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Register a new userDeep Learning for Automated Classification of Tuberculosis-Related Chest X-Ray: Dataset Specificity Limits Diagnostic Performance Generalizability
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Added by
Krit Pongpirul
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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Machine learning has been an emerging tool for various aspects of infectious diseases including tuberculosis surveillance and detection. However, WHO provided no recommendations on using computer-aided tuberculosis detection software because of the small number of studies, methodological limitations, and limited generalizability of the findings. To quantify the generalizability of the machine-learning model, we developed a Deep Convolutional Neural Network (DCNN) model using a TB-specific CXR dataset of one population (National Library of Medicine Shenzhen No.3 Hospital) and tested it with non-TB-specific CXR dataset of another population (National Institute of Health Clinical Centers). The findings suggested that a supervised deep learning model developed by using the training dataset from one population may not have the same diagnostic performance in another population. Technical specification of CXR images, disease severity distribution, overfitting, and overdiagnosis should be examined before implementation in other settings.
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Chest X-rays are the most commonly performed diagnostic examination to detect cardiopulmonary abnormalities. However, the presence of bony structures such as ribs and clavicles can obscure subtle abnormalities, resulting in diagnostic errors. This study aims to build a deep learning-based bone suppression model that identifies and removes these occluding bony structures in frontal CXRs to assist in reducing errors in radiological interpretation, including DL workflows, related to detecting manifestations consistent with tuberculosis (TB). Several bone suppression models with various deep architectures are trained and optimized using the proposed combined loss function and their performances are evaluated in a cross-institutional test setting. The best-performing model is used to suppress bones in the publicly available Shenzhen and Montgomery TB CXR collections. A VGG-16 model is pretrained on a large collection of publicly available CXRs. The CXR-pretrained model is then fine-tuned individually on the non-bone-suppressed and bone-suppressed CXRs of Shenzhen and Montgomery TB CXR collections to classify them as showing normal lungs or TB manifestations. The performances of these models are compared using several performance metrics, analyzed for statistical significance, and their predictions are qualitatively interpreted through class-selective relevance maps. It is observed that the models trained on bone-suppressed CXRs significantly outperformed (p<0.05) the models trained on the non-bone-suppressed CXRs. Models trained on bone-suppressed CXRs improved detection of TB-consistent findings and resulted in compact clustering of the data points in the feature space signifying that bone suppression improved the model sensitivity toward TB classification.
Tuberculosis (TB) is a chronic lung disease that occurs due to bacterial infection and is one of the top 10 leading causes of death. Accurate and early detection of TB is very important, otherwise, it could be life-threatening. In this work, we have detected TB reliably from the chest X-ray images using image pre-processing, data augmentation, image segmentation, and deep-learning classification techniques. Several public databases were used to create a database of 700 TB infected and 3500 normal chest X-ray images for this study. Nine different deep CNNs (ResNet18, ResNet50, ResNet101, ChexNet, InceptionV3, Vgg19, DenseNet201, SqueezeNet, and MobileNet), which were used for transfer learning from their pre-trained initial weights and trained, validated and tested for classifying TB and non-TB normal cases. Three different experiments were carried out in this work: segmentation of X-ray images using two different U-net models, classification using X-ray images, and segmented lung images. The accuracy, precision, sensitivity, F1-score, specificity in the detection of tuberculosis using X-ray images were 97.07 %, 97.34 %, 97.07 %, 97.14 % and 97.36 % respectively. However, segmented lungs for the classification outperformed than whole X-ray image-based classification and accuracy, precision, sensitivity, F1-score, specificity were 99.9 %, 99.91 %, 99.9 %, 99.9 %, and 99.52 % respectively. The paper also used a visualization technique to confirm that CNN learns dominantly from the segmented lung regions results in higher detection accuracy. The proposed method with state-of-the-art performance can be useful in the computer-aided faster diagnosis of tuberculosis.
The gold standard for COVID-19 is RT-PCR, testing facilities for which are limited and not always optimally distributed. Test results are delayed, which impacts treatment. Expert radiologists, one of whom is a co-author, are able to diagnose COVID-19 positivity from Chest X-Rays (CXR) and CT scans, that can facilitate timely treatment. Such diagnosis is particularly valuable in locations lacking radiologists with sufficient expertise and familiarity with COVID-19 patients. This paper has two contributions. One, we analyse literature on CXR based COVID-19 diagnosis. We show that popular choices of dataset selection suffer from data homogeneity, leading to misleading results. We compile and analyse a viable benchmark dataset from multiple existing heterogeneous sources. Such a benchmark is important for realistically testing models. Our second contribution relates to learning from imbalanced data. Datasets for COVID X-Ray classification face severe class imbalance, since most subjects are COVID -ve. Twin Support Vector Machines (Twin SVM) and Twin Neural Networks (Twin NN) have, in recent years, emerged as effective ways of handling skewed data. We introduce a state-of-the-art technique, termed as Twin Augmentation, for modifying popular pre-trained deep learning models. Twin Augmentation boosts the performance of a pre-trained deep neural network without requiring re-training. Experiments show, that across a multitude of classifiers, Twin Augmentation is very effective in boosting the performance of given pre-trained model for classification in imbalanced settings.
CXRs are a crucial and extraordinarily common diagnostic tool, leading to heavy research for CAD solutions. However, both high classification accuracy and meaningful model predictions that respect and incorporate clinical taxonomies are crucial for CAD usability. To this end, we present a deep HMLC approach for CXR CAD. Different than other hierarchical systems, we show that first training the network to model conditional probability directly and then refining it with unconditional probabilities is key in boosting performance. In addition, we also formulate a numerically stable cross-entropy loss function for unconditional probabilities that provides concrete performance improvements. Finally, we demonstrate that HMLC can be an effective means to manage missing or incomplete labels. To the best of our knowledge, we are the first to apply HMLC to medical imaging CAD. We extensively evaluate our approach on detecting abnormality labels from the CXR arm of the PLCO dataset, which comprises over $198,000$ manually annotated CXRs. When using complete labels, we report a mean AUC of 0.887, the highest yet reported for this dataset. These results are supported by ancillary experiments on the PadChest dataset, where we also report significant improvements, 1.2% and 4.1% in AUC and AP, respectively over strong flat classifiers. Finally, we demonstrate that our HMLC approach can much better handle incompletely labelled data. These performance improvements, combined with the inherent usefulness of taxonomic predictions, indicate that our approach represents a useful step forward for CXR CAD.
Robotic weed control has seen increased research of late with its potential for boosting productivity in agriculture. Majority of works focus on developing robotics for croplands, ignoring the weed management problems facing rangeland stock farmers. Perhaps the greatest obstacle to widespread uptake of robotic weed control is the robust classification of weed species in their natural environment. The unparalleled successes of deep learning make it an ideal candidate for recognising various weed species in the complex rangeland environment. This work contributes the first large, public, multiclass image dataset of weed species from the Australian rangelands; allowing for the development of robust classification methods to make robotic weed control viable. The DeepWeeds dataset consists of 17,509 labelled images of eight nationally significant weed species native to eight locations across northern Australia. This paper presents a baseline for classification performance on the dataset using the benchmark deep learning models, Inception-v3 and ResNet-50. These models achieved an average classification accuracy of 95.1% and 95.7%, respectively. We also demonstrate real time performance of the ResNet-50 architecture, with an average inference time of 53.4 ms per image. These strong results bode well for future field implementation of robotic weed control methods in the Australian rangelands.
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