Efficient Pneumonia Detection in Chest Xray Images Using Deep Transfer Learning

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.

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Effectiveness of transfer learning for enhancing tumor classification with a convolutional neural network on frozen sections

Scientific Reports ◽

10.1038/s41598-020-78129-0 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Young-Gon Kim ◽

Sungchul Kim ◽

Cristina Eunbee Cho ◽

In Hye Song ◽

Hee Jin Lee ◽

...

Keyword(s):

Neural Network ◽

Deep Learning ◽

Convolutional Neural Network ◽

Transfer Learning ◽

Frozen Section ◽

Medical Center ◽

External Validation ◽

Model Performance ◽

Classification Model ◽

Training Dataset

AbstractFast and accurate confirmation of metastasis on the frozen tissue section of intraoperative sentinel lymph node biopsy is an essential tool for critical surgical decisions. However, accurate diagnosis by pathologists is difficult within the time limitations. Training a robust and accurate deep learning model is also difficult owing to the limited number of frozen datasets with high quality labels. To overcome these issues, we validated the effectiveness of transfer learning from CAMELYON16 to improve performance of the convolutional neural network (CNN)-based classification model on our frozen dataset (N = 297) from Asan Medical Center (AMC). Among the 297 whole slide images (WSIs), 157 and 40 WSIs were used to train deep learning models with different dataset ratios at 2, 4, 8, 20, 40, and 100%. The remaining, i.e., 100 WSIs, were used to validate model performance in terms of patch- and slide-level classification. An additional 228 WSIs from Seoul National University Bundang Hospital (SNUBH) were used as an external validation. Three initial weights, i.e., scratch-based (random initialization), ImageNet-based, and CAMELYON16-based models were used to validate their effectiveness in external validation. In the patch-level classification results on the AMC dataset, CAMELYON16-based models trained with a small dataset (up to 40%, i.e., 62 WSIs) showed a significantly higher area under the curve (AUC) of 0.929 than those of the scratch- and ImageNet-based models at 0.897 and 0.919, respectively, while CAMELYON16-based and ImageNet-based models trained with 100% of the training dataset showed comparable AUCs at 0.944 and 0.943, respectively. For the external validation, CAMELYON16-based models showed higher AUCs than those of the scratch- and ImageNet-based models. Model performance for slide feasibility of the transfer learning to enhance model performance was validated in the case of frozen section datasets with limited numbers.

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The Effectiveness of Image Augmentation in Deep Learning Networks for Detecting COVID-19: A Geometric Transformation Perspective

Frontiers in Medicine ◽

10.3389/fmed.2021.629134 ◽

2021 ◽

Vol 8 ◽

Author(s):

Mohamed Elgendi ◽

Muhammad Umer Nasir ◽

Qunfeng Tang ◽

David Smith ◽

John-Paul Grenier ◽

...

Keyword(s):

Deep Learning ◽

Data Augmentation ◽

Learning Algorithms ◽

Training Dataset ◽

Geometric Transformation ◽

Detection Accuracy ◽

X Rays ◽

X Ray ◽

Testing Dataset ◽

The Impact

Chest X-ray imaging technology used for the early detection and screening of COVID-19 pneumonia is both accessible worldwide and affordable compared to other non-invasive technologies. Additionally, deep learning methods have recently shown remarkable results in detecting COVID-19 on chest X-rays, making it a promising screening technology for COVID-19. Deep learning relies on a large amount of data to avoid overfitting. While overfitting can result in perfect modeling on the original training dataset, on a new testing dataset it can fail to achieve high accuracy. In the image processing field, an image augmentation step (i.e., adding more training data) is often used to reduce overfitting on the training dataset, and improve prediction accuracy on the testing dataset. In this paper, we examined the impact of geometric augmentations as implemented in several recent publications for detecting COVID-19. We compared the performance of 17 deep learning algorithms with and without different geometric augmentations. We empirically examined the influence of augmentation with respect to detection accuracy, dataset diversity, augmentation methodology, and network size. Contrary to expectation, our results show that the removal of recently used geometrical augmentation steps actually improved the Matthews correlation coefficient (MCC) of 17 models. The MCC without augmentation (MCC = 0.51) outperformed four recent geometrical augmentations (MCC = 0.47 for Data Augmentation 1, MCC = 0.44 for Data Augmentation 2, MCC = 0.48 for Data Augmentation 3, and MCC = 0.49 for Data Augmentation 4). When we retrained a recently published deep learning without augmentation on the same dataset, the detection accuracy significantly increased, with a χMcNemar′s statistic2=163.2 and a p-value of 2.23 × 10−37. This is an interesting finding that may improve current deep learning algorithms using geometrical augmentations for detecting COVID-19. We also provide clinical perspectives on geometric augmentation to consider regarding the development of a robust COVID-19 X-ray-based detector.

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A Novel Transfer Learning Based Approach for Pneumonia Detection in Chest X-ray Images

Applied Sciences ◽

10.3390/app10020559 ◽

2020 ◽

Vol 10 (2) ◽

pp. 559 ◽

Cited By ~ 56

Author(s):

Vikash Chouhan ◽

Sanjay Kumar Singh ◽

Aditya Khamparia ◽

Deepak Gupta ◽

Prayag Tiwari ◽

...

Keyword(s):

Transfer Learning ◽

Medical Center ◽

Network Models ◽

Ensemble Model ◽

X Rays ◽

Neural Network Models ◽

Learning Framework ◽

Unseen Data ◽

Chest X Ray ◽

Bacteria And Fungi

Pneumonia is among the top diseases which cause most of the deaths all over the world. Virus, bacteria and fungi can all cause pneumonia. However, it is difficult to judge the pneumonia just by looking at chest X-rays. The aim of this study is to simplify the pneumonia detection process for experts as well as for novices. We suggest a novel deep learning framework for the detection of pneumonia using the concept of transfer learning. In this approach, features from images are extracted using different neural network models pretrained on ImageNet, which then are fed into a classifier for prediction. We prepared five different models and analyzed their performance. Thereafter, we proposed an ensemble model that combines outputs from all pretrained models, which outperformed individual models, reaching the state-of-the-art performance in pneumonia recognition. Our ensemble model reached an accuracy of 96.4% with a recall of 99.62% on unseen data from the Guangzhou Women and Children’s Medical Center dataset.

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Detection of coronavirus disease from X-ray images using deep learning and transfer learning algorithms

Journal of X-Ray Science and Technology ◽

10.3233/xst-200720 ◽

2020 ◽

Vol 28 (5) ◽

pp. 841-850

Author(s):

Saleh Albahli ◽

Waleed Albattah

Keyword(s):

Deep Learning ◽

Transfer Learning ◽

Data Augmentation ◽

Medical Image Analysis ◽

Image Data ◽

Network Models ◽

Learning Models ◽

X Ray ◽

Study Results ◽

Chest X Ray

OBJECTIVE: This study aims to employ the advantages of computer vision and medical image analysis to develop an automated model that has the clinical potential for early detection of novel coronavirus (COVID-19) infected disease. METHOD: This study applied transfer learning method to develop deep learning models for detecting COVID-19 disease. Three existing state-of-the-art deep learning models namely, Inception ResNetV2, InceptionNetV3 and NASNetLarge, were selected and fine-tuned to automatically detect and diagnose COVID-19 disease using chest X-ray images. A dataset involving 850 images with the confirmed COVID-19 disease, 500 images of community-acquired (non-COVID-19) pneumonia cases and 915 normal chest X-ray images was used in this study. RESULTS: Among the three models, InceptionNetV3 yielded the best performance with accuracy levels of 98.63% and 99.02% with and without using data augmentation in model training, respectively. All the performed networks tend to overfitting (with high training accuracy) when data augmentation is not used, this is due to the limited amount of image data used for training and validation. CONCLUSION: This study demonstrated that a deep transfer learning is feasible to detect COVID-19 disease automatically from chest X-ray by training the learning model with chest X-ray images mixed with COVID-19 patients, other pneumonia affected patients and people with healthy lungs, which may help doctors more effectively make their clinical decisions. The study also gives an insight to how transfer learning was used to automatically detect the COVID-19 disease. In future studies, as the amount of available dataset increases, different convolution neutral network models could be designed to achieve the goal more efficiently.

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Graphsite: ligand-binding site classification using deep graph neural network

10.1101/2021.12.06.471420 ◽

2021 ◽

Author(s):

Wentao Shi ◽

Manali Singha ◽

Limeng Pu ◽

J. Ram Ramanujam ◽

Michal Brylinski

Keyword(s):

Neural Networks ◽

Deep Learning ◽

Ligand Binding ◽

Small Molecules ◽

Binding Site ◽

Binding Sites ◽

Graph Representation ◽

Test Accuracy ◽

Learning Models ◽

Unseen Data

Binding sites are concave surfaces on proteins that bind to small molecules called ligands. Types of molecules that bind to the protein determine its biological function. Meanwhile, the binding process between small molecules and the protein is also crucial to various biological functionalities. Therefore, identifying and classifying such binding sites would enormously contribute to biomedical applications such as drug repurposing. Deep learning is a modern artificial intelligence technology. It utilizes deep neural networks to handle complex tasks such as image classification and language translation. Previous work has proven the capability of deep learning models handle binding sites wherein the binding sites are represented as pixels or voxels. Graph neural networks (GNNs) are deep learning models that operate on graphs. GNNs are promising for handling binding sites related tasks - provided there is an adequate graph representation to model the binding sties. In this communication, we describe a GNN-based computational method, GraphSite, that utilizes a novel graph representation of ligand-binding sites. A state-of-the-art GNN model is trained to capture the intrinsic characteristics of these binding sites and classify them. Our model generalizes well to unseen data and achieves test accuracy of 81.28\% on classifying 14 binding site classes.

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Comparison of Classification Models Based on Deep learning on COVID-19 Chest X-Rays

Journal of Physics Conference Series ◽

10.1088/1742-6596/2161/1/012078 ◽

2022 ◽

Vol 2161 (1) ◽

pp. 012078

Author(s):

Pallavi R Mane ◽

Rajat Shenoy ◽

Ghanashyama Prabhu

Keyword(s):

Deep Learning ◽

Transfer Learning ◽

State Of The Art ◽

Cost Effective ◽

X Rays ◽

The Novel ◽

Learning Models ◽

X Ray ◽

Chest X Ray ◽

Fine Tune

Abstract COVID -19, is a deadly, dangerous and contagious disease caused by the novel corona virus. It is very important to detect COVID-19 infection accurately as quickly as possible to avoid the spreading. Deep learning methods can significantly improve the efficiency and accuracy of reading Chest X-Rays (CXRs). The existing Deep learning models with further fine tune provide cost effective, rapid, and better classification results. This paper tries to deploy well studied AI tools with modification on X-ray images to classify COVID 19. This research performs five experiments to classify COVID-19 CXRs from Normal and Viral Pneumonia CXRs using Convolutional Neural Networks (CNN). Four experiments were performed on state-of-the-art pre-trained models using transfer learning and one experiment was performed using a CNN designed from scratch. Dataset used for the experiments consists of chest X-Ray images from the Kaggle dataset and other publicly accessible sources. The data was split into three parts while 90% retained for training the models, 5% each was used in validation and testing of the constructed models. The four transfer learning models used were Inception, Xception, ResNet, and VGG19, that resulted in the test accuracies of 93.07%, 94.8%, 67.5%, and 91.1% respectively and our CNN model resulted in 94.6%.

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COVID-19 Pneumonia Detection Using Optimized Deep Learning Techniques

Diagnostics ◽

10.3390/diagnostics11111972 ◽

2021 ◽

Vol 11 (11) ◽

pp. 1972

Author(s):

Abul Bashar ◽

Ghazanfar Latif ◽

Ghassen Ben Brahim ◽

Nazeeruddin Mohammad ◽

Jaafar Alghazo

Keyword(s):

Deep Learning ◽

Transfer Learning ◽

Data Augmentation ◽

Learning Algorithm ◽

The Body ◽

X Rays ◽

X Ray ◽

Clinical Observations ◽

Dataset Size ◽

Chest X Ray

It became apparent that mankind has to learn to live with and adapt to COVID-19, especially because the developed vaccines thus far do not prevent the infection but rather just reduce the severity of the symptoms. The manual classification and diagnosis of COVID-19 pneumonia requires specialized personnel and is time consuming and very costly. On the other hand, automatic diagnosis would allow for real-time diagnosis without human intervention resulting in reduced costs. Therefore, the objective of this research is to propose a novel optimized Deep Learning (DL) approach for the automatic classification and diagnosis of COVID-19 pneumonia using X-ray images. For this purpose, a publicly available dataset of chest X-rays on Kaggle was used in this study. The dataset was developed over three stages in a quest to have a unified COVID-19 entities dataset available for researchers. The dataset consists of 21,165 anterior-to-posterior and posterior-to-anterior chest X-ray images classified as: Normal (48%), COVID-19 (17%), Lung Opacity (28%) and Viral Pneumonia (6%). Data Augmentation was also applied to increase the dataset size to enhance the reliability of results by preventing overfitting. An optimized DL approach is implemented in which chest X-ray images go through a three-stage process. Image Enhancement is performed in the first stage, followed by Data Augmentation stage and in the final stage the results are fed to the Transfer Learning algorithms (AlexNet, GoogleNet, VGG16, VGG19, and DenseNet) where the images are classified and diagnosed. Extensive experiments were performed under various scenarios, which led to achieving the highest classification accuracy of 95.63% through the application of VGG16 transfer learning algorithm on the augmented enhanced dataset with freeze weights. This accuracy was found to be better as compared to the results reported by other methods in the recent literature. Thus, the proposed approach proved superior in performance as compared with that of other similar approaches in the extant literature, and it made a valuable contribution to the body of knowledge. Although the results achieved so far are promising, further work is planned to correlate the results of the proposed approach with clinical observations to further enhance the efficiency and accuracy of COVID-19 diagnosis.

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

10.1101/2020.11.07.20227504 ◽

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.

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Large-Scale Printed Chinese Character Recognition for ID Cards Using Deep Learning and Few Samples Transfer Learning

10.20944/preprints202112.0376.v1 ◽

2021 ◽

Author(s):

Yi-Quan Li ◽

Hao-Sen Chang ◽

Daw-Tung Lin

Keyword(s):

Neural Networks ◽

Deep Learning ◽

Transfer Learning ◽

Character Recognition ◽

Large Scale ◽

Data Augmentation ◽

Training Data ◽

Fine Tuning ◽

Training Dataset ◽

Model Parameters

In the field of computer vision, large-scale image classification tasks are both important and highly challenging. With the ongoing advances in deep learning and optical character recognition (OCR) technologies, neural networks designed to perform large-scale classification play an essential role in facilitating OCR systems. In this study, we developed an automatic OCR system designed to identify up to 13,070 large-scale printed Chinese characters by using deep learning neural networks and fine-tuning techniques. The proposed framework comprises four components, including training dataset synthesis and background simulation, image preprocessing and data augmentation, the process of training the model, and transfer learning. The training data synthesis procedure is composed of a character font generation step and a background simulation process. Three background models are proposed to simulate the factors of the background noise and anti-counterfeiting patterns on ID cards. To expand the diversity of the synthesized training dataset, rotation and zooming data augmentation are applied. A massive dataset comprising more than 19.6 million images was thus created to accommodate the variations in the input images and improve the learning capacity of the CNN model. Subsequently, we modified the GoogLeNet neural architecture by replacing the FC layer with a global average pooling layer to avoid overfitting caused by a massive amount of training data. Consequently, the number of model parameters was reduced. Finally, we employed the transfer learning technique to further refine the CNN model using a small number of real data samples. Experimental results show that the overall recognition performance of the proposed approach is significantly better than that of prior methods and thus demonstrate the effectiveness of proposed framework, which exhibited a recognition accuracy as high as 99.39% on the constructed real ID card dataset.

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Data augmentation and transfer learning to classify malware images in a deep learning context

Journal of Computer Virology and Hacking Techniques ◽

10.1007/s11416-021-00381-3 ◽

2021 ◽

Author(s):

Niccolò Marastoni ◽

Roberto Giacobazzi ◽

Mila Dalla Preda

Keyword(s):

Neural Network ◽

Deep Learning ◽

Transfer Learning ◽

Data Augmentation ◽

Short Term Memory ◽

State Of The Art ◽

Learning Models ◽

Learning Context ◽

Automatic Feature Extraction ◽

Augmentation Techniques

AbstractIn the past few years, malware classification techniques have shifted from shallow traditional machine learning models to deeper neural network architectures. The main benefit of some of these is the ability to work with raw data, guaranteed by their automatic feature extraction capabilities. This results in less technical expertise needed while building the models, thus less initial pre-processing resources. Nevertheless, such advantage comes with its drawbacks, since deep learning models require huge quantities of data in order to generate a model that generalizes well. The amount of data required to train a deep network without overfitting is often unobtainable for malware analysts. We take inspiration from image-based data augmentation techniques and apply a sequence of semantics-preserving syntactic code transformations (obfuscations) to a small dataset of programs to generate a larger dataset. We then design two learning models, a convolutional neural network and a bi-directional long short-term memory, and we train them on images extracted from compiled binaries of the newly generated dataset. Through transfer learning we then take the features learned from the obfuscated binaries and train the models against two state of the art malware datasets, each containing around 10 000 samples. Our models easily achieve up to 98.5% accuracy on the test set, which is on par or better than the present state of the art approaches, thus validating the approach.

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