pt-sk/ml_research_abs huggingface dataset:
Automatic scoring of COVID-19 severity in X-ray imaging based on a novel deep learning workflow.
Authors: Viacheslav VDanilov, DianaLitmanovich, AlexProutski, AlexanderKirpich, DatoNefaridze, AlexKarpovsky, YuriyGankin
Journal: Scientific reports

In this study, we propose a two-stage workflow used for the segmentation and scoring of lung diseases. The workflow inherits quantification, qualification, and visual assessment of lung diseases on X-ray images estimated by radiologists and clinicians. It requires the fulfillment of two core stages devoted to lung and disease segmentation as well as an additional post-processing stage devoted to scoring. The latter integrated block is utilized, mainly, for the estimation of segment scores and computes the overall severity score of a patient. The models of the proposed workflow were trained and tested on four publicly available X-ray datasets of COVID-19 patients and two X-ray datasets of patients with no pulmonary pathology. Based on a combined dataset consisting of 580 COVID-19 patients and 784 patients with no disorders, our best-performing algorithm is based on a combination of DeepLabV3 + , for lung segmentation, and MA-Net, for disease segmentation. The proposed algorithms' mean absolute error (MAE) of 0.30 is significantly reduced in comparison to established COVID-19 algorithms; BS-net and COVID-Net-S, possessing MAEs of 2.52 and 1.83 respectively. Moreover, the proposed two-stage workflow was not only more accurate but also computationally efficient, it was approximately 11 times faster than the mentioned methods. In summary, we proposed an accurate, time-efficient, and versatile approach for segmentation and scoring of lung diseases illustrated for COVID-19 and with broader future applications for pneumonia, tuberculosis, pneumothorax, amongst others.
Mortality Prediction Analysis among COVID-19 Inpatients Using Clinical Variables and Deep Learning Chest Radiography Imaging Features.
Authors: Xuan VNguyen, EnginDikici, SemaCandemir, Robyn LBall, Luciano MPrevedello
Journal: Tomography (Ann Arbor, Mich.)

The emergence of the COVID-19 pandemic over a relatively brief interval illustrates the need for rapid data-driven approaches to facilitate clinical decision making. We examined a machine learning process to predict inpatient mortality among COVID-19 patients using clinical and chest radiographic data. Modeling was performed with a de-identified dataset of encounters prior to widespread vaccine availability. Non-imaging predictors included demographics, pre-admission clinical history, and past medical history variables. Imaging features were extracted from chest radiographs by applying a deep convolutional neural network with transfer learning. A multi-layer perceptron combining 64 deep learning features from chest radiographs with 98 patient clinical features was trained to predict mortality. The Local Interpretable Model-Agnostic Explanations (LIME) method was used to explain model predictions. Non-imaging data alone predicted mortality with an ROC-AUC of 0.87 ± 0.03 (mean ± SD), while the addition of imaging data improved prediction slightly (ROC-AUC: 0.91 ± 0.02). The application of LIME to the combined imaging and clinical model found HbA1c values to contribute the most to model prediction (17.1 ± 1.7%), while imaging contributed 8.8 ± 2.8%. Age, gender, and BMI contributed 8.7%, 8.2%, and 7.1%, respectively. Our findings demonstrate a viable explainable AI approach to quantify the contributions of imaging and clinical data to COVID mortality predictions.
Federated Learning Approach with Pre-Trained Deep Learning Models for COVID-19 Detection from Unsegmented CT images.
Authors: Lucian MihaiFlorescu, Costin TeodorStreba, Mircea-SebastianŞerbănescu, MădălinMămuleanu, Dan NicolaeFlorescu, Rossy VlăduţTeică, Raluca ElenaNica, Ioana AndreeaGheonea
Journal: Life (Basel, Switzerland)

(1) Background: Coronavirus disease 2019 (COVID-19) is an infectious disease caused by SARS-CoV-2. Reverse transcription polymerase chain reaction (RT-PCR) remains the current gold standard for detecting SARS-CoV-2 infections in nasopharyngeal swabs. In Romania, the first reported patient to have contracted COVID-19 was officially declared on 26 February 2020. (2) Methods: This study proposes a federated learning approach with pre-trained deep learning models for COVID-19 detection. Three clients were locally deployed with their own dataset. The goal of the clients was to collaborate in order to obtain a global model without sharing samples from the dataset. The algorithm we developed was connected to our internal picture archiving and communication system and, after running backwards, it encountered chest CT changes suggestive for COVID-19 in a patient investigated in our medical imaging department on the 28 January 2020. (4) Conclusions: Based on our results, we recommend using an automated AI-assisted software in order to detect COVID-19 based on the lung imaging changes as an adjuvant diagnostic method to the current gold standard (RT-PCR) in order to greatly enhance the management of these patients and also limit the spread of the disease, not only to the general population but also to healthcare professionals.
Bag of Tricks for Improving Deep Learning Performance on Multimodal Image Classification.
Authors: Steve AAdeshina, Adeyinka PAdedigba
Journal: Bioengineering (Basel, Switzerland)

A comprehensive medical image-based diagnosis is usually performed across various image modalities before passing a final decision; hence, designing a deep learning model that can use any medical image modality to diagnose a particular disease is of great interest. The available methods are multi-staged, with many computational bottlenecks in between. This paper presents an improved end-to-end method of multimodal image classification using deep learning models. We present top research methods developed over the years to improve models trained from scratch and transfer learning approaches. We show that when fully trained, a model can first implicitly discriminate the imaging modality and then diagnose the relevant disease. Our developed models were applied to COVID-19 classification from chest X-ray, CT scan, and lung ultrasound image modalities. The model that achieved the highest accuracy correctly maps all input images to their respective modality, then classifies the disease achieving overall 91.07% accuracy.
A Novel Deep Learning and Ensemble Learning Mechanism for Delta-Type COVID-19 Detection.
Authors: Habib UllahKhan, SulaimanKhan, ShahNazir
Journal: Frontiers in public health

Recently, the novel coronavirus disease 2019 (COVID-19) has posed many challenges to the research community by presenting grievous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that results in a huge number of mortalities and high morbidities worldwide. Furthermore, the symptoms-based variations in virus type add new challenges for the research and practitioners to combat. COVID-19-infected patients comprise trenchant radiographic visual features, including dry cough, fever, dyspnea, fatigue, etc. Chest X-ray is considered a simple and non-invasive clinical adjutant that performs a key role in the identification of these ocular responses related to COVID-19 infection. Nevertheless, the defined availability of proficient radiologists to understand the X-ray images and the elusive aspects of disease radiographic replies to remnant the biggest bottlenecks in manual diagnosis. To address these issues, the proposed research study presents a hybrid deep learning model for the accurate diagnosing of Delta-type COVID-19 infection using X-ray images. This hybrid model comprises visual geometry group 16 (VGG16) and a support vector machine (SVM), where the VGG16 is accustomed to the identification process, while the SVM is used for the severity-based analysis of the infected people. An overall accuracy rate of 97.37% is recorded for the assumed model. Other performance metrics such as the area under the curve (AUC), precision, F-score, misclassification rate, and confusion matrix are used for validation and analysis purposes. Finally, the applicability of the presumed model is assimilated with other relevant techniques. The high identification rates shine the applicability of the formulated hybrid model in the targeted research domain.
A Deep Learning and Handcrafted Based Computationally Intelligent Technique for Effective COVID-19 Detection from X-ray/CT-scan Imaging.
Authors: MohammedHabib, MuhammadRamzan, Sajid AliKhan
Journal: Journal of grid computing

The world has witnessed dramatic changes because of the advent of COVID19 in the last few days of 2019. During the last more than two years, COVID-19 has badly affected the world in diverse ways. It has not only affected human health and mortality rate but also the economic condition on a global scale. There is an urgent need today to cope with this pandemic and its diverse effects. Medical imaging has revolutionized the treatment of various diseases during the last four decades. Automated detection and classification systems have proven to be of great assistance to the doctors and scientific community for the treatment of various diseases. In this paper, a novel framework for an efficient COVID-19 classification system is proposed which uses the hybrid feature extraction approach. After preprocessing image data, two types of features i.e., deep learning and handcrafted, are extracted. For Deep learning features, two pre-trained models namely ResNet101 and DenseNet201 are used. Handcrafted features are extracted using Weber Local Descriptor (WLD). The Excitation component of WLD is utilized and features are reduced using DCT. Features are extracted from both models, handcrafted features are fused, and significant features are selected using entropy. Experiments have proven the effectiveness of the proposed model. A comprehensive set of experiments have been performed and results are compared with the existing well-known methods. The proposed technique has performed better in terms of accuracy and time.
An efficient deep learning-based framework for tuberculosis detection using chest X-ray images.
Authors: AhmedIqbal, MuhammadUsman, ZohairAhmed
Journal: Tuberculosis (Edinburgh, Scotland)

Early diagnosis of tuberculosis (TB) is an essential and challenging task to prevent disease, decrease mortality risk, and stop transmission to other people. The chest X-ray (CXR) is the top choice for lung disease screening in clinics because it is cost-effective and easily accessible in most countries. However, manual screening of CXR images is a heavy burden for radiologists, resulting in a high rate of inter-observer variances. Hence, proposing a cost-effective and accurate computer aided diagnosis (CAD) system for TB diagnosis is challenging for researchers. In this research, we proposed an efficient and straightforward deep learning network called TBXNet, which can accurately classify a large number of TB CXR images. The network is based on five dual convolutions blocks with varying filter sizes of 32, 64, 128, 256 and 512, respectively. The dual convolution blocks are fused with a pre-trained layer in the fusion layer of the network. In addition, the pre-trained layer is utilized for transferring pre-trained knowledge into the fusion layer. The proposed TBXNet has achieved an accuracy of 98.98%, and 99.17% on Dataset A and Dataset B, respectively. Furthermore, the generalizability of the proposed work is validated against Dataset C, which is based on normal, tuberculous, pneumonia, and COVID-19 CXR images. The TBXNet has obtained the highest results in Precision (95.67%), Recall (95.10%), F1-score (95.38%), and Accuracy (95.10%), which is comparatively better than all other state-of-the-art methods.
Multi-population generalizability of a deep learning-based chest radiograph severity score for COVID-19.
Authors: Matthew DLi, Nishanth TArun, MehakAggarwal, SharutGupta, PraveerSingh, Brent PLittle, Dexter PMendoza, Gustavo C ACorradi, Marcelo STakahashi, Suely FFerraciolli, Marc DSucci, MinLang, Bernardo CBizzo, IttaiDayan, Felipe CKitamura, JayashreeKalpathy-Cramer
Journal: Medicine

To tune and test the generalizability of a deep learning-based model for assessment of COVID-19 lung disease severity on chest radiographs (CXRs) from different patient populations. A published convolutional Siamese neural network-based model previously trained on hospitalized patients with COVID-19 was tuned using 250 outpatient CXRs. This model produces a quantitative measure of COVID-19 lung disease severity (pulmonary x-ray severity (PXS) score). The model was evaluated on CXRs from 4 test sets, including 3 from the United States (patients hospitalized at an academic medical center (N = 154), patients hospitalized at a community hospital (N = 113), and outpatients (N = 108)) and 1 from Brazil (patients at an academic medical center emergency department (N = 303)). Radiologists from both countries independently assigned reference standard CXR severity scores, which were correlated with the PXS scores as a measure of model performance (Pearson R). The Uniform Manifold Approximation and Projection (UMAP) technique was used to visualize the neural network results. Tuning the deep learning model with outpatient data showed high model performance in 2 United States hospitalized patient datasets (R = 0.88 and R = 0.90, compared to baseline R = 0.86). Model performance was similar, though slightly lower, when tested on the United States outpatient and Brazil emergency department datasets (R = 0.86 and R = 0.85, respectively). UMAP showed that the model learned disease severity information that generalized across test sets. A deep learning model that extracts a COVID-19 severity score on CXRs showed generalizable performance across multiple populations from 2 continents, including outpatients and hospitalized patients.
Ftl-CoV19: A Transfer Learning Approach to Detect COVID-19.
Authors: TarishiSingh, PraneetSaurabh, DhananjayBisen, LalitKane, MayankPathak, G RSinha
Journal: Computational intelligence and neuroscience

COVID-19 is an infectious and contagious disease caused by the new coronavirus. The total number of cases is over 19 million and continues to grow. A common symptom noticed among COVID-19 patients is lung infection that results in breathlessness, and the lack of essential resources such as testing, oxygen, and ventilators enhances its severity. Chest X-ray can be used to design and develop a COVID-19 detection mechanism for a quicker diagnosis using AI and machine learning techniques. Due to this silver lining, various new COVID-19 detection techniques and prediction models have been introduced in recent times based on chest radiography images. However, due to a high level of unpredictability and the absence of essential data, standard models have showcased low efficiency and also suffer from overheads and complexities. This paper proposes a model fine tuning transfer learning-coronavirus 19 (Ftl-CoV19) for COVID-19 detection through chest X-rays, which embraces the ideas of transfer learning in pretrained VGG16 model with including combination of convolution, max pooling, and dense layer at different stages of model. Ftl-CoV19 reported promising experimental results; it observed training and validation accuracy of 98.82% and 99.27% with precision of 100%, recall of 98%, and F1 score of 99%. These results outperformed other conventional state of arts such as CNN, ResNet50, InceptionV3, and Xception.
Automated diagnosis and prognosis of COVID-19 pneumonia from initial ER chest X-rays using deep learning.
Authors: Jordan HChamberlin, GilbertoAquino, SophiaNance, AndrewWortham, NathanLeaphart, NamrataPaladugu, SeanBrady, HenryBaird, MatthewFiegel, LoganFitzpatrick, MadisonKocher, FlorinGhesu, AwaisMansoor, PhilippHoelzer, MathisZimmermann, W EnnisJames, D JamesonDennis, Brian AHouston, Ismail MKabakus, DhirajBaruah, U JosephSchoepf, Jeremy RBurt
Journal: BMC infectious diseases

Airspace disease as seen on chest X-rays is an important point in triage for patients initially presenting to the emergency department with suspected COVID-19 infection. The purpose of this study is to evaluate a previously trained interpretable deep learning algorithm for the diagnosis and prognosis of COVID-19 pneumonia from chest X-rays obtained in the ED.
This retrospective study included 2456 (50% RT-PCR positive for COVID-19) adult patients who received both a chest X-ray and SARS-CoV-2 RT-PCR test from January 2020 to March of 2021 in the emergency department at a single U.S.
A total of 2000 patients were included as an additional training cohort and 456 patients in the randomized internal holdout testing cohort for a previously trained Siemens AI-Radiology Companion deep learning convolutional neural network algorithm. Three cardiothoracic fellowship-trained radiologists systematically evaluated each chest X-ray and generated an airspace disease area-based severity score which was compared against the same score produced by artificial intelligence. The interobserver agreement, diagnostic accuracy, and predictive capability for inpatient outcomes were assessed. Principal statistical tests used in this study include both univariate and multivariate logistic regression.
Overall ICC was 0.820 (95% CI 0.790-0.840). The diagnostic AUC for SARS-CoV-2 RT-PCR positivity was 0.890 (95% CI 0.861-0.920) for the neural network and 0.936 (95% CI 0.918-0.960) for radiologists. Airspace opacities score by AI alone predicted ICU admission (AUC = 0.870) and mortality (0.829) in all patients. Addition of age and BMI into a multivariate log model improved mortality prediction (AUC = 0.906).
The deep learning algorithm provides an accurate and interpretable assessment of the disease burden in COVID-19 pneumonia on chest radiographs. The reported severity scores correlate with expert assessment and accurately predicts important clinical outcomes. The algorithm contributes additional prognostic information not currently incorporated into patient management.
Simplified Transfer Learning for Chest Radiography Models Using Less Data.
Authors: Andrew BSellergren, ChristinaChen, ZaidNabulsi, YuanzhenLi, AaronMaschinot, AaronSarna, JennyHuang, CharlesLau, Sreenivasa RajuKalidindi, MozziyarEtemadi, FlorenciaGarcia-Vicente, DavidMelnick, YunLiu, KrishEswaran, DanielTse, NeeralBeladia, DilipKrishnan, ShravyaShetty
Journal: Radiology

Background Developing deep learning models for radiology requires large data sets and substantial computational resources. Data set size limitations can be further exacerbated by distribution shifts, such as rapid changes in patient populations and standard of care during the COVID-19 pandemic. A common partial mitigation is transfer learning by pretraining a "generic network" on a large nonmedical data set and then fine-tuning on a task-specific radiology data set. Purpose To reduce data set size requirements for chest radiography deep learning models by using an advanced machine learning approach (supervised contrastive [SupCon] learning) to generate chest radiography networks. Materials and Methods SupCon helped generate chest radiography networks from 821 544 chest radiographs from India and the United States. The chest radiography networks were used as a starting point for further machine learning model development for 10 prediction tasks (eg, airspace opacity, fracture, tuberculosis, and COVID-19 outcomes) by using five data sets comprising 684 955 chest radiographs from India, the United States, and China. Three model development setups were tested (linear classifier, nonlinear classifier, and fine-tuning the full network) with different data set sizes from eight to 8
COVID-19 Classification from Chest X-Ray Images: A Framework of Deep Explainable Artificial Intelligence.
Authors: Muhammad AttiqueKhan, MariumAzhar, KainatIbrar, AbdullahAlqahtani, ShtwaiAlsubai, AdelBinbusayyis, Ye JinKim, ByoungcholChang
Journal: Computational intelligence and neuroscience

COVID-19 detection and classification using chest X-ray images is a current hot research topic based on the important application known as medical image analysis. To halt the spread of COVID-19, it is critical to identify the infection as soon as possible. Due to time constraints and the expertise of radiologists, manually diagnosing this infection from chest X-ray images is a difficult and time-consuming process. Artificial intelligence techniques have had a significant impact on medical image analysis and have also introduced several techniques for COVID-19 diagnosis. Deep learning and explainable AI have shown significant popularity among AL techniques for COVID-19 detection and classification. In this work, we propose a deep learning and explainable AI technique for the diagnosis and classification of COVID-19 using chest X-ray images. Initially, a hybrid contrast enhancement technique is proposed and applied to the original images that are later utilized for the training of two modified deep learning models. The deep transfer learning concept is selected for the training of pretrained modified models that are later employed for feature extraction. Features of both deep models are fused using improved canonical correlation analysis that is further optimized using a hybrid algorithm named Whale-Elephant Herding. Through this algorithm, the best features are selected and classified using an extreme learning machine (ELM). Moreover, the modified deep models are utilized for Grad-CAM visualization. The experimental process was conducted on three publicly available datasets and achieved accuracies of 99.1, 98.2, and 96.7%, respectively. Moreover, the ablation study was performed and showed that the proposed accuracy is better than the other methods.
A Deep Learning Approach to Identify Chest Computed Tomography Features for Prediction of SARS-CoV-2 Infection Outcomes.
Authors: AmirhosseinSahebkar, MitraAbbasifard, SamiraChaibakhsh, Paul CGuest, Mohamad AminPourhoseingholi, AmirVahedian-Azimi, PrashantKesharwani, TannazJamialahmadi
Journal: Methods in molecular biology (Clifton, N.J.)

There is still an urgent need to develop effective treatments to help minimize the cases of severe COVID-19. A number of tools have now been developed and applied to address these issues, such as the use of non-contrast chest computed tomography (CT) for evaluation and grading of the associated lung damage. Here we used a deep learning approach for predicting the outcome of 1078 patients admitted into the Baqiyatallah Hospital in Tehran, Iran, suffering from COVID-19 infections in the first wave of the pandemic. These were classified into two groups of non-severe and severe cases according to features on their CT scans with accuracies of approximately 0.90. We suggest that incorporation of molecular and/or clinical features, such as multiplex immunoassay or laboratory findings, will increase accuracy and sensitivity of the model for COVID-19 -related predictions.