. ML-based supervised algorithms (Naïve Bays, Support Vector Machine, Bagging, Random Forest, K-nearest neighbors, Decision Tree and Ensemble Meta voting) were utilized. The optimal model was selected based on precision, recall and area-under-curve (AUC) by randomizing the training/validation, followed by testing using the test set.
Nine pertinent features (2 shape, 1 first-order, and 6 second-order) were obtained after features selection for both phases. In diagnostic task, the performance of 3-class classification using Random Forest was 0.909±0.026, 0.907±0.056, 0.902±0.044, 0.939±0.031, and 0.982±0.010 for precision, recall, F1-score, accuracy, and AUC, respectively. The severity prediction task using Random Forest achieved 0.868±0.123 precision, 0.865±0.121 recall, 0.853±0.139 F1-score, 0.934±0.024 accuracy, and 0.969±0.022 AUC.
The two-phase ML-based model accurately classified COVID-19 and pneumonia patients using CT radiomics, and adequately predicted severity of lungs involvement. This 2-steps model showed great potential in assessing COVID-19 CT images towards improved management of patients.
Development and validation of chest CT-based imaging biomarkers for early stage COVID-19 screening.
Authors: Xiao-PingLiu, XuYang, MiaoXiong, XuanyuMao, XiaoqingJin, ZhiqiangLi, ShuangZhou, HangChang
Journal: Frontiers in public health

Coronavirus Disease 2019 (COVID-19) is currently a global pandemic, and early screening is one of the key factors for COVID-19 control and treatment. Here, we developed and validated chest CT-based imaging biomarkers for COVID-19 patient screening from two independent hospitals with 419 patients. We identified the vasculature-like signals from CT images and found that, compared to healthy and community acquired pneumonia (CAP) patients, COVID-19 patients display a significantly higher abundance of these signals. Furthermore, unsupervised feature learning led to the discovery of clinical-relevant imaging biomarkers from the vasculature-like signals for accurate and sensitive COVID-19 screening that have been double-blindly validated in an independent hospital (sensitivity: 0.941, specificity: 0.920, AUC: 0.971, accuracy 0.931, F1 score: 0.929). Our findings could open a new avenue to assist screening of COVID-19 patients.
RadImageNet: An Open Radiologic Deep Learning Research Dataset for Effective Transfer Learning.
Authors: XueyanMei, ZelongLiu, Philip MRobson, BrettMarinelli, MingqianHuang, AmishDoshi, AdamJacobi, ChendiCao, Katherine ELink, ThomasYang, YingWang, HayitGreenspan, TimothyDeyer, Zahi AFayad, YangYang
Journal: Radiology. Artificial intelligence

To demonstrate the value of pretraining with millions of radiologic images compared with ImageNet photographic images on downstream medical applications when using transfer learning.
This retrospective study included patients who underwent a radiologic study between 2005 and 2020 at an outpatient imaging facility. Key images and associated labels from the studies were retrospectively extracted from the original study interpretation. These images were used for RadImageNet model training with random weight initiation. The RadImageNet models were compared with ImageNet models using the area under the receiver operating characteristic curve (AUC) for eight classification tasks and using Dice scores for two segmentation problems.
The RadImageNet database consists of 1.35 million annotated medical images in 131 872 patients who underwent CT, MRI, and US for musculoskeletal, neurologic, oncologic, gastrointestinal, endocrine, abdominal, and pulmonary pathologic conditions. For transfer learning tasks on small datasets-thyroid nodules (US), breast masses (US), anterior cruciate ligament injuries (MRI), and meniscal tears (MRI)-the RadImageNet models demonstrated a significant advantage (
RadImageNet pretrained models demonstrated better interpretability compared with ImageNet models, especially for smaller radiologic datasets.
Deep learning models for COVID-19 chest x-ray classification: Preventing shortcut learning using feature disentanglement.
Authors: AnusuaTrivedi, CalebRobinson, MarianBlazes, AnthonyOrtiz, JocelynDesbiens, SunilGupta, RahulDodhia, Pavan KBhatraju, W ConradLiles, JayashreeKalpathy-Cramer, Aaron YLee, Juan MLavista Ferres
Journal: PloS one

In response to the COVID-19 global pandemic, recent research has proposed creating deep learning based models that use chest radiographs (CXRs) in a variety of clinical tasks to help manage the crisis. However, the size of existing datasets of CXRs from COVID-19+ patients are relatively small, and researchers often pool CXR data from multiple sources, for example, using different x-ray machines in various patient populations under different clinical scenarios. Deep learning models trained on such datasets have been shown to overfit to erroneous features instead of learning pulmonary characteristics in a phenomenon known as shortcut learning. We propose adding feature disentanglement to the training process. This technique forces the models to identify pulmonary features from the images and penalizes them for learning features that can discriminate between the original datasets that the images come from. We find that models trained in this way indeed have better generalization performance on unseen data; in the best case we found that it improved AUC by 0.13 on held out data. We further find that this outperforms masking out non-lung parts of the CXRs and performing histogram equalization, both of which are recently proposed methods for removing biases in CXR datasets.
Automatic Detection of Cases of COVID-19 Pneumonia from Chest X-ray Images and Deep Learning Approaches.
Authors: FahimaHajjej, SarraAyouni, MalekHasan, TanvirAbir
Journal: Computational intelligence and neuroscience

Machine learning has already been used as a resource for disease detection and health care as a complementary tool to help with various daily health challenges. The advancement of deep learning techniques and a large amount of data-enabled algorithms to outperform medical teams in certain imaging tasks, such as pneumonia detection, skin cancer classification, hemorrhage detection, and arrhythmia detection. Automated diagnostics, which are enabled by images extracted from patient examinations, allow for interesting experiments to be conducted. This research differs from the related studies that were investigated in the experiment. These works are capable of binary categorization into two categories. COVID-Net, for example, was able to identify a positive case of COVID-19 or a healthy person with 93.3% accuracy. Another example is CHeXNet, which has a 95% accuracy rate in detecting cases of pneumonia or a healthy state in a patient. Experiments revealed that the current study was more effective than the previous studies in detecting a greater number of categories and with a higher percentage of accuracy. The results obtained during the model's development were not only viable but also excellent, with an accuracy of nearly 96% when analyzing a chest X-ray with three possible diagnoses in the two experiments conducted.
Biomarkers extracted by fully automated body composition analysis from chest CT correlate with SARS-CoV-2 outcome severity.
Authors: RenéHosch, SimoneKattner, Marc MoritzBerger, ThorstenBrenner, JohannesHaubold, JensKleesiek, SvenKoitka, LennardKroll, AnisaKureishi, NilsFlaschel, FelixNensa
Journal: Scientific reports

The complex process of manual biomarker extraction from body composition analysis (BCA) has far restricted the analysis of SARS-CoV-2 outcomes to small patient cohorts and a limited number of tissue types. We investigate the association of two BCA-based biomarkers with the development of severe SARS-CoV-2 infections for 918 patients (354 female, 564 male) regarding disease severity and mortality (186 deceased). Multiple tissues, such as muscle, bone, or adipose tissue are used and acquired with a deep-learning-based, fully-automated BCA from computed tomography images of the chest. The BCA features and markers were univariately analyzed with a Shapiro-Wilk and two-sided Mann-Whitney-U test. In a multivariate approach, obtained markers were adjusted by a defined set of laboratory parameters promoted by other studies. Subsequently, the relationship between the markers and two endpoints, namely severity and mortality, was investigated with regard to statistical significance. The univariate approach showed that the muscle volume was significant for female (p
AI in Health Science: A Perspective.
Authors: RaghavMishra, KajalChaudhary, IshaMishra
Journal: Current pharmaceutical biotechnology

By helping practitioners understand complicated and varied types of data, Artificial Intelligence (AI) has influenced medical practice deeply. It is the use of a computer to mimic intelligent behaviour. Many medical professions, particularly those reliant on imaging or surgery, are progressively developing AI. While AI cognitive component outperforms human intellect, it lacks awareness, emotions, intuition, and adaptability. With minimum human participation, AI is quickly growing in healthcare, and numerous AI applications have been created to address current issues. This article explains AI, its various elements and how to utilize them in healthcare. It also offers practical suggestions for developing an AI strategy to assist the digital healthcare transition.
COVID-19 Semantic Pneumonia Segmentation and Classification Using Artificial Intelligence.
Authors: Mohammed JAbdulaal, Ibrahim MMehedi, Abdullah MAbusorrah, Abdulah JezaAljohani, Ahmad HMilyani, Md MasudRana, MohamedMahmoud
Journal: Contrast media & molecular imaging

Coronavirus 2019 (COVID-19) has become a pandemic. The seriousness of COVID-19 can be realized from the number of victims worldwide and large number of deaths. This paper presents an efficient deep semantic segmentation network (DeepLabv3Plus). Initially, the dynamic adaptive histogram equalization is utilized to enhance the images. Data augmentation techniques are then used to augment the enhanced images. The second stage builds a custom convolutional neural network model using several pretrained ImageNet models and compares them to repeatedly trim the best-performing models to reduce complexity and improve memory efficiency. Several experiments were done using different techniques and parameters. Furthermore, the proposed model achieved an average accuracy of 99.6% and an area under the curve of 0.996 in the COVID-19 detection. This paper will discuss how to train a customized smart convolutional neural network using various parameters on a set of chest X-rays with an accuracy of 99.6%.
A novel multimodal fusion framework for early diagnosis and accurate classification of COVID-19 patients using X-ray images and speech signal processing techniques.
Authors: SantoshKumar, Mithilesh KumarChaube, Saeed HamoodAlsamhi, Sachin KumarGupta, MohsenGuizani, RaffaeleGravina, GiancarloFortino
Journal: Computer methods and programs in biomedicine

COVID-19 outbreak has become one of the most challenging problems for human being. It is a communicable disease caused by a new coronavirus strain, which infected over 375 million people already and caused almost 6 million deaths. This paper aims to develop and design a framework for early diagnosis and fast classification of COVID-19 symptoms using multimodal Deep Learning techniques.
we collected chest X-ray and cough sample data from open source datasets, Cohen and datasets and local hospitals. The features are extracted from the chest X-ray images are extracted from chest X-ray datasets. We also used cough audio datasets from Coswara project and local hospitals. The publicly available Coughvid DetectNow and Virufy datasets are used to evaluate COVID-19 detection based on speech sounds, respiratory, and cough. The collected audio data comprises slow and fast breathing, shallow and deep coughing, spoken digits, and phonation of sustained vowels. Gender, geographical location, age, preexisting medical conditions, and current health status (COVID-19 and Non-COVID-19) are recorded.
The proposed framework uses the selection algorithm of the pre-trained network to determine the best fusion model characterized by the pre-trained chest X-ray and cough models. Third, deep chest X-ray fusion by discriminant correlation analysis is used to fuse discriminatory features from the two models. The proposed framework achieved recognition accuracy, specificity, and sensitivity of 98.91%, 96.25%, and 97.69%, respectively. With the fusion method we obtained 94.99% accuracy.
This paper examines the effectiveness of well-known ML architectures on a joint collection of chest-X-rays and cough samples for early classification of COVID-19. It shows that existing methods can effectively used for diagnosis and suggesting that the fusion learning paradigm could be a crucial asset in diagnosing future unknown illnesses. The proposed framework supports health informatics basis on early diagnosis, clinical decision support, and accurate prediction.