Dataset Information

Deep CNN Model Using CT Radiomics Feature Mapping Recognizes EGFR Gene Mutation Status of Lung Adenocarcinoma.

ABSTRACT: To recognize the epidermal growth factor receptor (EGFR) gene mutation status in lung adenocarcinoma (LADC) has become a prerequisite of deciding whether EGFR-tyrosine kinase inhibitor (EGFR-TKI) medicine can be used. Polymerase chain reaction assay or gene sequencing is for measuring EGFR status, however, the tissue samples by surgery or biopsy are required. We propose to develop deep learning models to recognize EGFR status by using radiomics features extracted from non-invasive CT images. Preoperative CT images, EGFR mutation status and clinical data have been collected in a cohort of 709 patients (the primary cohort) and an independent cohort of 205 patients. After 1,037 CT-based radiomics features are extracted from each lesion region, 784 discriminative features are selected for analysis and construct a feature mapping. One Squeeze-and-Excitation (SE) Convolutional Neural Network (SE-CNN) has been designed and trained to recognize EGFR status from the radiomics feature mapping. SE-CNN model is trained and validated by using 638 patients from the primary cohort, tested by using the rest 71 patients (the internal test cohort), and further tested by using the independent 205 patients (the external test cohort). Furthermore, SE-CNN model is compared with machine learning (ML) models using radiomics features, clinical features, and both features. EGFR(-) patients show the smaller age, higher odds of female, larger lesion volumes, and lower odds of subtype of acinar predominant adenocarcinoma (APA), compared with EGFR(+). The most discriminative features are for texture (614, 78.3%) and the features of first order of intensity (158, 20.1%) and the shape features (12, 1.5%) follow. SE-CNN model can recognize EGFR mutation status with an AUC of 0.910 and 0.841 for the internal and external test cohorts, respectively. It outperforms the CNN model without SE, the fine-tuned VGG16 and VGG19, three ML models, and the state-of-art models. Utilizing radiomics feature mapping extracted from non-invasive CT images, SE-CNN can precisely recognize EGFR mutation status of LADC patients. The proposed method combining radiomics features and deep leaning is superior to ML methods and can be expanded to other medical applications. The proposed SE-CNN model may help make decision on usage of EGFR-TKI medicine.

SUBMITTER: Zhang B

PROVIDER: S-EPMC7907520 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Deep CNN Model Using CT Radiomics Feature Mapping Recognizes EGFR Gene Mutation Status of Lung Adenocarcinoma.

Zhang Baihua B Qi Shouliang S Pan Xiaohuan X Li Chen C Yao Yudong Y Qian Wei W Guan Yubao Y

Frontiers in oncology 20210212

To recognize the epidermal growth factor receptor (EGFR) gene mutation status in lung adenocarcinoma (LADC) has become a prerequisite of deciding whether EGFR-tyrosine kinase inhibitor (EGFR-TKI) medicine can be used. Polymerase chain reaction assay or gene sequencing is for measuring EGFR status, however, the tissue samples by surgery or biopsy are required. We propose to develop deep learning models to recognize EGFR status by using radiomics features extracted from non-invasive CT images. Pre ...[more]

PMID: 33643902

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Project description:Purpose: This study aimed to compare the performance of radiomics and deep learning in predicting EGFR mutation status in patients with lung cancer based on PET/CT images, and tried to explore a model with excellent prediction performance to accurately predict EGFR mutation status in patients with non-small cell lung cancer (NSCLC). Method: PET/CT images of 194 NSCLC patients from Xijing Hospital were collected and divided into a training set and a validation set according to the ratio of 7:3. Statistics were made on patients' clinical characteristics, and a large number of features were extracted based on their PET/CT images (4306 radiomics features and 2048 deep learning features per person) with the pyradiomics toolkit and 3D convolutional neural network. Then a radiomics model (RM), a deep learning model (DLM), and a hybrid model (HM) were established. The performance of the three models was compared by receiver operating characteristic (ROC) curves, sensitivity, specificity, accuracy, calibration curves, and decision curves. In addition, a nomogram based on a deep learning score (DS) and the most significant clinical characteristic was plotted. Result: In the training set composed of 138 patients (64 with EGFR mutation and 74 without EGFR mutation), the area under the ROC curve (AUC) of HM (0.91, 95% CI: 0.86-0.96) was higher than that of RM (0.82, 95% CI: 0.75-0.89) and DLM (0.90, 95% CI: 0.85-0.95). In the validation set composed of 57 patients (32 with EGFR mutation and 25 without EGFR mutation), the AUC of HM (0.85, 95% CI: 0.77-0.93) was also higher than that of RM (0.68, 95% CI: 0.52-0.84) and DLM (0.79, 95% CI: 0.67-0.91). In all, HM achieved better diagnostic performance in predicting EGFR mutation status in NSCLC patients than two other models. Conclusion: Our study showed that the deep learning model based on PET/CT images had better performance than radiomics model in diagnosing EGFR mutation status of NSCLC patients based on PET/CT images. Combined with the most statistically significant clinical characteristic (smoking) and deep learning features, our hybrid model had better performance in predicting EGFR mutation types of patients than two other models, which could enable NSCLC patients to choose more personalized treatment schemes.

Project description:ObjectiveThis paper puts forward a new method for automatic segmentation of bony orbit as well as automatic extraction and classification of aging features of segmented orbit contour based on depth learning, with which the aging mode of bony orbit contour is preliminarily validated.MethodThree-dimensional reconstruction was carried out by using the craniofacial Computed Tomography scanning data of 595 adult Mongolians at different ages (119 young males, 78 young females, 109 middle-aged males, 89 middle-aged females, 95 elderly males, and 105 elderly females), the craniofacial images were exported, orbit contour images were obtained with U-Net segmentation network, and then the orbit contour features of young group, the middle-aged group and the elderly group were classified with the classification network. Next, contour area, height, and other features put forward in existing research were automatically calculated by using the connected component shape description method; and it was validated whether the aging features of the bony orbit only occur to partial or the whole orbit.ResultsWith the method put forward in this paper, high-precision identification (97.94% and 99.18%) of 3 categories in the male and female group experiments. In the meanwhile, it was found in the comparison experiment with other features that bony orbit contour definitely has features relating to aging, but these features only occur to partial areas of the orbit, which enables the convolutional neural network to achieve good identification effects. And, bone resorption of the superior orbital rim of males is more obvious than that of the inferior orbital rim, but the overall shape features like the bony orbit area and height do not change significantly along with the increase of the age.ConclusionsU-Net can realize high-precision segmentation of the orbit contour, and with the Convolutional Neural Network-based orbit contour sorting algorithm, the aging degree of the bony orbit can be identified precisely. It is preliminarily validated that the aging mode of Mongolian bony orbit contour is that the bone resorption of the superior orbital rim is more obvious than that of the inferior orbital rim, and the change of the orbit area, perimeter, height and circularity is not obvious in the aging process.

Project description:ObjectivesTo compare image quality of deep learning reconstruction (AiCE) for radiomics feature extraction with filtered back projection (FBP), hybrid iterative reconstruction (AIDR 3D), and model-based iterative reconstruction (FIRST).MethodsEffects of image reconstruction on radiomics features were investigated using a phantom that realistically mimicked a 65-year-old patient's abdomen with hepatic metastases. The phantom was scanned at 18 doses from 0.2 to 4 mGy, with 20 repeated scans per dose. Images were reconstructed with FBP, AIDR 3D, FIRST, and AiCE. Ninety-three radiomics features were extracted from 24 regions of interest, which were evenly distributed across three tissue classes: normal liver, metastatic core, and metastatic rim. Features were analyzed in terms of their consistent characterization of tissues within the same image (intraclass correlation coefficient ≥ 0.75), discriminative power (Kruskal-Wallis test p value < 0.05), and repeatability (overall concordance correlation coefficient ≥ 0.75).ResultsThe median fraction of consistent features across all doses was 6%, 8%, 6%, and 22% with FBP, AIDR 3D, FIRST, and AiCE, respectively. Adequate discriminative power was achieved by 48%, 82%, 84%, and 92% of features, and 52%, 20%, 17%, and 39% of features were repeatable, respectively. Only 5% of features combined consistency, discriminative power, and repeatability with FBP, AIDR 3D, and FIRST versus 13% with AiCE at doses above 1 mGy and 17% at doses ≥ 3 mGy. AiCE was the only reconstruction technique that enabled extraction of higher-order features.ConclusionsAiCE more than doubled the yield of radiomics features at doses typically used clinically. Inconsistent tissue characterization within CT images contributes significantly to the poor stability of radiomics features.Key points• Image quality of CT images reconstructed with filtered back projection and iterative methods is inadequate for the majority of radiomics features due to inconsistent tissue characterization, low discriminative power, or low repeatability. • Deep learning reconstruction enhances image quality for radiomics and more than doubled the feature yield at doses that are typically used in clinical CT imaging. • Image reconstruction algorithms can optimize image quality for more reliable quantification of tissues in CT images.

Dataset Information

Deep CNN Model Using CT Radiomics Feature Mapping Recognizes EGFR Gene Mutation Status of Lung Adenocarcinoma.

Publications

Deep CNN Model Using CT Radiomics Feature Mapping Recognizes EGFR Gene Mutation Status of Lung Adenocarcinoma.

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