Radiomics-guided deep neural networks stratify lung adenocarcinoma prognosis from CT scans
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ABSTRACT:
SUBMITTER: Cho H
PROVIDER: S-EPMC8590002 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Research on Coronavirus Disease 2019 (COVID-19) detection methods has increased in the last months as more accurate automated toolkits are required. Recent studies show that CT scan images contain useful information to detect the COVID-19 disease. However, the scarcity of large and well balanced datasets limits the possibility of using detection approaches in real diagnostic contexts as they are unable to generalize. Indeed, the performance of these models quickly becomes inadequate when applied to samples captured in different contexts (e.g., different equipment or populations) from those used in the training phase. In this paper, a novel ensemble-based approach for more accurate COVID-19 disease detection using CT scan images is proposed. This work exploits transfer learning using pre-trained deep networks (e.g., VGG, Xception, and ResNet) evolved with a genetic algorithm, combined into an ensemble architecture for the classification of clustered images of lung lobes. The study is validated on a new dataset obtained as an integration of existing ones. The results of the experimental evaluation show that the ensemble classifier ensures effective performance, also exhibiting better generalization capabilities.
| S-EPMC8494191 | biostudies-literature
Project description:Accurately detecting and examining lung nodules early is key in diagnosing lung cancers and thus one of the best ways to prevent lung cancer deaths. Radiologists spend countless hours detecting small spherical-shaped nodules in computed tomography (CT) images. In addition, even after detecting nodule candidates, a considerable amount of effort and time is required for them to determine whether they are real nodules. The aim of this paper is to introduce a high performance nodule classification method that uses three dimensional deep convolutional neural networks (DCNNs) and an ensemble method to distinguish nodules between non-nodules. In this paper, we use a three dimensional deep convolutional neural network (3D DCNN) with shortcut connections and a 3D DCNN with dense connections for lung nodule classification. The shortcut connections and dense connections successfully alleviate the gradient vanishing problem by allowing the gradient to pass quickly and directly. Connections help deep structured networks to obtain general as well as distinctive features of lung nodules. Moreover, we increased the dimension of DCNNs from two to three to capture 3D features. Compared with shallow 3D CNNs used in previous studies, deep 3D CNNs more effectively capture the features of spherical-shaped nodules. In addition, we use an alternative ensemble method called the checkpoint ensemble method to boost performance. The performance of our nodule classification method is compared with that of the state-of-the-art methods which were used in the LUng Nodule Analysis 2016 Challenge. Our method achieves higher competition performance metric (CPM) scores than the state-of-the-art methods using deep learning. In the experimental setup ESB-ALL, the 3D DCNN with shortcut connections and the 3D DCNN with dense connections using the checkpoint ensemble method achieved the highest CPM score of 0.910. The result demonstrates that our method of using a 3D DCNN with shortcut connections, a 3D DCNN with dense connections, and the checkpoint ensemble method is effective for capturing 3D features of nodules and distinguishing nodules between non-nodules.
| S-EPMC6276244 | biostudies-other
Project description:Error estimation in nonlinear medical image registration is a nontrivial problem that is important for validation of registration methods. We propose a supervised method for estimation of registration errors in nonlinear registration of three-dimensional (3-D) images. The method is based on a 3-D convolutional neural network that learns to estimate registration errors from a pair of image patches. By applying the network to patches centered around every voxel, we construct registration error maps. The network is trained using a set of representative images that have been synthetically transformed to construct a set of image pairs with known deformations. The method is evaluated on deformable registrations of inhale-exhale pairs of thoracic CT scans. Using ground truth target registration errors on manually annotated landmarks, we evaluate the method's ability to estimate local registration errors. Estimation of full domain error maps is evaluated using a gold standard approach. The two evaluation approaches show that we can train the network to robustly estimate registration errors in a predetermined range, with subvoxel accuracy. We achieved a root-mean-square deviation of 0.51 mm from gold standard registration errors and of 0.66 mm from ground truth landmark registration errors.
| S-EPMC5943620 | biostudies-other
Project description:Quantitative single-photon emission computed tomography/computed tomography (SPECT/CT) using Tc-99m pertechnetate aids in evaluating salivary gland function. However, gland segmentation and quantitation of gland uptake is challenging. We develop a salivary gland SPECT/CT with automated segmentation using a deep convolutional neural network (CNN). The protocol comprises SPECT/CT at 20 min, sialagogue stimulation, and SPECT at 40 min post-injection of Tc-99m pertechnetate (555 MBq). The 40-min SPECT was reconstructed using the 20-min CT after misregistration correction. Manual salivary gland segmentation for %injected dose (%ID) by human experts proved highly reproducible, but took 15 min per scan. An automatic salivary segmentation method was developed using a modified 3D U-Net for end-to-end learning from the human experts (n = 333). The automatic segmentation performed comparably with human experts in voxel-wise comparison (mean Dice similarity coefficient of 0.81 for parotid and 0.79 for submandibular, respectively) and gland %ID correlation (R2 = 0.93 parotid, R2 = 0.95 submandibular) with an operating time less than 1 min. The algorithm generated results that were comparable to the reference data. In conclusion, with the aid of a CNN, we developed a quantitative salivary gland SPECT/CT protocol feasible for clinical applications. The method saves analysis time and manual effort while reducing patients' radiation exposure.
| S-EPMC8035179 | biostudies-literature
Project description:BackgroundRecent studies indicate that bladder cancer is among the top 10 most common cancers in the world (Saginala et al. 2022). Bladder cancer frequently reoccurs, and prognostic judgments may vary among clinicians. As a favorable prognosis may help to inform less aggressive treatment plans, classification of histopathology slides is essential for the accurate prognosis and effective treatment of bladder cancer patients. Developing automated and accurate histopathology image analysis methods can help pathologists determine the prognosis of patients with bladder cancer.Materials and methodsIn this study, we introduced Bladder4Net, a deep learning pipeline, to classify whole-slide histopathology images of bladder cancer into two classes: low-risk (combination of PUNLMP and low-grade tumors) and high-risk (combination of high-grade and invasive tumors). This pipeline consists of four convolutional neural network (CNN)-based classifiers to address the difficulties of identifying PUNLMP and invasive classes. We evaluated our pipeline on 182 independent whole-slide images from the New Hampshire Bladder Cancer Study (NHBCS) (Karagas et al., 1998; Sverrisson et al., 2014; Sverrisson et al., 2014) collected from 1994 to 2004 and 378 external digitized slides from The Cancer Genome Atlas (TCGA) database (https://www.cancer.gov/tcga).ResultsThe weighted average F1-score of our approach was 0.91 (95% confidence interval (CI): 0.86-0.94) on the NHBCS dataset and 0.99 (95% CI: 0.97-1.00) on the TCGA dataset. Additionally, we computed Kaplan-Meier survival curves for patients who were predicted as high risk versus those predicted as low risk. For the NHBCS test set, patients predicted as high risk had worse overall survival than those predicted as low risk, with a log-rank p-value of 0.004.ConclusionsIf validated through prospective trials, our model could be used in clinical settings to improve patient care.
| S-EPMC9577122 | biostudies-literature
Project description: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.
| S-EPMC7907520 | biostudies-literature
Project description:Objectives: The aim of this study is to develop a scar detection method for routine computed tomography angiography (CTA) imaging using deep convolutional neural networks (CNN), which relies solely on anatomical information as input and is compatible with existing clinical workflows. Background: Identifying cardiac patients with scar tissue is important for assisting diagnosis and guiding interventions. Late gadolinium enhancement (LGE) magnetic resonance imaging (MRI) is the gold standard for scar imaging; however, there are common instances where it is contraindicated. CTA is an alternative imaging modality that has fewer contraindications and is faster than Cardiovascular magnetic resonance imaging but is unable to reliably image scar. Methods: A dataset of LGE MRI (200 patients, 83 with scar) was used to train and validate a CNN to detect ischemic scar slices using segmentation masks as input to the network. MRIs were segmented to produce 3D left ventricle meshes, which were sampled at points along the short axis to extract anatomical masks, with scar labels from LGE as ground truth. The trained CNN was tested with an independent CTA dataset (25 patients, with ground truth established with paired LGE MRI). Automated segmentation was performed to provide the same input format of anatomical masks for the network. The CNN was compared against manual reading of the CTA dataset by 3 experts. Results: Note that 84.7% cross-validated accuracy (AUC: 0.896) for detecting scar slices in the left ventricle on the MRI data was achieved. The trained network was tested against the CTA-derived data, with no further training, where it achieved an 88.3% accuracy (AUC: 0.901). The automated pipeline outperformed the manual reading by clinicians. Conclusion: Automatic ischemic scar detection can be performed from a routine cardiac CTA, without any scar-specific imaging or contrast agents. This requires only a single acquisition in the cardiac cycle. In a clinical setting, with near zero additional cost, scar presence could be detected to triage images, reduce reading times, and guide clinical decision-making.
| S-EPMC8283258 | biostudies-literature
Project description:Cross-sectional X-ray imaging has become the standard for staging most solid organ malignancies. However, for some malignancies such as urinary bladder cancer, the ability to accurately assess local extent of the disease and understand response to systemic chemotherapy is limited with current imaging approaches. In this study, we explored the feasibility that radiomics-based predictive models using pre- and post-treatment computed tomography (CT) images might be able to distinguish between bladder cancers with and without complete chemotherapy responses. We assessed three unique radiomics-based predictive models, each of which employed different fundamental design principles ranging from a pattern recognition method via deep-learning convolution neural network (DL-CNN), to a more deterministic radiomics feature-based approach and then a bridging method between the two, utilizing a system which extracts radiomics features from the image patterns. Our study indicates that the computerized assessment using radiomics information from the pre- and post-treatment CT of bladder cancer patients has the potential to assist in assessment of treatment response.
| S-EPMC5562694 | biostudies-other
Project description:In reconstructive craniofacial surgery, the bilateral symmetry of the midplane of the facial skeleton plays an important role in surgical planning. Surgeons can take advantage of the intact side of the face as a template for the malformed side by accurately locating the midplane to assist in the preparation of the surgical procedure. However, despite its importance, the location of the midline is still a subjective procedure. The aim of this study was to present a 3D technique using a convolutional neural network and geometric moments to automatically calculate the craniofacial midline symmetry of the facial skeleton from CT scans. To perform this task, a total of 195 skull images were assessed to validate the proposed technique. In the symmetry planes, the technique was found to be reliable and provided good accuracy. However, further investigations to improve the results of asymmetric images may be carried out.
| S-EPMC7999007 | biostudies-literature
Project description:Objective:To demonstrate and test the validity of a novel deep-learning-based system for the automated detection of pulmonary nodules. Materials and Methods:The proposed system uses 2 3D deep learning models, 1 for each of the essential tasks of computer-aided nodule detection: candidate generation and false positive reduction. A total of 888 scans from the LIDC-IDRI dataset were used for training and evaluation. Results:Results for candidate generation on the test data indicated a detection rate of 94.77% with 30.39 false positives per scan, while the test results for false positive reduction exhibited a sensitivity of 94.21% with 1.789 false positives per scan. The overall system detection rate on the test data was 89.29% with 1.789 false positives per scan. Discussion:An extensive and rigorous validation was conducted to assess the performance of the proposed system. The system demonstrated a novel combination of 3D deep neural network architectures and demonstrates the use of deep learning for both candidate generation and false positive reduction to be evaluated with a substantial test dataset. The results strongly support the ability of deep learning pulmonary nodule detection systems to generalize to unseen data. The source code and trained model weights have been made available. Conclusion:A novel deep-neural-network-based pulmonary nodule detection system is demonstrated and validated. The results provide comparison of the proposed deep-learning-based system over other similar systems based on performance.
| S-EPMC6188511 | biostudies-literature