pt-sk/ml_research_abs huggingface dataset:
Automated processing of social media content for radiologists: applied deep learning to radiological content on twitter during COVID-19 pandemic.
Authors: ShikharKhurana, RohanChopra, BhartiKhurana
Journal: Emergency radiology

The purpose of this study was to develop an automated process to analyze multimedia content on Twitter during the COVID-19 outbreak and classify content for radiological significance using deep learning (DL).
Using Twitter search features, all tweets containing keywords from both "radiology" and "COVID-19" were collected for the period January 01, 2020 up to April 24, 2020. The resulting dataset comprised of 8354 tweets. Images were classified as (i) images with text (ii) radiological content (e.g., CT scan snapshots, X-ray images), and (iii) non-medical content like personal images or memes. We trained our deep learning model using Convolutional Neural Networks (CNN) on training dataset of 1040 labeled images drawn from all three classes. We then trained another DL classifier for segmenting images into categories based on human anatomy. All software used is open-source and adapted for this research. The diagnostic performance of the algorithm was assessed by comparing results on a test set of 1885 images.
Our analysis shows that in COVID-19 related tweets on radiology, nearly 32% had textual images, another 24% had radiological content, and 44% were not of radiological significance. Our results indicated a 92% accuracy in classifying images originally labeled as chest X-ray or chest CT and a nearly 99% accurate classification of images containing medically relevant text. With larger training dataset and algorithmic tweaks, the accuracy can be further improved.
Applying DL on rich textual images and other metadata in tweets we can process and classify content for radiological significance in real time.
COVID-19 diagnosis from chest X-ray images using transfer learning: Enhanced performance by debiasing dataloader.
Authors: ÇağínPolat, OnurKaraman, CerenKaraman, GüneyKorkmaz, Mehmet CanBalcı, Sevim ErcanKelek
Journal: Journal of X-ray science and technology

Chest X-ray imaging has been proved as a powerful diagnostic method to detect and diagnose COVID-19 cases due to its easy accessibility, lower cost and rapid imaging time.
This study aims to improve efficacy of screening COVID-19 infected patients using chest X-ray images with the help of a developed deep convolutional neural network model (CNN) entitled nCoV-NET.
To train and to evaluate the performance of the developed model, three datasets were collected from resources of "ChestX-ray14", "COVID-19 image data collection", and "Chest X-ray collection from Indiana University," respectively. Overall, 299 COVID-19 pneumonia cases and 1,522 non-COVID 19 cases are involved in this study. To overcome the probable bias due to the unbalanced cases in two classes of the datasets, ResNet, DenseNet, and VGG architectures were re-trained in the fine-tuning stage of the process to distinguish COVID-19 classes using a transfer learning method. Lastly, the optimized final nCoV-NET model was applied to the testing dataset to verify the performance of the proposed model.
Although the performance parameters of all re-trained architectures were determined close to each other, the final nCOV-NET model optimized by using DenseNet-161 architecture in the transfer learning stage exhibits the highest performance for classification of COVID-19 cases with the accuracy of 97.1 %. The Activation Mapping method was used to create activation maps that highlights the crucial areas of the radiograph to improve causality and intelligibility.
This study demonstrated that the proposed CNN model called nCoV-NET can be utilized for reliably detecting COVID-19 cases using chest X-ray images to accelerate the triaging and save critical time for disease control as well as assisting the radiologist to validate their initial diagnosis.
Deep Learning Models for Predicting Severe Progression in COVID-19-Infected Patients: Retrospective Study.
Authors: Thao ThiHo, JongminPark, TaewooKim, ByunggeonPark, JaeheeLee, Jin YoungKim, Ki BeomKim, SooyoungChoi, Young HwanKim, Jae-KwangLim, SanghunChoi
Journal: JMIR medical informatics

Many COVID-19 patients rapidly progress to respiratory failure with a broad range of severities. Identification of high-risk cases is critical for early intervention.
The aim of this study is to develop deep learning models that can rapidly identify high-risk COVID-19 patients based on computed tomography (CT) images and clinical data.
We analyzed 297 COVID-19 patients from five hospitals in Daegu, South Korea. A mixed artificial convolutional neural network (ACNN) model, combining an artificial neural network for clinical data and a convolutional neural network for 3D CT imaging data, was developed to classify these cases as either high risk of severe progression (ie, event) or low risk (ie, event-free).
Using the mixed ACNN model, we were able to obtain high classification performance using novel coronavirus pneumonia lesion images (ie, 93.9% accuracy, 80.8% sensitivity, 96.9% specificity, and 0.916 area under the curve [AUC] score) and lung segmentation images (ie, 94.3% accuracy, 74.7% sensitivity, 95.9% specificity, and 0.928 AUC score) for event versus event-free groups.
Our study successfully differentiated high-risk cases among COVID-19 patients using imaging and clinical features. The developed model can be used as a predictive tool for interventions in aggressive therapies.
Multi-window back-projection residual networks for reconstructing COVID-19 CT super-resolution images.
Authors: DefuQiu, YuhuCheng, XuesongWang, XiaoqiangZhang
Journal: Computer methods and programs in biomedicine

With the increasing problem of coronavirus disease 2019 (COVID-19) in the world, improving the image resolution of COVID-19 computed tomography (CT) becomes a very important task. At present, single-image super-resolution (SISR) models based on convolutional neural networks (CNN) generally have problems such as the loss of high-frequency information and the large size of the model due to the deep network structure.
In this work, we propose an optimization model based on multi-window back-projection residual network (MWSR), which outperforms most of the state-of-the-art methods. Firstly, we use multi-window to refine the same feature map at the same time to obtain richer high/low frequency information, and fuse and filter out the features needed by the deep network. Then, we develop a back-projection network based on the dilated convolution, using up-projection and down-projection modules to extract image features. Finally, we merge several repeated and continuous residual modules with global features, merge the information flow through the network, and input them to the reconstruction module.
The proposed method shows the superiority over the state-of-the-art methods on the benchmark dataset, and generates clear COVID-19 CT super-resolution images.
Both subjective visual effects and objective evaluation indicators are improved, and the model specifications are optimized. Therefore, the MWSR method can improve the clarity of CT images of COVID-19 and effectively assist the diagnosis and quantitative assessment of COVID-19.
Distant Domain Transfer Learning for Medical Imaging.
Authors: ShutengNiu, MerylLiu, YongxinLiu, JianWang, HoubingSong
Journal: IEEE journal of biomedical and health informatics

Medical image processing is one of the most important topics in the Internet of Medical Things (IoMT). Recently, deep learning methods have carried out state-of-the-art performances on medical imaging tasks. In this paper, we propose a novel transfer learning framework for medical image classification. Moreover, we apply our method COVID-19 diagnosis with lung Computed Tomography (CT) images. However, well-labeled training data sets cannot be easily accessed due to the disease's novelty and privacy policies. The proposed method has two components: reduced-size Unet Segmentation model and Distant Feature Fusion (DFF) classification model. This study is related to a not well-investigated but important transfer learning problem, termed Distant Domain Transfer Learning (DDTL). In this study, we develop a DDTL model for COVID-19 diagnosis using unlabeled Office-31, Caltech-256, and chest X-ray image data sets as the source data, and a small set of labeled COVID-19 lung CT as the target data. The main contributions of this study are: 1) the proposed method benefits from unlabeled data in distant domains which can be easily accessed, 2) it can effectively handle the distribution shift between the training data and the testing data, 3) it has achieved 96% classification accuracy, which is 13% higher classification accuracy than "non-transfer" algorithms, and 8% higher than existing transfer and distant transfer algorithms.
Explainable COVID-19 Detection Using Chest CT Scans and Deep Learning.
Authors: HammamAlshazly, ChristophLinse, ErhardtBarth, ThomasMartinetz
Journal: Sensors (Basel, Switzerland)

This paper explores how well deep learning models trained on chest CT images can diagnose COVID-19 infected people in a fast and automated process. To this end, we adopted advanced deep network architectures and proposed a transfer learning strategy using custom-sized input tailored for each deep architecture to achieve the best performance. We conducted extensive sets of experiments on two CT image datasets, namely, the SARS-CoV-2 CT-scan and the COVID19-CT. The results show superior performances for our models compared with previous studies. Our best models achieved average accuracy, precision, sensitivity, specificity, and F1-score values of 99.4%, 99.6%, 99.8%, 99.6%, and 99.4% on the SARS-CoV-2 dataset, and 92.9%, 91.3%, 93.7%, 92.2%, and 92.5% on the COVID19-CT dataset, respectively. For better interpretability of the results, we applied visualization techniques to provide visual explanations for the models' predictions. Feature visualizations of the learned features show well-separated clusters representing CT images of COVID-19 and non-COVID-19 cases. Moreover, the visualizations indicate that our models are not only capable of identifying COVID-19 cases but also provide accurate localization of the COVID-19-associated regions, as indicated by well-trained radiologists.
An Efficient Method for Coronavirus Detection Through X-rays Using Deep Neural Network.
Authors: P SrinivasaRao, PradeepBheemavarapu, P S LathaKalyampudi, T V MadhusudhanaRao
Journal: Current medical imaging

Coronavirus (COVID-19) is a group of infectious diseases caused by related viruses called coronaviruses. In humans, the seriousness of infection caused by a coronavirus in the respiratory tract can vary from mild to lethal. A serious illness can be developed in old people and those with underlying medical problems like diabetes, cardiovascular disease, cancer, and chronic respiratory disease. For the diagnosis of coronavirus disease, due to the growing number of cases, a limited number of test kits for COVID-19 are available in the hospitals. Hence, it is important to implement an automated system as an immediate alternative diagnostic option to pause the spread of COVID-19 in the population.
This paper proposes a deep learning model for the classification of coronavirus infected patient detection using chest X-ray radiographs.
A fully connected convolutional neural network model is developed to classify healthy and diseased X-ray radiographs. The proposed neural network model consists of seven convolutional layers with the rectified linear unit, softmax (last layer) activation functions, and max-pooling layers which were trained using the publicly available COVID-19 dataset.
For validation of the proposed model, the publicly available chest X-ray radiograph dataset consisting of COVID-19 and normal patient's images were used. Considering the performance of the results that are evaluated based on various evaluation metrics such as precision, recall, MSE, RMSE and accuracy, it is seen that the accuracy of the proposed CNN model is 98.07%.
Diabetic Retinopathy Screening Using Artificial Intelligence and Handheld Smartphone-Based Retinal Camera.
Authors: Fernando KornMalerbi, Rafael ErnaneAndrade, Paulo HenriqueMorales, José AugustoStuchi, DiegoLencione, Jean Vitorde Paulo, Mayana PereiraCarvalho, Fabrícia SilvaNunes, Roseanne MontargilRocha, Daniel AFerraz, RubensBelfort
Journal: Journal of diabetes science and technology

Portable retinal cameras and deep learning (DL) algorithms are novel tools adopted by diabetic retinopathy (DR) screening programs. Our objective is to evaluate the diagnostic accuracy of a DL algorithm and the performance of portable handheld retinal cameras in the detection of DR in a large and heterogenous type 2 diabetes population in a real-world, high burden setting.
Participants underwent fundus photographs of both eyes with a portable retinal camera (Phelcom Eyer). Classification of DR was performed by human reading and a DL algorithm (PhelcomNet), consisting of a convolutional neural network trained on a dataset of fundus images captured exclusively with the portable device; both methods were compared. We calculated the area under the curve (AUC), sensitivity, and specificity for more than mild DR.
A total of 824 individuals with type 2 diabetes were enrolled at Itabuna Diabetes Campaign, a subset of 679 (82.4%) of whom could be fully assessed. The algorithm sensitivity/specificity was 97.8 % (95% CI 96.7-98.9)/61.4 % (95% CI 57.7-65.1); AUC was 0·89. All false negative cases were classified as moderate non-proliferative diabetic retinopathy (NPDR) by human grading.
The DL algorithm reached a good diagnostic accuracy for more than mild DR in a real-world, high burden setting. The performance of the handheld portable retinal camera was adequate, with over 80% of individuals presenting with images of sufficient quality. Portable devices and artificial intelligence tools may increase coverage of DR screening programs.
A novel deep learning-based quantification of serial chest computed tomography in Coronavirus Disease 2019 (COVID-19).
Authors: FengPan, LinLi, BoLiu, TianheYe, LingliLi, DehanLiu, ZezhenDing, GuangfengChen, BoLiang, LianYang, ChuanshengZheng
Journal: Scientific reports

This study aims to explore and compare a novel deep learning-based quantification with the conventional semi-quantitative computed tomography (CT) scoring for the serial chest CT scans of COVID-19. 95 patients with confirmed COVID-19 and a total of 465 serial chest CT scans were involved, including 61 moderate patients (moderate group, 319 chest CT scans) and 34 severe patients (severe group, 146 chest CT scans). Conventional CT scoring and deep learning-based quantification were performed for all chest CT scans for two study goals: (1) Correlation between these two estimations; (2) Exploring the dynamic patterns using these two estimations between moderate and severe groups. The Spearman's correlation coefficient between these two estimation methods was 0.920 (p < 0.001). predicted pulmonary involvement (CT score and percent of pulmonary lesions calculated using deep learning-based quantification) increased more rapidly and reached a higher peak on 23rd days from symptom onset in severe group, which reached a peak on 18th days in moderate group with faster absorption of the lesions. The deep learning-based quantification for COVID-19 showed a good correlation with the conventional CT scoring and demonstrated a potential benefit in the estimation of disease severities of COVID-19.
COV19-CNNet and COV19-ResNet: Diagnostic Inference Engines for Early Detection of COVID-19.
Authors: AyturkKeles, Mustafa BerkKeles, AliKeles
Journal: Cognitive computation

Chest CT is used in the COVID-19 diagnosis process as a significant complement to the reverse transcription polymerase chain reaction (RT-PCR) technique. However, it has several drawbacks, including long disinfection and ventilation times, excessive radiation effects, and high costs. While X-ray radiography is more useful for detecting COVID-19, it is insensitive to the early stages of the disease. We have developed inference engines that will turn X-ray machines into powerful diagnostic tools by using deep learning technology to detect COVID-19. We named these engines COV19-CNNet and COV19-ResNet. The former is based on convolutional neural network architecture; the latter is on residual neural network (ResNet) architecture. This research is a retrospective study. The database consists of 210 COVID-19, 350 viral pneumonia, and 350 normal (healthy) chest X-ray (CXR) images that were created using two different data sources. This study was focused on the problem of multi-class classification (COVID-19, viral pneumonia, and normal), which is a rather difficult task for the diagnosis of COVID-19. The classification accuracy levels for COV19-ResNet and COV19-CNNet were 97.61% and 94.28%, respectively. The inference engines were developed from scratch using new and special deep neural networks without pre-trained models, unlike other studies in the field. These powerful diagnostic engines allow for the early detection of COVID-19 as well as distinguish it from viral pneumonia with similar radiological appearances. Thus, they can help in fast recovery at the early stages, prevent the COVID-19 outbreak from spreading, and contribute to reducing pressure on health-care systems worldwide.
Chest X-ray image phase features for improved diagnosis of COVID-19 using convolutional neural network.
Authors: XiaoQi, Lloyd GBrown, David JForan, JohnNosher, IlkerHacihaliloglu
Journal: International journal of computer assisted radiology and surgery

Recently, the outbreak of the novel coronavirus disease 2019 (COVID-19) pandemic has seriously endangered human health and life. In fighting against COVID-19, effective diagnosis of infected patient is critical for preventing the spread of diseases. 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. In order to reduce intra- and inter-observer variability, during radiological assessment, computer-aided diagnostic tools have been used in order to supplement medical decision making and subsequent management. 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 8851 normal (healthy), 6045 pneumonia, and 3323 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. Future work will involve further evaluation of the proposed method on a larger-size COVID-19 dataset as they become available.
Accurately Differentiating Between Patients With COVID-19, Patients With Other Viral Infections, and Healthy Individuals: Multimodal Late Fusion Learning Approach.
Authors: MingXu, LiuOuyang, LeiHan, KaiSun, TingtingYu, QianLi, HuaTian, LidaSafarnejad, HengdongZhang, YueGao, Forrest ShengBao, YuanfangChen, PatrickRobinson, YaorongGe, BaoliZhu, JieLiu, ShiChen
Journal: Journal of medical Internet research

Effectively identifying patients with COVID-19 using nonpolymerase chain reaction biomedical data is critical for achieving optimal clinical outcomes. Currently, there is a lack of comprehensive understanding in various biomedical features and appropriate analytical approaches for enabling the early detection and effective diagnosis of patients with COVID-19.
We aimed to combine low-dimensional clinical and lab testing data, as well as high-dimensional computed tomography (CT) imaging data, to accurately differentiate between healthy individuals, patients with COVID-19, and patients with non-COVID viral pneumonia, especially at the early stage of infection.
In this study, we recruited 214 patients with nonsevere COVID-19, 148 patients with severe COVID-19, 198 noninfected healthy participants, and 129 patients with non-COVID viral pneumonia. The participants' clinical information (ie, 23 features), lab testing results (ie, 10 features), and CT scans upon admission were acquired and used as 3 input feature modalities. To enable the late fusion of multimodal features, we constructed a deep learning model to extract a 10-feature high-level representation of CT scans. We then developed 3 machine learning models (ie, k-nearest neighbor, random forest, and support vector machine models) based on the combined 43 features from all 3 modalities to differentiate between the following 4 classes: nonsevere, severe, healthy, and viral pneumonia.
Multimodal features provided substantial performance gain from the use of any single feature modality. All 3 machine learning models had high overall prediction accuracy (95.4%-97.7%) and high class-specific prediction accuracy (90.6%-99.9%).
Compared to the existing binary classification benchmarks that are often focused on single-feature modality, this study's hybrid deep learning-machine learning framework provided a novel and effective breakthrough for clinical applications. Our findings, which come from a relatively large sample size, and analytical workflow will supplement and assist with clinical decision support for current COVID-19 diagnostic methods and other clinical applications with high-dimensional multimodal biomedical features.
Fast automated detection of COVID-19 from medical images using convolutional neural networks.
Authors: ShuangLiang, HuixiangLiu, YuGu, XiuhuaGuo, HongjunLi, LiLi, ZhiyuanWu, MengyangLiu, LixinTao
Journal: Communications biology

Coronavirus disease 2019 (COVID-19) is a global pandemic posing significant health risks. The diagnostic test sensitivity of COVID-19 is limited due to irregularities in specimen handling. We propose a deep learning framework that identifies COVID-19 from medical images as an auxiliary testing method to improve diagnostic sensitivity. We use pseudo-coloring methods and a platform for annotating X-ray and computed tomography images to train the convolutional neural network, which achieves a performance similar to that of experts and provides high scores for multiple statistical indices (F1 scores > 96.72% (0.9307, 0.9890) and specificity >99.33% (0.9792, 1.0000)). Heatmaps are used to visualize the salient features extracted by the neural network. The neural network-based regression provides strong correlations between the lesion areas in the images and five clinical indicators, resulting in high accuracy of the classification framework. The proposed method represents a potential computer-aided diagnosis method for COVID-19 in clinical practice.