Dataset Information

An ensemble deep learning model for risk stratification of invasive lung adenocarcinoma using thin-slice CT.

ABSTRACT: Lung cancer screening using computed tomography (CT) has increased the detection rate of small pulmonary nodules and early-stage lung adenocarcinoma. It would be clinically meaningful to accurate assessment of the nodule histology by CT scans with advanced deep learning algorithms. However, recent studies mainly focus on predicting benign and malignant nodules, lacking of model for the risk stratification of invasive adenocarcinoma. We propose an ensemble multi-view 3D convolutional neural network (EMV-3D-CNN) model to study the risk stratification of lung adenocarcinoma. We include 1075 lung nodules (≤30 mm and ≥4 mm) with preoperative thin-section CT scans and definite pathology confirmed by surgery. Our model achieves a state-of-art performance of 91.3% and 92.9% AUC for diagnosis of benign/malignant and pre-invasive/invasive nodules, respectively. Importantly, our model outperforms senior doctors in risk stratification of invasive adenocarcinoma with 77.6% accuracy [i.e., Grades 1, 2, 3]). It provides detailed predictive histological information for the surgical management of pulmonary nodules. Finally, for user-friendly access, the proposed model is implemented as a web-based system ( https://seeyourlung.com.cn ).

SUBMITTER: Zhou J

PROVIDER: S-EPMC10322969 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature

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An ensemble deep learning model for risk stratification of invasive lung adenocarcinoma using thin-slice CT.

Zhou Jing J Hu Bin B Feng Wei W Zhang Zhang Z Fu Xiaotong X Shao Handie H Wang Hansheng H Jin Longyu L Ai Siyuan S Ji Ying Y

NPJ digital medicine 20230705 1

Lung cancer screening using computed tomography (CT) has increased the detection rate of small pulmonary nodules and early-stage lung adenocarcinoma. It would be clinically meaningful to accurate assessment of the nodule histology by CT scans with advanced deep learning algorithms. However, recent studies mainly focus on predicting benign and malignant nodules, lacking of model for the risk stratification of invasive adenocarcinoma. We propose an ensemble multi-view 3D convolutional neural netwo ...[more]

PMID: 37407729

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Project description:Using nephrographic phase CT images combined with pathology diagnosis, we aim to develop and validate a fusion feature-based stacking ensemble machine learning model to distinguish malignant renal neoplasms from cystic renal lesions (CRLs). This retrospective research includes 166 individuals with CRLs for model training and 47 individuals with CRLs in another institution for model testing. Histopathology results are adopted as diagnosis criterion. Nephrographic phase CT scans are selected to build the fusion feature-based machine learning algorithms. The pretrained 3D-ResNet50 CNN model and radiomics methods are selected to extract deep features and radiomics features, respectively. Fivefold cross-validated least absolute shrinkage and selection operator (LASSO) regression methods are adopted to identify the most discriminative candidate features in the development cohort. Intraclass correlation coefficients and interclass correlation coefficients are employed to evaluate feature's reproducibility. Pearson correlation coefficients for normal distribution features and Spearman's rank correlation coefficients for non-normal distribution features are used to eliminate redundant features. After that, stacking ensemble machine learning models are developed in the training cohort. The area under the receiver operator characteristic curve (ROC), calibration curve, and decision curve analysis (DCA) are adopted in the testing cohort to evaluate the performance of each model. The stacking ensemble machine learning algorithm reached excellent diagnostic performance in the testing dataset. The calibration plot shows good stability when using the stacking ensemble model. Net benefits presented by DCA are higher than the Bosniak 2019 version classification when employing any machine learning algorithm. The fusion feature-based machine learning algorithm accurately distinguishes malignant renal neoplasms from CRLs, which outperformed the Bosniak 2019 version classification, and proves to be more applicable for clinical decision-making.

Project description:ObjectivesAlthough CT scanners generally allow dynamic acquisition of thin slices (1 mm), thick slice (≥5 mm) reconstruction is commonly used for stroke imaging to reduce data, processing time, and noise level. Thin slice CT perfusion (CTP) reconstruction may suffer less from partial volume effects, and thus yield more accurate quantitative results with increased resolution. Before thin slice protocols are to be introduced clinically, it needs to be ensured that this does not affect overall CTP constancy. We studied the influence of thin slice reconstruction on average perfusion values by comparing it with standard thick slice reconstruction.Materials and methodsFrom 50 patient studies, absolute and relative hemisphere averaged estimates of cerebral blood volume (CBV), cerebral blood flow (CBF), mean transit time (MTT), and permeability-surface area product (PS) were analyzed using 0.8, 2.4, 4.8, and 9.6 mm slice reconstructions. Specifically, the influence of Gaussian and bilateral filtering, the arterial input function (AIF), and motion correction on the perfusion values was investigated.ResultsBilateral filtering gave noise levels comparable to isotropic Gaussian filtering, with less partial volume effects. Absolute CBF, CBV and PS were 22%, 14% and 46% lower with 0.8 mm than with 4.8 mm slices. If the AIF and motion correction were based on thin slices prior to reconstruction of thicker slices, these differences reduced to 3%, 4% and 3%. The effect of slice thickness on relative values was very small.ConclusionsThis study shows that thin slice reconstruction for CTP with unaltered acquisition protocol gives relative perfusion values without clinically relevant bias. It does however affect absolute perfusion values, of which CBF and CBV are most sensitive. Partial volume effects in large arteries and veins lead to overestimation of these values. The effects of reconstruction slice thickness should be taken into account when absolute perfusion values are used for clinical decision making.

Project description:ObjectivesQuantitative CT imaging is an important emphysema biomarker, especially in smoking cohorts, but does not always correlate to radiologists' visual CT assessments. The objectives were to develop and validate a neural network-based slice-wise whole-lung emphysema score (SWES) for chest CT, to validate SWES on unseen CT data, and to compare SWES with a conventional quantitative CT method.Materials and methodsSeparate cohorts were used for algorithm development and validation. For validation, thin-slice CT stacks from 474 participants in the prospective cross-sectional Swedish CArdioPulmonary bioImage Study (SCAPIS) were included, 395 randomly selected and 79 from an emphysema cohort. Spirometry (FEV1/FVC) and radiologists' visual emphysema scores (sum-visual) obtained at inclusion in SCAPIS were used as reference tests. SWES was compared with a commercially available quantitative emphysema scoring method (LAV950) using Pearson's correlation coefficients and receiver operating characteristics (ROC) analysis.ResultsSWES correlated more strongly with the visual scores than LAV950 (r = 0.78 vs. r = 0.41, p < 0.001). The area under the ROC curve for the prediction of airway obstruction was larger for SWES than for LAV950 (0.76 vs. 0.61, p = 0.007). SWES correlated more strongly with FEV1/FVC than either LAV950 or sum-visual in the full cohort (r = - 0.69 vs. r = - 0.49/r = - 0.64, p < 0.001/p = 0.007), in the emphysema cohort (r = - 0.77 vs. r = - 0.69/r = - 0.65, p = 0.03/p = 0.002), and in the random sample (r = - 0.39 vs. r = - 0.26/r = - 0.25, p = 0.001/p = 0.007).ConclusionThe slice-wise whole-lung emphysema score (SWES) correlates better than LAV950 with radiologists' visual emphysema scores and correlates better with airway obstruction than do LAV950 and radiologists' visual scores.Clinical relevance statementThe slice-wise whole-lung emphysema score provides quantitative emphysema information for CT imaging that avoids the disadvantages of threshold-based scores and is correlated more strongly with reference tests than LAV950 and reader visual scores.Key points• A slice-wise whole-lung emphysema score (SWES) was developed to quantify emphysema in chest CT images. • SWES identified visual emphysema and spirometric airflow limitation significantly better than threshold-based score (LAV950). • SWES improved emphysema quantification in CT images, which is especially useful in large-scale research.

Project description:BackgroundPreoperative prediction models for histologic subtype and grade of stage IA lung adenocarcinoma (LUAD) according to the update of the WHO Classification of Tumors of the Lung in 2021 and the 2020 new grade system are yet to be explored. We aim to develop the noninvasive pathology and grade evaluation approach for patients with stage IA LUAD via CT-based radiomics approach and evaluate their performance in clinical practice.MethodsChest CT scans were retrospectively collected from patients who were diagnosed with stage IA LUAD and underwent complete resection at two hospitals. A deep learning segmentation algorithm was first applied to assist lesion delineation. Expansion strategies such as bounding-box annotations were further applied. Radiomics features were then extracted and selected followed by radiomics modeling based on four classic machine learning algorithms for histologic subtype classification and grade stratification. The area under the receiver operating characteristic curve (AUC) was used to evaluate model performance.ResultsThe study included 294 and 145 patients with stage IA LUAD from two hospitals for radiomics analysis, respectively. For classification of four histological subtypes, multilayer perceptron (MLP) algorithm presented no annotation strategy preference and achieved the average AUC of 0.855, 0.922, and 0.720 on internal, independent, and external test sets with 1-pixel expansion annotation. Bounding-box annotation strategy also enabled MLP an acceptable and stable accuracy among test sets. Meanwhile, logistic regression was selected for grade stratification and achieved the average AUC of 0.928, 0.837, and 0.748 on internal, independent, and external test sets with optimal annotation strategies.ConclusionsDL-enhanced radiomics models had great potential to predict the fine histological subtypes and grades of early-stage LUADs based on CT images, which might serve as a promising noninvasive approach for the diagnosis and management of early LUADs.

Dataset Information

An ensemble deep learning model for risk stratification of invasive lung adenocarcinoma using thin-slice CT.

Publications

An ensemble deep learning model for risk stratification of invasive lung adenocarcinoma using thin-slice CT.

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