Automatic Prediction of MGMT Status in Glioblastoma via Deep Learning-Based MR Image Analysis
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ABSTRACT:
SUBMITTER: Chen X
PROVIDER: S-EPMC7530505 | biostudies-literature | 2020 Jan
REPOSITORIES: biostudies-literature
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Project description:PurposeMost radiomic studies use the features extracted from the manually drawn tumor contours for classification or survival prediction. However, large interobserver segmentation variations lead to inconsistent features and hence introduce more challenges in constructing robust prediction models. Here, we proposed an automatic workflow for glioblastoma (GBM) survival prediction based on multimodal magnetic resonance (MR) images.Methods and materialsTwo hundred eighty-five patients with glioma (210 GBM, 75 low-grade glioma) were included. One hundred sixty-three of the patients with GBM had overall survival data. Every patient had 4 preoperative MR images and manually drawn tumor contours. A 3-dimensional convolutional neural network, VGG-Seg, was trained and validated using 122 patients with glioma for automatic GBM segmentation. The trained VGG-Seg was applied to the remaining 163 patients with GBM to generate their autosegmented tumor contours. The handcrafted and deep learning (DL)-based radiomic features were extracted from the autosegmented contours using explicitly designed algorithms and a pretrained convolutional neural network, respectively. One hundred sixty-three patients with GBM were randomly split into training (n = 122) and testing (n = 41) sets for survival analysis. Cox regression models were trained to construct the handcrafted and DL-based signatures. The prognostic powers of the 2 signatures were evaluated and compared.ResultsThe VGG-Seg achieved a mean Dice coefficient of 0.86 across 163 patients with GBM for GBM segmentation. The handcrafted signature achieved a C-index of 0.64 (95% confidence interval, 0.55-0.73), whereas the DL-based signature achieved a C-index of 0.67 (95% confidence interval, 0.57-0.77). Unlike the handcrafted signature, the DL-based signature successfully stratified testing patients into 2 prognostically distinct groups.ConclusionsThe VGG-Seg generated accurate GBM contours from 4 MR images. The DL-based signature achieved a numerically higher C-index than the handcrafted signature and significant patient stratification. The proposed automatic workflow demonstrated the potential of improving patient stratification and survival prediction in patients with GBM.
| S-EPMC8377554 | biostudies-literature
Project description:BackgroundThe study aims to explore MRI phenotypes that predict glioblastoma's (GBM) methylation status of the promoter region of MGMT gene (pMGMT) by qualitatively assessing contrast-enhanced T1-weighted intensity images.MethodsA total of 193 histologically and molecularly confirmed GBMs at the Kansai Network for Molecular Diagnosis of Central Nervous Tumors (KANSAI) were used as an exploratory cohort. From the Cancer Imaging Archive/Cancer Genome Atlas (TCGA) 93 patients were used as validation cohorts. "Thickened structure" was defined as the solid tumor component presenting circumferential extension or occupying >50% of the tumor volume. "Methylated contrast phenotype" was defined as indistinct enhancing circumferential border, heterogenous enhancement, or nodular enhancement. Inter-rater agreement was assessed, followed by an investigation of the relationship between radiological findings and pMGMT methylation status.ResultsFleiss's Kappa coefficient for "Thickened structure" was 0.68 for the exploratory and 0.55 for the validation cohort, and for "Methylated contrast phenotype," 0.30 and 0.39, respectively. The imaging feature, the presence of "Thickened structure" and absence of "Methylated contrast phenotype," was significantly predictive of pMGMT unmethylation both for the exploratory (p = .015, odds ratio = 2.44) and for the validation cohort (p = .006, odds ratio = 7.83). The sensitivities and specificities of the imaging feature, the presence of "Thickened structure," and the absence of "Methylated contrast phenotype" for predicting pMGMT unmethylation were 0.29 and 0.86 for the exploratory and 0.25 and 0.96 for the validation cohort.ConclusionsThe present study showed that qualitative assessment of contrast-enhanced T1-weighted intensity images helps predict GBM's pMGMT methylation status.
| S-EPMC10896622 | biostudies-literature
Project description:Predictive models based on gene expression are already a part of medical decision making for selected situations such as early breast cancer treatment. Most of these models are based on measures that do not capture critical aspects of gene splicing, butwith RNA sequencing it is possible to capture some of these aspects of alternative splicing and use them to improve clinical predictions. Building on previous models to predict cigarette smoking status, we show that measures of alternative splicing significantly improve the accuracy of these predictive models.
2020-12-31 | GSE158699 | GEO
Project description:Automatic medical image segmentation plays a critical role in scientific research and medical care. Existing high-performance deep learning methods typically rely on large training datasets with high-quality manual annotations, which are difficult to obtain in many clinical applications. Here, we introduce Annotation-effIcient Deep lEarning (AIDE), an open-source framework to handle imperfect training datasets. Methodological analyses and empirical evaluations are conducted, and we demonstrate that AIDE surpasses conventional fully-supervised models by presenting better performance on open datasets possessing scarce or noisy annotations. We further test AIDE in a real-life case study for breast tumor segmentation. Three datasets containing 11,852 breast images from three medical centers are employed, and AIDE, utilizing 10% training annotations, consistently produces segmentation maps comparable to those generated by fully-supervised counterparts or provided by independent radiologists. The 10-fold enhanced efficiency in utilizing expert labels has the potential to promote a wide range of biomedical applications.
| S-EPMC8501087 | biostudies-literature
Project description:To develop a deep learning system based on 3D convolutional neural networks (CNNs), and to automatically predict EGFR-mutant pulmonary adenocarcinoma in CT images. A dataset of 579 nodules with EGFR mutation status labels of mutant (Mut) or wild-type (WT) was retrospectively analyzed. A deep learning system, namely 3D DenseNets, was developed to process 3D patches of nodules from CT data, and learn strong representations with supervised end-to-end training. The 3D DenseNets were trained with a training subset of 348 nodules and tuned with a development subset of 116 nodules. A strong data augmentation technique, mixup, was used for better generalization. We evaluated our model on a holdout subset of 115 nodules. An independent public dataset of 37 nodules from the cancer imaging archive (TCIA) was also used to test the generalization of our method. Conventional radiomics analysis was also performed for comparison. Our method achieved promising performance on predicting EGFR mutation status, with AUCs of 75.8% and 75.0% for our holdout test set and public test set, respectively. Moreover, strong relations were found between deep learning feature and conventional radiomics, while deep learning worked through an enhanced radiomics manner, that is, deep learned radiomics (DLR), in terms of robustness, compactness and expressiveness. The proposed deep learning system predicts EGFR-mutant of lung adenocarcinomas in CT images noninvasively and automatically, indicating its potential to help clinical decision-making by identifying eligible patients of pulmonary adenocarcinoma for EGFR-targeted therapy.
| S-EPMC6601587 | biostudies-literature
Project description:BackgroundA variety of external factors might seriously degrade PET image quality and lead to inconsistent results. The aim of this study is to explore a potential PET image quality assessment (QA) method with deep learning (DL).MethodsA total of 89 PET images were acquired from Peking Union Medical College Hospital (PUMCH) in China in this study. Ground-truth quality for images was assessed by two senior radiologists and classified into five grades (grade 1, grade 2, grade 3, grade 4, and grade 5). Grade 5 is the best image quality. After preprocessing, the Dense Convolutional Network (DenseNet) was trained to automatically recognize optimal- and poor-quality PET images. Accuracy (ACC), sensitivity, specificity, receiver operating characteristic curve (ROC), and area under the ROC Curve (AUC) were used to evaluate the diagnostic properties of all models. All indicators of models were assessed using fivefold cross-validation. An image quality QA tool was developed based on our deep learning model. A PET QA report can be automatically obtained after inputting PET images.ResultsFour tasks were generated. Task2 showed worst performance in AUC,ACC, specificity and sensitivity among 4 tasks, and task1 showed unstable performance between training and testing and task3 showed low specificity in both training and testing. Task 4 showed the best diagnostic properties and discriminative performance between poor image quality (grade 1, grade 2) and good quality (grade 3, grade 4, grade 5) images. The automated quality assessment of task 4 showed ACC = 0.77, specificity = 0.71, and sensitivity = 0.83, in the train set; ACC = 0.85, specificity = 0.79, and sensitivity = 0.91, in the test set, respectively. The ROC measuring performance of task 4 had an AUC of 0.86 in the train set and 0.91 in the test set. The image QA tool could output basic information of images, scan and reconstruction parameters, typical instances of PET images, and deep learning score.ConclusionsThis study highlights the feasibility of the assessment of image quality in PET images using a deep learning model, which may assist with accelerating clinical research by reliably assessing image quality.
| S-EPMC10243071 | biostudies-literature
Project description:The study objective was to investigate the performance of a dedicated convolutional neural network (CNN) optimized for wrist cartilage segmentation from 2D MR images. CNN utilized a planar architecture and patch-based (PB) training approach that ensured optimal performance in the presence of a limited amount of training data. The CNN was trained and validated in 20 multi-slice MRI datasets acquired with two different coils in 11 subjects (healthy volunteers and patients). The validation included a comparison with the alternative state-of-the-art CNN methods for the segmentation of joints from MR images and the ground-truth manual segmentation. When trained on the limited training data, the CNN outperformed significantly image-based and PB-U-Net networks. Our PB-CNN also demonstrated a good agreement with manual segmentation (Sørensen-Dice similarity coefficient [DSC] = 0.81) in the representative (central coronal) slices with a large amount of cartilage tissue. Reduced performance of the network for slices with a very limited amount of cartilage tissue suggests the need for fully 3D convolutional networks to provide uniform performance across the joint. The study also assessed inter- and intra-observer variability of the manual wrist cartilage segmentation (DSC = 0.78-0.88 and 0.9, respectively). The proposed deep learning-based segmentation of the wrist cartilage from MRI could facilitate research of novel imaging markers of wrist osteoarthritis to characterize its progression and response to therapy.
| S-EPMC7784718 | biostudies-literature
Project description:Cancer research has seen explosive development exploring deep learning (DL) techniques for analysing magnetic resonance imaging (MRI) images for predicting brain tumours. We have observed a substantial gap in explanation, interpretability, and high accuracy for DL models. Consequently, we propose an explanation-driven DL model by utilising a convolutional neural network (CNN), local interpretable model-agnostic explanation (LIME), and Shapley additive explanation (SHAP) for the prediction of discrete subtypes of brain tumours (meningioma, glioma, and pituitary) using an MRI image dataset. Unlike previous models, our model used a dual-input CNN approach to prevail over the classification challenge with images of inferior quality in terms of noise and metal artifacts by adding Gaussian noise. Our CNN training results reveal 94.64% accuracy as compared to other state-of-the-art methods. We used SHAP to ensure consistency and local accuracy for interpretation as Shapley values examine all future predictions applying all possible combinations of inputs. In contrast, LIME constructs sparse linear models around each prediction to illustrate how the model operates in the immediate area. Our emphasis for this study is interpretability and high accuracy, which is critical for realising disparities in predictive performance, helpful in developing trust, and essential in integration into clinical practice. The proposed method has a vast clinical application that could potentially be used for mass screening in resource-constraint countries.
| S-EPMC8964286 | biostudies-literature
Project description:Patch clamp recording of neurons is a labor-intensive and time-consuming procedure. Here, we demonstrate a tool that fully automatically performs electrophysiological recordings in label-free tissue slices. The automation covers the detection of cells in label-free images, calibration of the micropipette movement, approach to the cell with the pipette, formation of the whole-cell configuration, and recording. The cell detection is based on deep learning. The model is trained on a new image database of neurons in unlabeled brain tissue slices. The pipette tip detection and approaching phase use image analysis techniques for precise movements. High-quality measurements are performed on hundreds of human and rodent neurons. We also demonstrate that further molecular and anatomical analysis can be performed on the recorded cells. The software has a diary module that automatically logs patch clamp events. Our tool can multiply the number of daily measurements to help brain research.
| S-EPMC7875980 | biostudies-literature
Project description:IntroductionThe primary objective of this study was to develop an end-to-end model that can accurately identify corneal endothelial cells and diagnose keratoconus based on corneal endothelial images acquired from a non-contact specular microscope.MethodsThis was a retrospective case-control study performed at the Refractive Surgery Center of West China Hospital. A total of 403 keratoconus eyes (221 patients) and 370 myopic eyes (185 normal controls) were consecutively recruited from January 2021 to September 2022. Specular microscopy was used to image and measure the morphometric parameters of the corneal endothelial cells. A Fully Convolutional Network model with a ResNet50 (FCN_ResNet50) was established to perform the endothelial segmentation. The images were then classified using an ensemble machine learning system consisting of four pre-trained deep learning networks: DenseNet121, ResNet50, Inception_v3, and MobileNet_v2. The performance of the models was evaluated based on different metrics, such as accuracy, intersection over union (IoU), and mean IoU.ResultsWe established a fully end-to-end deep-learning model for the segmentation of endothelial and diagnosis of keratoconus. For endothelial segmentation, the accuracy of the FCN_ResNet50 model achieved near 90% with mean IoU converging to about 80%. The ensemble machine learning system can achieve over 92% accuracy, and > 98% area under curve (AUC) values to diagnose keratoconus with endothelial cell images. In addition, we constructed a diagnostic model based on deep-learning features and developed an associated nomogram which manifested an excellent performance for diagnosis and monitoring the progression of keratoconus.ConclusionsOur research developed an end-to-end model to automatically identify and assess corneal endothelial morphological changes in keratoconus eyes. Moreover, we also constructed a novel nomogram, which can provide valuable information for the diagnosis, monitoring, and management of the disease.
| S-EPMC10640564 | biostudies-literature