scholarly journals Challenges of Deep Learning Methods for COVID-19 Detection Using Public Datasets

2020 ◽  
Author(s):  
Md. Kamrul Hasan ◽  
Md. Ashraful Alam ◽  
Lavsen Dahal ◽  
Md. Toufick E Elahi ◽  
Shidhartho Roy ◽  
...  
Keyword(s):  
Deep Learning ◽  
Training Dataset ◽  
Clinical Settings ◽  
X Rays ◽  
Imaging Data ◽  
Learning Models ◽  
Test Set ◽  
Public Data ◽  
Independent Test ◽  
Public Datasets

ABSTRACTA large number of studies in the past months have proposed deep learning-based Artificial Intelligence (AI) tools for automated detection of COVID-19 using publicly available datasets of Chest X-rays (CXRs) or CT scans for training and evaluation. Most of these studies report high accuracy when classifying COVID-19 patients from normal or other commonly occurring pneumonia cases. However, these results are often obtained on cross-validation studies without an independent test set coming from a separate dataset and have biases such as the two classes to be predicted come from two completely different datasets. In this work, we investigate potential overfitting and biases in such studies by designing different experimental setups within the available public data constraints and highlight the challenges and limitations of developing deep learning models with such datasets. We propose a deep learning architecture for COVID-19 classification that combines two very popular classification networks, ResNet and Xception, and use it to carry out the experiments to investigate challenges and limitations. The results show that the deep learning models can overestimate their performance due to biases in the experimental design and overfitting to the training dataset. We compare the proposed architecture to state-of-the-art methods utilizing an independent test set for evaluation, where some of the identified bias and overfitting issues are reduced. Although our proposed deep learning architecture gives the best performance with our best possible setup, we highlight the challenges in comparing and interpreting various deep learning algorithms’ results. While the deep learning-based methods using chest imaging data show promise in being helpful for clinical management and triage of COVID-19 patients, our experiments suggest that a larger, more comprehensive database with less bias is necessary for developing tools applicable in real clinical settings.

scholarly journals Efficient Pneumonia Detection in Chest Xray Images Using Deep Transfer Learning

Diagnostics ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 417 ◽  
Author(s):  
Mohammad Farukh Hashmi ◽  
Satyarth Katiyar ◽  
Avinash G Keskar ◽  
Neeraj Dhanraj Bokde ◽  
Zong Woo Geem
Keyword(s):  
Deep Learning ◽  
Transfer Learning ◽  
Data Augmentation ◽  
Medical Center ◽  
Training Dataset ◽  
Test Accuracy ◽  
X Rays ◽  
Learning Models ◽  
Novel Approach ◽  
Unseen Data

Pneumonia causes the death of around 700,000 children every year and affects 7% of the global population. Chest X-rays are primarily used for the diagnosis of this disease. However, even for a trained radiologist, it is a challenging task to examine chest X-rays. There is a need to improve the diagnosis accuracy. In this work, an efficient model for the detection of pneumonia trained on digital chest X-ray images is proposed, which could aid the radiologists in their decision making process. A novel approach based on a weighted classifier is introduced, which combines the weighted predictions from the state-of-the-art deep learning models such as ResNet18, Xception, InceptionV3, DenseNet121, and MobileNetV3 in an optimal way. This approach is a supervised learning approach in which the network predicts the result based on the quality of the dataset used. Transfer learning is used to fine-tune the deep learning models to obtain higher training and validation accuracy. Partial data augmentation techniques are employed to increase the training dataset in a balanced way. The proposed weighted classifier is able to outperform all the individual models. Finally, the model is evaluated, not only in terms of test accuracy, but also in the AUC score. The final proposed weighted classifier model is able to achieve a test accuracy of 98.43% and an AUC score of 99.76 on the unseen data from the Guangzhou Women and Children’s Medical Center pneumonia dataset. Hence, the proposed model can be used for a quick diagnosis of pneumonia and can aid the radiologists in the diagnosis process.

scholarly journals Shallow Convolutional Neural Network for COVID-19 Outbreak Screening using Chest X-rays

2020 ◽  
Author(s):  
Himadri Mukherjee ◽  
Subhankar Ghosh ◽  
Ankita Dhar ◽  
Sk. Md. Obaidullah ◽  
KC Santosh ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Mass Screening ◽  
False Positive ◽  
False Positive Rate ◽  
Experimental Tests ◽  
X Rays ◽  
Imaging Data ◽  
Learning Models

<div><div><div><p>Among radiological imaging data, chest X-rays are of great use in observing COVID-19 mani- festations. For mass screening, using chest X-rays, a computationally efficient AI-driven tool is the must to detect COVID-19 positive cases from non-COVID ones. For this purpose, we proposed a light-weight Convolutional Neural Network (CNN)-tailored shallow architecture that can automatically detect COVID-19 positive cases using chest X-rays, with no false positive. The shallow CNN-tailored architecture was designed with fewer parameters as compared to other deep learning models, which was validated using 130 COVID-19 positive chest X-rays. In this study, in addition to COVID-19 positive cases, another set of non-COVID-19 cases (exactly similar to the size of COVID-19 set) was taken into account, where MERS, SARS, Pneumonia, and healthy chest X-rays were used. In experimental tests, to avoid possible bias, 5-fold cross validation was followed. Using 260 chest X-rays, the proposed model achieved an accuracy of an accuracy of 96.92%, sensitivity of 0.942, where AUC was 0.9869. Further, the reported false positive rate was 0 for 130 COVID-19 positive cases. This stated that proposed tool could possibly be used for mass screening. Note to be confused, it does not include any clinical implications. Using the exact same set of chest X-rays collection, the current results were better than other deep learning models and state-of-the-art works.</p></div></div></div>

scholarly journals Shallow Convolutional Neural Network for COVID-19 Outbreak Screening using Chest X-rays

2020 ◽  
Author(s):  
Himadri Mukherjee ◽  
Subhankar Ghosh ◽  
Ankita Dhar ◽  
Sk. Md. Obaidullah ◽  
KC Santosh ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Mass Screening ◽  
False Positive ◽  
False Positive Rate ◽  
Experimental Tests ◽  
X Rays ◽  
Imaging Data ◽  
Learning Models

<div><div><div><p>Among radiological imaging data, chest X-rays are of great use in observing COVID-19 mani- festations. For mass screening, using chest X-rays, a computationally efficient AI-driven tool is the must to detect COVID-19 positive cases from non-COVID ones. For this purpose, we proposed a light-weight Convolutional Neural Network (CNN)-tailored shallow architecture that can automatically detect COVID-19 positive cases using chest X-rays, with no false positive. The shallow CNN-tailored architecture was designed with fewer parameters as compared to other deep learning models, which was validated using 130 COVID-19 positive chest X-rays. In this study, in addition to COVID-19 positive cases, another set of non-COVID-19 cases (exactly similar to the size of COVID-19 set) was taken into account, where MERS, SARS, Pneumonia, and healthy chest X-rays were used. In experimental tests, to avoid possible bias, 5-fold cross validation was followed. Using 260 chest X-rays, the proposed model achieved an accuracy of an accuracy of 96.92%, sensitivity of 0.942, where AUC was 0.9869. Further, the reported false positive rate was 0 for 130 COVID-19 positive cases. This stated that proposed tool could possibly be used for mass screening. Note to be confused, it does not include any clinical implications. Using the exact same set of chest X-rays collection, the current results were better than other deep learning models and state-of-the-art works.</p></div></div></div>

scholarly journals Evaluation of the feasibility of explainable computer-aided detection of cardiomegaly on chest radiographs using deep learning

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mu Sook Lee ◽  
Yong Soo Kim ◽  
Minki Kim ◽  
Muhammad Usman ◽  
Shi Sub Byon ◽  
...  
Keyword(s):  
Deep Learning ◽  
Diagnostic Performance ◽  
Absolute Error ◽  
Training Dataset ◽  
Computer Aided Detection ◽  
Test Dataset ◽  
Cardiothoracic Ratio ◽  
Computer Aided ◽  
Chest X Ray ◽  
Public Datasets

AbstractWe examined the feasibility of explainable computer-aided detection of cardiomegaly in routine clinical practice using segmentation-based methods. Overall, 793 retrospectively acquired posterior–anterior (PA) chest X-ray images (CXRs) of 793 patients were used to train deep learning (DL) models for lung and heart segmentation. The training dataset included PA CXRs from two public datasets and in-house PA CXRs. Two fully automated segmentation-based methods using state-of-the-art DL models for lung and heart segmentation were developed. The diagnostic performance was assessed and the reliability of the automatic cardiothoracic ratio (CTR) calculation was determined using the mean absolute error and paired t-test. The effects of thoracic pathological conditions on performance were assessed using subgroup analysis. One thousand PA CXRs of 1000 patients (480 men, 520 women; mean age 63 ± 23 years) were included. The CTR values derived from the DL models and diagnostic performance exhibited excellent agreement with reference standards for the whole test dataset. Performance of segmentation-based methods differed based on thoracic conditions. When tested using CXRs with lesions obscuring heart borders, the performance was lower than that for other thoracic pathological findings. Thus, segmentation-based methods using DL could detect cardiomegaly; however, the feasibility of computer-aided detection of cardiomegaly without human intervention was limited.

Deep learning to predict subtypes of poorly differentiated lung cancer from biopsy whole slide images.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 8536-8536
Author(s):  
Gouji Toyokawa ◽  
Fahdi Kanavati ◽  
Seiya Momosaki ◽  
Kengo Tateishi ◽  
Hiroaki Takeoka ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Deep Learning ◽  
Learning Model ◽  
Test Set ◽  
Cancer Subtypes ◽  
Independent Test ◽  
Poorly Differentiated ◽  
Test Sets ◽  
Deep Learning Model ◽  
Whole Slide Images

8536 Background: Lung cancer is the leading cause of cancer-related death in many countries, and its prognosis remains unsatisfactory. Since treatment approaches differ substantially based on the subtype, such as adenocarcinoma (ADC), squamous cell carcinoma (SCC) and small cell lung cancer (SCLC), an accurate histopathological diagnosis is of great importance. However, if the specimen is solely composed of poorly differentiated cancer cells, distinguishing between histological subtypes can be difficult. The present study developed a deep learning model to classify lung cancer subtypes from whole slide images (WSIs) of transbronchial lung biopsy (TBLB) specimens, in particular with the aim of using this model to evaluate a challenging test set of indeterminate cases. Methods: Our deep learning model consisted of two separately trained components: a convolutional neural network tile classifier and a recurrent neural network tile aggregator for the WSI diagnosis. We used a training set consisting of 638 WSIs of TBLB specimens to train a deep learning model to classify lung cancer subtypes (ADC, SCC and SCLC) and non-neoplastic lesions. The training set consisted of 593 WSIs for which the diagnosis had been determined by pathologists based on the visual inspection of Hematoxylin-Eosin (HE) slides and of 45 WSIs of indeterminate cases (64 ADCs and 19 SCCs). We then evaluated the models using five independent test sets. For each test set, we computed the receiver operator curve (ROC) area under the curve (AUC). Results: We applied the model to an indeterminate test set of WSIs obtained from TBLB specimens that pathologists had not been able to conclusively diagnose by examining the HE-stained specimens alone. Overall, the model achieved ROC AUCs of 0.993 (confidence interval [CI] 0.971-1.0) and 0.996 (0.981-1.0) for ADC and SCC, respectively. We further evaluated the model using five independent test sets consisting of both TBLB and surgically resected lung specimens (combined total of 2490 WSIs) and obtained highly promising results with ROC AUCs ranging from 0.94 to 0.99. Conclusions: In this study, we demonstrated that a deep learning model could be trained to predict lung cancer subtypes in indeterminate TBLB specimens. The extremely promising results obtained show that if deployed in clinical practice, a deep learning model that is capable of aiding pathologists in diagnosing indeterminate cases would be extremely beneficial as it would allow a diagnosis to be obtained sooner and reduce costs that would result from further investigations.

scholarly journals Covid-19 detection via deep neural network and occlusion sensitivity maps

2021 ◽  
Author(s):  
Noor Ahmad ◽  
Muhammad Aminu ◽  
Mohd Halim Mohd Noor
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Deep Neural Network ◽  
State Of The Art ◽  
Color Images ◽  
Fine Tuning ◽  
Training Dataset ◽  
Learning Approaches ◽  
Learning Models ◽  
Sensitivity Maps

Deep learning approaches have attracted a lot of attention in the automatic detection of Covid-19 and transfer learning is the most common approach. However, majority of the pre-trained models are trained on color images, which can cause inefficiencies when fine-tuning the models on Covid-19 images which are often grayscale. To address this issue, we propose a deep learning architecture called CovidNet which requires a relatively smaller number of parameters. CovidNet accepts grayscale images as inputs and is suitable for training with limited training dataset. Experimental results show that CovidNet outperforms other state-of-the-art deep learning models for Covid-19 detection.

scholarly journals Pseudoprogression in Patients with Glioblastoma: Assessment by Using Volume-weighted Voxel-based Multiparametric Clustering of MR Imaging Data in an Independent Test Set

Radiology ◽  
2015 ◽  
Vol 275 (3) ◽  
pp. 792-802 ◽  
Author(s):  
Ji Eun Park ◽  
Ho Sung Kim ◽  
Myeong Ju Goh ◽  
Sang Joon Kim ◽  
Jeong Hoon Kim
Keyword(s):  
Mr Imaging ◽  
Imaging Data ◽  
Test Set ◽  
Independent Test

scholarly journals Covid-19 detection via deep neural network and occlusion sensitivity maps

2021 ◽  
Author(s):  
Noor Ahmad ◽  
Muhammad Aminu ◽  
Mohd Halim Mohd Noor
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Deep Neural Network ◽  
State Of The Art ◽  
Color Images ◽  
Fine Tuning ◽  
Training Dataset ◽  
Learning Approaches ◽  
Learning Models ◽  
Sensitivity Maps

Deep learning approaches have attracted a lot of attention in the automatic detection of Covid-19 and transfer learning is the most common approach. However, majority of the pre-trained models are trained on color images, which can cause inefficiencies when fine-tuning the models on Covid-19 images which are often grayscale. To address this issue, we propose a deep learning architecture called CovidNet which requires a relatively smaller number of parameters. CovidNet accepts grayscale images as inputs and is suitable for training with limited training dataset. Experimental results show that CovidNet outperforms other state-of-the-art deep learning models for Covid-19 detection.

scholarly journals Detecting Coronavirus from Chest X-rays Using Transfer Learning

COVID ◽  
2021 ◽  
Vol 1 (1) ◽  
pp. 403-415
Author(s):  
Abeer Badawi ◽  
Khalid Elgazzar
Keyword(s):  
Deep Learning ◽  
Binary Classification ◽  
Healthcare Providers ◽  
Large Set ◽  
X Rays ◽  
Learning Models ◽  
X Ray ◽  
Chest X Ray ◽  
Multi Class Classification ◽  
Novel Coronavirus

Coronavirus disease (COVID-19) is an illness caused by a novel coronavirus family. One of the practical examinations for COVID-19 is chest radiography. COVID-19 infected patients show abnormalities in chest X-ray images. However, examining the chest X-rays requires a specialist with high experience. Hence, using deep learning techniques in detecting abnormalities in the X-ray images is presented commonly as a potential solution to help diagnose the disease. Numerous research has been reported on COVID-19 chest X-ray classification, but most of the previous studies have been conducted on a small set of COVID-19 X-ray images, which created an imbalanced dataset and affected the performance of the deep learning models. In this paper, we propose several image processing techniques to augment COVID-19 X-ray images to generate a large and diverse dataset to boost the performance of deep learning algorithms in detecting the virus from chest X-rays. We also propose innovative and robust deep learning models, based on DenseNet201, VGG16, and VGG19, to detect COVID-19 from a large set of chest X-ray images. A performance evaluation shows that the proposed models outperform all existing techniques to date. Our models achieved 99.62% on the binary classification and 95.48% on the multi-class classification. Based on these findings, we provide a pathway for researchers to develop enhanced models with a balanced dataset that includes the highest available COVID-19 chest X-ray images. This work is of high interest to healthcare providers, as it helps to better diagnose COVID-19 from chest X-rays in less time with higher accuracy.

scholarly journals Pre-trained deep learning models in automatic COVID-19 diagnosis

2021 ◽  
Vol 22 (3) ◽  
pp. 1540
Author(s):  
Ahmed Wasif Reza ◽  
Md Mahamudul Hasan ◽  
Nazla Nowrin ◽  
Mir Moynuddin Ahmed Shibly
Keyword(s):  
Deep Learning ◽  
Open Source ◽  
Healthcare Professionals ◽  
Automated System ◽  
Primary Concern ◽  
X Rays ◽  
Learning Models ◽  
Efficient System ◽  
Empirical Results ◽  
History Of

Coronavirus Disease (COVID-19) is a devastating pandemic in the history of mankind. It is a highly contagious flu that can spread from human to human without revealing any symptoms. For being so contagious, detecting patients with it and isolating them has become the primary concern for healthcare professionals. This study presented an alternative way to identify COVID-19 patients by doing an automatic examination of chest X-rays of the patients. To develop such an efficient system, six pre-trained deep learning models were used. Those models were: VGG16, InceptionV3, Xception, DenseNet201, InceptionResNetV2, and EfficientNetB4. Those models were developed on two open-source datasets that have chest X-rays of patients diagnosed with COVID-19. Among the models, EfficientNetB4 achieved better performances on both datasets with 96% and 97% of accuracies. The empirical results were also exemplary. This type of automated system can help us fight this dangerous virus outbreak.

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