Learning-to-augment strategy using noisy and denoised data: Improving generalizability of deep CNN for the detection of COVID-19 in X-ray images

Deep learning with noisy labels in medical prediction problems: a scoping review

OBJECTIVES

Medical research faces substantial challenges from noisy labels attributed to factors like inter-expert variability and machine-extracted labels. Despite this, the adoption of label noise management remains limited, and label noise is largely ignored. To this end, there is a critical need to conduct a scoping review focusing on the problem space. This scoping review aims to comprehensively review label noise management in deep learning-based medical prediction problems, which includes label noise detection, label noise handling, and evaluation. Research involving label uncertainty is also included.

METHODS

Our scoping review follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We searched 4 databases, including PubMed, IEEE Xplore, Google Scholar, and Semantic Scholar. Our search terms include "noisy label AND medical/healthcare/clinical," "uncertainty AND medical/healthcare/clinical," and "noise AND medical/healthcare/clinical."

RESULTS

A total of 60 papers met inclusion criteria between 2016 and 2023. A series of practical questions in medical research are investigated. These include the sources of label noise, the impact of label noise, the detection of label noise, label noise handling techniques, and their evaluation. Categorization of both label noise detection methods and handling techniques are provided.

DISCUSSION

From a methodological perspective, we observe that the medical community has been up to date with the broader deep-learning community, given that most techniques have been evaluated on medical data. We recommend considering label noise as a standard element in medical research, even if it is not dedicated to handling noisy labels. Initial experiments can start with easy-to-implement methods, such as noise-robust loss functions, weighting, and curriculum learning.

Deep learning-based automated kidney and cyst segmentation of autosomal dominant polycystic kidney disease using single vs. multi-institutional data

PURPOSE

This study aimed to investigate if a deep learning model trained with a single institution's data has comparable accuracy to that trained with multi-institutional data for segmenting kidney and cyst regions in magnetic resonance (MR) images of patients affected by autosomal dominant polycystic kidney disease (ADPKD).

METHODS

We used TensorFlow with a Keras custom UNet on 2D slices of 756 MRI images of kidneys with ADPKD obtained from four institutions in the Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease (CRISP) study. The ground truth was determined via a manual plus global thresholding method. Five models were trained with 80 % of all institutional data (n = 604) and each institutional data (n = 232, 172, 148, or 52), respectively, and validated with 10 % and tested on an unseen 10 % of the data. The model's performance was evaluated using the Dice Similarity Coefficient (DSC).

RESULTS

The DSCs by the model trained with all institutional data ranged from 0.92 to 0.95 for kidney image segmentation, only 1-2 % higher than those by the models trained with single institutional data (0.90-0.93).In cyst segmentation, however, the DSCs by the model trained with all institutional data ranged from 0.83 to 0.89, which were 2-20 % higher than those by the models trained with single institutional data (0.66-0.86).

CONCLUSION

The UNet performance, when trained with a single institutional dataset, exhibited similar accuracy to the model trained on a multi-institutional dataset. Segmentation accuracy increases with models trained on larger sample sizes, especially in more complex cyst segmentation.

Classification of Monkeypox Images Using LIME-Enabled Investigation of Deep Convolutional Neural Network

In this research, we demonstrate a Deep Convolutional Neural Network-based classification model for the detection of monkeypox. Monkeypox can be difficult to diagnose clinically in its early stages since it resembles both chickenpox and measles in symptoms. The early diagnosis of monkeypox helps doctors cure it more quickly. Therefore, pre-trained models are frequently used in the diagnosis of monkeypox, because the manual analysis of a large number of images is labor-intensive and prone to inaccuracy. Therefore, finding the monkeypox virus requires an automated process. The large layer count of convolutional neural network (CNN) architectures enables them to successfully conceptualize the features on their own, thereby contributing to better performance in image classification. The scientific community has recently articulated significant attention in employing artificial intelligence (AI) to diagnose monkeypox from digital skin images due primarily to AI's success in COVID-19 identification. The VGG16, VGG19, ResNet50, ResNet101, DenseNet201, and AlexNet models were used in our proposed method to classify patients with monkeypox symptoms with other diseases of a similar kind (chickenpox, measles, and normal). The majority of images in our research are collected from publicly available datasets. This study suggests an adaptive k-means clustering image segmentation technique that delivers precise segmentation results with straightforward operation. Our preliminary computational findings reveal that the proposed model could accurately detect patients with monkeypox. The best overall accuracy achieved by ResNet101 is 94.25%, with an AUC of 98.59%. Additionally, we describe the categorization of our model utilizing feature extraction using Local Interpretable Model-Agnostic Explanations (LIME), which provides a more in-depth understanding of particular properties that distinguish the monkeypox virus.

Detection of the rotator cuff tears using a novel convolutional neural network from magnetic resonance image (MRI)

The rotator cuff tear is a common situation for basketballers, handballers, or other athletes that strongly use their shoulders. This injury can be diagnosed precisely from a magnetic resonance (MR) image. In this paper, a novel deep learning-based framework is proposed to diagnose rotator cuff tear from MRI images of patients suspected of the rotator cuff tear. First, we collected 150 shoulders MRI images from two classes of rotator cuff tear patients and healthy ones with the same numbers. These images were observed by an orthopedic specialist and then tagged and used as input in the various configurations of the Convolutional Neural Network (CNN). At this stage, five different configurations of convolutional networks have been examined. Then, in the next step, the selected network with the highest accuracy is used to extract the deep features and classify the two classes of rotator cuff tear and healthy. Also, MRI images are feed to two quick pre-trained CNNs (MobileNetv2 and SqueezeNet) to compare with the proposed CNN. Finally, the evaluation is performed using the 5-fold cross-validation method. Also, a specific Graphical User Interface (GUI) was designed in the MATLAB environment for simplicity, which allows for testing by detecting the image class. The proposed CNN achieved higher accuracy than the two mentioned pre-trained CNNs. The average accuracy, precision, sensitivity, and specificity achieved by the best selected CNN configuration are equal to 92.67%, 91.13%, 91.75%, and 92.22%, respectively. The deep learning algorithm could accurately rule out significant rotator cuff tear based on shoulder MRI.

Intelligent detection of citrus fruit pests using machine vision system and convolutional neural network through transfer learning technique

Plant pests and diseases play a significant role in reducing the quality of agricultural products. As one of the most important plant pathogens, pests like Mediterranean fruit fly cause significant damage to crops and thus annually farmers face a lot of loss in their products. Therefore, the use of modern and non-destructive methods such as machine vision systems and deep learning for early detection of pests in agricultural products is of particular importance. In this study, citrus fruit images were taken in three stages: 1) before pest infestation, 2) beginning of fruit infestation, and 3) eight days after the second stage, in natural light conditions (7000-11,000 lux). A total of 1519 images were prepared for all classes. To classify the images, 70% of the images were used for the network training stage, 10% and 20% of the images were used for the validation and testing stages. Four pre-trained CNN models, namely ResNet-50, GoogleNet, VGG-16 and AlexNet as well as the SGDm, RMSProp and Adam optimization algorithms were used to identify and classify healthy fruit and fruit infected with the Mediterranean fly. The results of evaluating the models in the pest outbreak stage showed that the VGG-16 model with the help of SGDm algorithm had the best efficiency with the highest detection accuracy and F1 of 98.33% and 98.36%, respectively. The evaluation of the third stage showed that the AlexNet model with the help of SGDm algorithm had the best result with the highest detection accuracy and F1 of 99.33% and 99.34%, respectively. AlexNet model using SGDm optimization algorithm had the shortest network training time (323 s). The results of this study showed that convolutional neural network method and machine vision system can be effective in controlling and managing pests in orchards and other agricultural products.

The effect of Gaussian noise on pneumonia detection on chest radiographs, using convolutional neural networks

INTRODUCTION

Chest X-rays (CXR) with under-exposure increase image noise and this may affect convolutional neural network (CNN) performance. This study aimed to train and validate CNNs for classifying pneumonia on CXR as normal or pneumonia acquired at different image noise levels.

METHODS

The study used the curated and publicly available "Chest X-Ray Pneumonia" dataset of 5856 AP CXR classified into 1583 normal, 4273 viral and bacterial pneumonia cases. Gaussian noise with zero mean was added to the images, at 5 image noise variance levels, corresponding to decreasing exposure. Each noise-level dataset was split into 80% for training, 10% for validation, and 10% for test data and then classified using custom trained sequential CNN architecture. Six classification tasks were developed for five Gaussian noise levels and the original dataset. Sensitivity, specificity, predictive values and accuracy were used as evaluation performance metrics.

RESULTS

CNN evaluation on the different datasets revealed no performance drop from the original dataset to the five datasets with different noise levels. Sensitivity, specificity and accuracy for the normal datasets were 98.7%, 76.1% and 90.2%. For the five Gaussian noise levels the sensitivity, specificity and accuracy ranged from 96.9% to 98.2%, 94.4%-98.7% and 96.8%-97.6%, respectively. A heat map was used for visual explanation of the CNNs.

CONCLUSION

The CNNs sensitivity maintained, and the specificity increased in distinguishing between normal and pneumonia CXR with the introduction of image noise.

IMPLICATIONS FOR PRACTICE

No performance drops of CNNs in distinguishing cases with and without pneumonia CXR with different Gaussian noise levels was observed. This has potential for decreasing radiation dose to patients or maintaining exposure parameters for patients that require additional radiographs.

A Novel Lightweight Approach to COVID-19 Diagnostics Based on Chest X-ray Images

Background: This paper presents a novel lightweight approach based on machine learning methods supporting COVID-19 diagnostics based on X-ray images. The presented schema offers effective and quick diagnosis of COVID-19. Methods: Real data (X-ray images) from hospital patients were used in this study. All labels, namely those that were COVID-19 positive and negative, were confirmed by a PCR test. Feature extraction was performed using a convolutional neural network, and the subsequent classification of samples used Random Forest, XGBoost, LightGBM and CatBoost. Results: The LightGBM model was the most effective in classifying patients on the basis of features extracted from X-ray images, with an accuracy of 1.00, a precision of 1.00, a recall of 1.00 and an F1-score of 1.00. Conclusion: The proposed schema can potentially be used as a support for radiologists to improve the diagnostic process. The presented approach is efficient and fast. Moreover, it is not excessively complex computationally.

Learning-to-augment incorporated noise-robust deep CNN for detection of COVID-19 in noisy X-ray images

Deep convolutional neural networks (CNNs) are used for the detection of COVID-19 in X-ray images. The detection performance of deep CNNs may be reduced by noisy X-ray images. To improve the robustness of a deep CNN against impulse noise, we propose a novel CNN approach using adaptive convolution, with the aim to ameliorate COVID-19 detection in noisy X-ray images without requiring any preprocessing for noise removal. This approach includes an impulse noise-map layer, an adaptive resizing layer, and an adaptive convolution layer to the conventional CNN framework. We also used a learning-to-augment strategy using noisy X-ray images to improve the generalization of a deep CNN. We have collected a dataset of 2093 chest X-ray images including COVID-19 (452 images), non-COVID pneumonia (621 images), and healthy ones (1020 images). The architecture of pre-trained networks such as SqueezeNet, GoogleNet, MobileNetv2, ResNet18, ResNet50, ShuffleNet, and EfficientNetb0 has been modified to increase their robustness to impulse noise. Validation on the noisy X-ray images using the proposed noise-robust layers and learning-to-augment strategy-incorporated ResNet50 showed 2% better classification accuracy compared with state-of-the-art method.

A privacy-aware method for COVID-19 detection in chest CT images using lightweight deep conventional neural network and blockchain

With the global spread of the COVID-19 epidemic, a reliable method is required for identifying COVID-19 victims. The biggest issue in detecting the virus is a lack of testing kits that are both reliable and affordable. Due to the virus's rapid dissemination, medical professionals have trouble finding positive patients. However, the next real-life issue is sharing data with hospitals around the world while considering the organizations' privacy concerns. The primary worries for training a global Deep Learning (DL) model are creating a collaborative platform and personal confidentiality. Another challenge is exchanging data with health care institutions while protecting the organizations' confidentiality. The primary concerns for training a universal DL model are creating a collaborative platform and preserving privacy. This paper provides a model that receives a small quantity of data from various sources, like organizations or sections of hospitals, and trains a global DL model utilizing blockchain-based Convolutional Neural Networks (CNNs). In addition, we use the Transfer Learning (TL) technique to initialize layers rather than initialize randomly and discover which layers should be removed before selection. Besides, the blockchain system verifies the data, and the DL method trains the model globally while keeping the institution's confidentiality. Furthermore, we gather the actual and novel COVID-19 patients. Finally, we run extensive experiments utilizing Python and its libraries, such as Scikit-Learn and TensorFlow, to assess the proposed method. We evaluated works using five different datasets, including Boukan Dr. Shahid Gholipour hospital, Tabriz Emam Reza hospital, Mahabad Emam Khomeini hospital, Maragheh Dr.Beheshti hospital, and Miandoab Abbasi hospital datasets, and our technique outperform state-of-the-art methods on average in terms of precision (2.7%), recall (3.1%), F1 (2.9%), and accuracy (2.8%).

An automated diagnosis and classification of COVID-19 from chest CT images using a transfer learning-based convolutional neural network

Researchers have developed more intelligent, highly responsive, and efficient detection methods owing to the COVID-19 demands for more widespread diagnosis. The work done deals with developing an AI-based framework that can help radiologists and other healthcare professionals diagnose COVID-19 cases at a high level of accuracy. However, in the absence of publicly available CT datasets, the development of such AI tools can prove challenging. Therefore, an algorithm for performing automatic and accurate COVID-19 classification using Convolutional Neural Network (CNN), pre-trained model, and Sparrow search algorithm (SSA) on CT lung images was proposed. The pre-trained CNN models used are SeresNext50, SeresNext101, SeNet154, MobileNet, MobileNetV2, MobileNetV3Small, and MobileNetV3Large. In addition, the SSA will be used to optimize the different CNN and transfer learning(TL) hyperparameters to find the best configuration for the pre-trained model used and enhance its performance. Two datasets are used in the experiments. There are two classes in the first dataset, while three in the second. The authors combined two publicly available COVID-19 datasets as the first dataset, namely the COVID-19 Lung CT Scans and COVID-19 CT Scan Dataset. In total, 14,486 images were included in this study. The authors analyzed the Large COVID-19 CT scan slice dataset in the second dataset, which utilized 17,104 images. Compared to other pre-trained models on both classes datasets, MobileNetV3Large pre-trained is the best model. As far as the three-classes dataset is concerned, a model trained on SeNet154 is the best available. Results show that, when compared to other CNN models like LeNet-5 CNN, COVID faster R–CNN, Light CNN, Fuzzy + CNN, Dynamic CNN, CNN and Optimized CNN, the proposed Framework achieves the best accuracy of 99.74% (two classes) and 98% (three classes).

Aleatory-aware deep uncertainty quantification for transfer learning

The user does not have any idea about the credibility of outcomes from deep neural networks (DNN) when uncertainty quantification (UQ) is not employed. However, current Deep UQ classification models capture mostly epistemic uncertainty. Therefore, this paper aims to propose an aleatory-aware Deep UQ method for classification problems. First, we train DNNs through transfer learning and collect numeric output posteriors for all training samples instead of logical outputs. Then we determine the probability of happening a certain class from K-nearest output posteriors of the same DNN in training samples. We name this probability as opacity score, as the paper focuses on the detection of opacity on X-ray images. This score reflects the level of aleatory on the sample. When the NN is certain on the classification of the sample, the probability of happening a class becomes much higher than the probabilities of others. Probabilities for different classes become close to each other for a highly uncertain classification outcome. To capture the epistemic uncertainty, we train multiple DNNs with different random initializations, model selection, and augmentations to observe the effect of these training parameters on prediction and uncertainty. To reduce execution time, we first obtain features from the pre-trained NN. Then we apply features to the ensemble of fully connected layers to get the distribution of opacity score during the test. We also train several ResNet and DenseNet DNNs to observe the effect of model selection on prediction and uncertainty. The paper also demonstrates a patient referral framework based on the proposed uncertainty quantification. The scripts of the proposed method are available at the following link: https://github.com/dipuk0506/Aleatory-aware-UQ.

COVID-19 diagnosis using state-of-the-art CNN architecture features and Bayesian Optimization

The coronavirus outbreak 2019, called COVID-19, which originated in Wuhan, negatively affected the lives of millions of people and many people died from this infection. To prevent the spread of the disease, which is still in effect, various restriction decisions have been taken all over the world. In addition, the number of COVID-19 tests has been increased to quarantine infected people. However, due to the problems encountered in the supply of RT-PCR tests and the ease of obtaining Computed Tomography and X-ray images, imaging-based methods have become very popular in the diagnosis of COVID-19. Therefore, studies using these images to classify COVID-19 have increased. This paper presents a classification method for computed tomography chest images in the COVID-19 Radiography Database using features extracted by popular Convolutional Neural Networks (CNN) models (AlexNet, ResNet18, ResNet50, Inceptionv3, Densenet201, Inceptionresnetv2, MobileNetv2, GoogleNet). The determination of hyperparameters of Machine Learning (ML) algorithms by Bayesian optimization, and ANN-based image segmentation are the two main contributions in this study. First of all, lung segmentation is performed automatically from the raw image with Artificial Neural Networks (ANNs). To ensure data diversity, data augmentation is applied to the COVID-19 classes, which are fewer than the other two classes. Then these images are applied as input to five different CNN models. The features extracted from each CNN model are given as input to four different ML algorithms, namely Support Vector Machine (SVM), k-Nearest Neighbors (k-NN), Naive Bayes (NB), and Decision Tree (DT) for classification. To achieve the most successful classification accuracy, the hyperparameters of each ML algorithm are determined using Bayesian optimization. With the classification made using these hyperparameters, the highest success is obtained as 96.29% with the DenseNet201 model and SVM algorithm. The Sensitivity, Precision, Specificity, MCC, and F1-Score metric values for this structure are 0.9642, 0.9642, 0.9812, 0.9641 and 0.9453, respectively. These results showed that ML methods with the most optimum hyperparameters can produce successful results.

A deep learning-based COVID-19 classification from chest X-ray image: case study

The novel corona virus disease (COVID-19) is a pandemic disease that is currently affecting over 200 countries around the world and more than 6 millions of people died in last 2 years. Early detection of COVID-19 can mitigate and control its spread. Reverse transcription polymerase chain reaction (RT-CPR), Chest X-ray (CXR) scan, and Computerized Tomography (CT) scan are used to identify the COVID-19. Chest X-ray image analysis is relatively time efficient than compared with RT-CPR and CT scan. Its cost-effectiveness make it a good choice for COVID-19 Classification. We propose a deep learning based Convolutional Neural Network model for detection of COVID-19 from CXR. Chest X-ray images are collected from various sources dataset for training with augmentation and evaluating our model, which is widely used for COVID-19 detection and diagnosis. A Deep Convolutional neural network (CNN) based model for analysis of COVID-19 with data augmentation is proposed, which uses the patient's chest X-ray images for the diagnosis of COVID-19 with an aim to help the physicians to assist the diagnostic process among high workload conditions. The overall accuracy of 93 percent for COVID-19 Classification is achieved by choosing best optimizer.

Greedy Autoaugment for classification of mycobacterium tuberculosis image via generalized deep CNN using mixed pooling based on minimum square rough entropy

Although tuberculosis (TB) is a disease whose cause, epidemiology and treatment are well known, some infected patients in many parts of the world are still not diagnosed by current methods, leading to further transmission in society. Creating an accurate image-based processing system for screening patients can help in the early diagnosis of this disease. We provided a dataset containing1078 confirmed negative and 469 positive Mycobacterium tuberculosis instances. An effective method using an improved and generalized convolutional neural network (CNN) was proposed for classifying TB bacteria in microscopic images. In the preprocessing phase, the insignificant parts of microscopic images are excluded with an efficient algorithm based on the square rough entropy (SRE) thresholding. Top 10 policies of data augmentation were selected with the proposed model based on the Greedy AutoAugment algorithm to resolve the overfitting problem. In order to improve the generalization of CNN, mixed pooling was used instead of baseline one. The results showed that employing generalized pooling, batch normalization, Dropout, and PReLU have improved the classification of Mycobacterium tuberculosis images. The output of classifiers such as Naïve Bayes-LBP, KNN-LBP, GBT-LBP, Naïve Bayes-HOG, KNN-HOG, SVM-HOG, GBT-HOG indicated that proposed CNN has the best results with an accuracy of 93.4%. The improvements of CNN based on the proposed model can yield promising results for diagnosing TB.

Detection of fraud in ginger powder using an automatic sorting system based on image processing technique and deep learning

Ginger is a well-known product in the food and pharmaceutical industries. Ginger is one of the spices which are adulterated for economic gain. The lack of marketability of grade 3 chickpeas (small and broken chickpeas) and their very low price have made them a good choice to be mixed with ginger in powder form and sold in the market. Demand for non-destructive methods of measuring food quality, such as machine vision and the growing need for food and spices, were the main motives to conduct this study. This study classified ginger powder images to detect fraud by improving convolutional neural networks (CNN) through a gated pooling function. The main approach to improving CNN is to use a pooling function that combines average pooling and max pooling. The Batch normalization (BN) technique is used in CNN to improve classification results. We show empirically that the combining operation used increases the accuracy of ginger powder classification compared to the baseline pooling method. For this purpose, 3360 image samples of ginger powder were prepared in 7 categories (pure ginger powder, chickpea powder, 10%, 20%, 30%, 40%, and 50% fraud in ginger powder). Moreover, MLP, Fuzzy, SVM, GBT, and EDT algorithms were used to compare the proposed CNN results with other classifiers. The results showed that using batch normalization based on gated pooling, the proposed CNN was able to grade the images of ginger powder with 99.70% accuracy compared to other classifiers. Therefore, it can be said that the CNN method and image processing technique effectively increase marketability, prevent ginger powder fraud, and promote traditional methods of ginger powder fraud detection.