Dataset Information

Computer-aided diagnosis of lung nodule classification between benign nodule, primary lung cancer, and metastatic lung cancer at different image size using deep convolutional neural network with transfer learning.

ABSTRACT: We developed a computer-aided diagnosis (CADx) method for classification between benign nodule, primary lung cancer, and metastatic lung cancer and evaluated the following: (i) the usefulness of the deep convolutional neural network (DCNN) for CADx of the ternary classification, compared with a conventional method (hand-crafted imaging feature plus machine learning), (ii) the effectiveness of transfer learning, and (iii) the effect of image size as the DCNN input. Among 1240 patients of previously-built database, computed tomography images and clinical information of 1236 patients were included. For the conventional method, CADx was performed by using rotation-invariant uniform-pattern local binary pattern on three orthogonal planes with a support vector machine. For the DCNN method, CADx was evaluated using the VGG-16 convolutional neural network with and without transfer learning, and hyperparameter optimization of the DCNN method was performed by random search. The best averaged validation accuracies of CADx were 55.9%, 68.0%, and 62.4% for the conventional method, the DCNN method with transfer learning, and the DCNN method without transfer learning, respectively. For image size of 56, 112, and 224, the best averaged validation accuracy for the DCNN with transfer learning were 60.7%, 64.7%, and 68.0%, respectively. DCNN was better than the conventional method for CADx, and the accuracy of DCNN improved when using transfer learning. Also, we found that larger image sizes as inputs to DCNN improved the accuracy of lung nodule classification.

SUBMITTER: Nishio M

PROVIDER: S-EPMC6063408 | biostudies-other | 2018

REPOSITORIES: biostudies-other

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Computer-aided diagnosis of lung nodule classification between benign nodule, primary lung cancer, and metastatic lung cancer at different image size using deep convolutional neural network with transfer learning.

Nishio Mizuho M Sugiyama Osamu O Yakami Masahiro M Ueno Syoko S Kubo Takeshi T Kuroda Tomohiro T Togashi Kaori K

PloS one 20180727 7

We developed a computer-aided diagnosis (CADx) method for classification between benign nodule, primary lung cancer, and metastatic lung cancer and evaluated the following: (i) the usefulness of the deep convolutional neural network (DCNN) for CADx of the ternary classification, compared with a conventional method (hand-crafted imaging feature plus machine learning), (ii) the effectiveness of transfer learning, and (iii) the effect of image size as the DCNN input. Among 1240 patients of previous ...[more]

PMID: 30052644

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Project description:ObjectiveIn this study, we evaluated a commercially available computer assisted diagnosis system (CAD). The deep learning algorithm of the CAD was trained with a lung cancer screening cohort and developed for detection, classification, quantification, and growth of actionable pulmonary nodules on chest CT scans. Here, we evaluated the CAD in a retrospective cohort of a routine clinical population.Materials and methodsIn total, a number of 337 scans of 314 different subjects with reported nodules of 3-30 mm in size were included into the evaluation. Two independent thoracic radiologists alternately reviewed scans with or without CAD assistance to detect, classify, segment, and register pulmonary nodules. A third, more experienced, radiologist served as an adjudicator. In addition, the cohort was analyzed by the CAD alone. The study cohort was divided into five different groups: 1) 178 CT studies without reported pulmonary nodules, 2) 95 studies with 1-10 pulmonary nodules, 23 studies from the same patients with 3) baseline and 4) follow-up studies, and 5) 18 CT studies with subsolid nodules. A reference standard for nodules was based on majority consensus with the third thoracic radiologist as required. Sensitivity, false positive (FP) rate and Dice inter-reader coefficient were calculated.ResultsAfter analysis of 470 pulmonary nodules, the sensitivity readings for radiologists without CAD and radiologist with CAD, were 71.9% (95% CI: 66.0%, 77.0%) and 80.3% (95% CI: 75.2%, 85.0%) (p < 0.01), with average FP rate of 0.11 and 0.16 per CT scan, respectively. Accuracy and kappa of CAD for classifying solid vs sub-solid nodules was 94.2% and 0.77, respectively. Average inter-reader Dice coefficient for nodule segmentation was 0.83 (95% CI: 0.39, 0.96) and 0.86 (95% CI: 0.51, 0.95) for CAD versus readers. Mean growth percentage discrepancy of readers and CAD alone was 1.30 (95% CI: 1.02, 2.21) and 1.35 (95% CI: 1.01, 4.99), respectively.ConclusionThe applied CAD significantly increased radiologist's detection of actionable nodules yet also minimally increasing the false positive rate. The CAD can automatically classify and quantify nodules and calculate nodule growth rate in a cohort of a routine clinical population. Results suggest this Deep Learning software has the potential to assist chest radiologists in the tasks of pulmonary nodule detection and management within their routine clinical practice.

Project description:Chest X-ray (CXR) imaging is one of the most feasible diagnosis modalities for early detection of the infection of COVID-19 viruses, which is classified as a pandemic according to the World Health Organization (WHO) report in December 2019. COVID-19 is a rapid natural mutual virus that belongs to the coronavirus family. CXR scans are one of the vital tools to early detect COVID-19 to monitor further and control its virus spread. Classification of COVID-19 aims to detect whether a subject is infected or not. In this article, a model is proposed for analyzing and evaluating grayscale CXR images called Chest X-Ray COVID Network (CXRVN) based on three different COVID-19 X-Ray datasets. The proposed CXRVN model is a lightweight architecture that depends on a single fully connected layer representing the essential features and thus reducing the total memory usage and processing time verse pre-trained models and others. The CXRVN adopts two optimizers: mini-batch gradient descent and Adam optimizer, and the model has almost the same performance. Besides, CXRVN accepts CXR images in grayscale that are a perfect image representation for CXR and consume less memory storage and processing time. Hence, CXRVN can analyze the CXR image with high accuracy in a few milliseconds. The consequences of the learning process focus on decision making using a scoring function called SoftMax that leads to high rate true-positive classification. The CXRVN model is trained using three different datasets and compared to the pre-trained models: GoogleNet, ResNet and AlexNet, using the fine-tuning and transfer learning technologies for the evaluation process. To verify the effectiveness of the CXRVN model, it was evaluated in terms of the well-known performance measures such as precision, sensitivity, F1-score and accuracy. The evaluation results based on sensitivity, precision, recall, accuracy, and F1 score demonstrated that, after GAN augmentation, the accuracy reached 96.7% in experiment 2 (Dataset-2) for two classes and 93.07% in experiment-3 (Dataset-3) for three classes, while the average accuracy of the proposed CXRVN model is 94.5%.

Project description:To develop a computer-aided detection (CADe) scheme for nodules in chest radiographs (CXRs) with a high sensitivity and a low false-positive (FP) rate.The authors developed a CADe scheme consisting of five major steps, which were developed for improving the overall performance of CADe schemes. First, to segment the lung fields accurately, the authors developed a multisegment active shape model. Then, a two-stage nodule-enhancement technique was developed for improving the conspicuity of nodules. Initial nodule candidates were detected and segmented by using the clustering watershed algorithm. Thirty-one shape-, gray-level-, surface-, and gradient-based features were extracted from each segmented candidate for determining the feature space, including one of the new features based on the Canny edge detector to eliminate a major FP source caused by rib crossings. Finally, a nonlinear support vector machine (SVM) with a Gaussian kernel was employed for classification of the nodule candidates.To evaluate and compare the scheme to other published CADe schemes, the authors used a publicly available database containing 140 nodules in 140 CXRs and 93 normal CXRs. The CADe scheme based on the SVM classifier achieved sensitivities of 78.6% (110/140) and 71.4% (100/140) with averages of 5.0 (1165/233) FPs/image and 2.0 (466/233) FPs/image, respectively, in a leave-one-out cross-validation test, whereas the CADe scheme based on a linear discriminant analysis classifier had a sensitivity of 60.7% (85/140) at an FP rate of 5.0 FPs/image. For nodules classified as "very subtle" and "extremely subtle," a sensitivity of 57.1% (24/42) was achieved at an FP rate of 5.0 FPs/image. When the authors used a database developed at the University of Chicago, the sensitivities was 83.3% (40/48) and 77.1% (37/48) at an FP rate of 5.0 (240/48) FPs/image and 2.0 (96/48) FPs/image, respectively.These results compare favorably to those described for other commercial and non-commercial CADe nodule detection systems.

Project description:Training deep Convolutional Neural Networks (CNNs) presents challenges in terms of memory requirements and computational resources, often resulting in issues such as model overfitting and lack of generalization. These challenges can only be mitigated by using an excessive number of training images. However, medical image datasets commonly suffer from data scarcity due to the complexities involved in their acquisition, preparation, and curation. To address this issue, we propose a compact and hybrid machine learning architecture based on the Morphological and Convolutional Neural Network (MCNN), followed by a Random Forest classifier. Unlike deep CNN architectures, the MCNN was specifically designed to achieve effective performance with medical image datasets limited to a few hundred samples. It incorporates various morphological operations into a single layer and uses independent neural networks to extract information from each signal channel. The final classification is obtained by utilizing a Random Forest classifier on the outputs of the last neural network layer. We compare the classification performance of our proposed method with three popular deep CNN architectures (ResNet-18, ShuffleNet-V2, and MobileNet-V2) using two training approaches: full training and transfer learning. The evaluation was conducted on two distinct medical image datasets: the ISIC dataset for melanoma classification and the ORIGA dataset for glaucoma classification. Results demonstrate that the MCNN method exhibits reliable performance in melanoma classification, achieving an AUC of 0.94 (95% CI: 0.91 to 0.97), outperforming the popular CNN architectures. For the glaucoma dataset, the MCNN achieved an AUC of 0.65 (95% CI: 0.53 to 0.74), which was similar to the performance of the popular CNN architectures. This study contributes to the understanding of mathematical morphology in shallow neural networks for medical image classification and highlights the potential of hybrid architectures in effectively learning from medical image datasets that are limited by a small number of case samples.

Project description:PURPOSE:Convolutional neural networks have become rapidly popular for image recognition and image analysis because of its powerful potential. In this paper, we developed a method for classifying subtypes of lung adenocarcinoma from pathological images using neural network whose that can evaluate phenotypic features from wider area to consider cellular distributions. METHODS:In order to recognize the types of tumors, we need not only to detail features of cells, but also to incorporate statistical distribution of the different types of cells. Variants of autoencoders as building blocks of pre-trained convolutional layers of neural networks are implemented. A sparse deep autoencoder which minimizes local information entropy on the encoding layer is then proposed and applied to images of size [Formula: see text]. We applied this model for feature extraction from pathological images of lung adenocarcinoma, which is comprised of three transcriptome subtypes previously defined by the Cancer Genome Atlas network. Since the tumor tissue is composed of heterogeneous cell populations, recognition of tumor transcriptome subtypes requires more information than local pattern of cells. The parameters extracted using this approach will then be used in multiple reduction stages to perform classification on larger images. RESULTS:We were able to demonstrate that these networks successfully recognize morphological features of lung adenocarcinoma. We also performed classification and reconstruction experiments to compare the outputs of the variants. The results showed that the larger input image that covers a certain area of the tissue is required to recognize transcriptome subtypes. The sparse autoencoder network with [Formula: see text] input provides a 98.9% classification accuracy. CONCLUSION:This study shows the potential of autoencoders as a feature extraction paradigm and paves the way for a whole slide image analysis tool to predict molecular subtypes of tumors from pathological features.

Dataset Information

Computer-aided diagnosis of lung nodule classification between benign nodule, primary lung cancer, and metastatic lung cancer at different image size using deep convolutional neural network with transfer learning.

Publications

Computer-aided diagnosis of lung nodule classification between benign nodule, primary lung cancer, and metastatic lung cancer at different image size using deep convolutional neural network with transfer learning.

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