Accuracy of Machine Learning Algorithms for the Classification of Molecular Features of Gliomas on MRI: A Systematic Literature Review and Meta-Analysis.
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ABSTRACT:
SUBMITTER: van Kempen EJ
PROVIDER: S-EPMC8198025 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Keratoconus is a noninflammatory disease characterized by thinning and bulging of the cornea, generally appearing during adolescence and slowly progressing, causing vision impairment. However, the detection of keratoconus remains difficult in the early stages of the disease because the patient does not feel any pain. Therefore, the development of a method for detecting this disease based on machine and deep learning methods is necessary for early detection in order to provide the appropriate treatment as early as possible to patients. Thus, the objective of this work is to determine the most relevant parameters with respect to the different classifiers used for keratoconus classification based on the keratoconus dataset of Harvard Dataverse. A total of 446 parameters are analyzed out of 3162 observations by 11 different feature selection algorithms. Obtained results showed that sequential forward selection (SFS) method provided a subset of 10 most relevant variables, thus, generating the highest classification performance by the application of random forest (RF) classifier, with an accuracy of 98% and 95% considering 2 and 4 keratoconus classes, respectively. Found classification accuracy applying RF classifier on the selected variables using SFS method achieves the accuracy obtained using all features of the original dataset.
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Project description:Background:To evaluate the association of multiparametric and multiregional MRI-features with key molecular characteristics in patients with newly-diagnosed glioblastoma. Methods:Retrospective data evaluation was approved by the local ethics committee of the University of Heidelberg (ethics approval number: S-320/2012) and informed consent was waived. Preoperative MRI-features were correlated with key molecular characteristics within a single-institutional cohort of 152 patients with newly-diagnosed glioblastoma. Preoperative MRI-features (n=31) included multiparametric (anatomical, diffusion-, perfusion-, and susceptibility-weighted images) and multiregional (contrast enhancing and non-enhancing FLAIR-hyperintense) information with (histogram) quantification of tumor volumes, volume ratios, apparent diffusion coefficients, cerebral blood flow / volume (CBF / CBV) and intratumoral susceptibility signals. Molecular characteristics determined with the Illumina Infinium HumanMethylation450 array included global DNA-methylation subgroups (e.g. mesenchymal (MES), RTK I “PGFRA”, RTK II “classic”), MGMT-promoter methylation status and hallmark copy-number-variations (EGFR-, PDGFRA-, MDM4- and CDK4-amplification; PTEN-, CDKN2A-, NF1- and RB1-loss). Univariate analyses (voxel-lesion-symptom-mapping for tumor location, Wilcoxon-test for all other MRI-features) as well as machine-learning models were applied to study the strength of association and discriminative value of MRI-features for predicting underlying molecular characteristics. Results: There was no tumor location predilection for any of the assessed molecular parameters (permutation-adjusted p>0.05 each). Univariate imaging parameter associations were noted for EGFR amplification and CDKN2A loss, both demonstrating increased nrCBV and nrCBF values (performance of these parameters, as assessed by the area under the ROC curve ranged from 63 to 69%, FDR-adjusted p<0.05, respectively). Subjecting all MRI-features to machine-learning-based classification allowed to predict EGFR amplification status and the RTK II “classic” GB subgroup with a moderate, yet significantly greater accuracy (63% for EGFR [p<0.01] and 61% for RTK II [p=0.01]) than the prediction by chance, whereas prediction accuracy for all other molecular parameters was non-significant (p>0.05, all models). Conclusions: In summary, we found univariate associations between established MRI-features and molecular characteristics, however not of sufficient strength to allow the generation of machine-learning classification models for reliable and clinically meaningful prediction of the assessed molecular characteristics in patients with newly-diagnosed glioblastoma.
2016-11-23 | GSE85539 | GEO
Project description:ObjectivesDifferent machine learning algorithms (MLAs) for automated segmentation of gliomas have been reported in the literature. Automated segmentation of different tumor characteristics can be of added value for the diagnostic work-up and treatment planning. The purpose of this study was to provide an overview and meta-analysis of different MLA methods.MethodsA systematic literature review and meta-analysis was performed on the eligible studies describing the segmentation of gliomas. Meta-analysis of the performance was conducted on the reported dice similarity coefficient (DSC) score of both the aggregated results as two subgroups (i.e., high-grade and low-grade gliomas). This study was registered in PROSPERO prior to initiation (CRD42020191033).ResultsAfter the literature search (n = 734), 42 studies were included in the systematic literature review. Ten studies were eligible for inclusion in the meta-analysis. Overall, the MLAs from the included studies showed an overall DSC score of 0.84 (95% CI: 0.82-0.86). In addition, a DSC score of 0.83 (95% CI: 0.80-0.87) and 0.82 (95% CI: 0.78-0.87) was observed for the automated glioma segmentation of the high-grade and low-grade gliomas, respectively. However, heterogeneity was considerably high between included studies, and publication bias was observed.ConclusionMLAs facilitating automated segmentation of gliomas show good accuracy, which is promising for future implementation in neuroradiology. However, before actual implementation, a few hurdles are yet to be overcome. It is crucial that quality guidelines are followed when reporting on MLAs, which includes validation on an external test set.Key points• MLAs from the included studies showed an overall DSC score of 0.84 (95% CI: 0.82-0.86), indicating a good performance. • MLA performance was comparable when comparing the segmentation results of the high-grade gliomas and the low-grade gliomas. • For future studies using MLAs, it is crucial that quality guidelines are followed when reporting on MLAs, which includes validation on an external test set.
| S-EPMC8589805 | biostudies-literature
Project description:BackgroundP53 mutation status is a pivotal biomarker for gliomas. Here, we developed a machine-learning model to predict p53 status in lower-grade gliomas based on radiomic features extracted from conventional magnetic resonance (MR) images.MethodsPreoperative MR images were retrospectively obtained from 272 patients with primary grade II/III gliomas. The patients were randomly allocated in a 2:1 ratio to a training (n = 180) or validation (n = 92) set. A total of 431 radiomic features were extracted from each patient. The lest absolute shrinkage and selection operator (LASSO) method was used for feature selection and radiomic signature construction. Subsequently, a machine-learning model to predict p53 status was established using the selected features and a Support Vector Machine classifier. The predictive performance of all individual features and the model was calculated using receiver operating characteristic curves in both the training and validation sets.ResultsThe p53-related radiomic signature was built using the LASSO algorithm; this procedure consisted of four first-order statistics or related wavelet features (including Maximum, Median, Minimum, and Uniformity), a shape and size-based feature (Spherical Disproportion), and ten textural features or related wavelet features (including Correlation, Run Percentage, and Sum Entropy). The prediction accuracies based on the area under the curve were 89.6% in the training set and 76.3% in the validation set, which were better than individual features.ConclusionsThese results demonstrate that MR image texture features are predictive of p53 mutation status in lower-grade gliomas. Thus, our procedure can be conveniently used to facilitate presurgical molecular pathological diagnosis.
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Project description:BackgroundArtificial intelligence and automated technology were first reported more than 70 years ago and nowadays provide unprecedented diagnostic accuracy, screening capacity, risk stratification, and workflow optimization. Diabetic retinopathy is an important cause of preventable blindness worldwide, and artificial intelligence technology provides precocious diagnosis, monitoring, and guide treatment. High-quality exams are fundamental in supervised artificial intelligence algorithms, but the lack of ground truth standards in retinal exams datasets is a problem.Main bodyIn this article, ETDRS, NHS, ICDR, SDGS diabetic retinopathy grading, and manual annotation are described and compared in publicly available datasets. The various DR labeling systems generate a fundamental problem for AI datasets. Possible solutions are standardization of DR classification and direct retinal-finding identifications.ConclusionReliable labeling methods also need to be considered in datasets with more trustworthy labeling.
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Project description:A relatively large number of studies have investigated the power of structural magnetic resonance imaging (sMRI) data to discriminate patients with schizophrenia from healthy controls. However, very few of them have also included patients with bipolar disorder, allowing the clinically relevant discrimination between both psychotic diagnostics. To assess the efficacy of sMRI data for diagnostic prediction in psychosis we objectively evaluated the discriminative power of a wide range of commonly used machine learning algorithms (ridge, lasso, elastic net and L0 norm regularized logistic regressions, a support vector classifier, regularized discriminant analysis, random forests and a Gaussian process classifier) on main sMRI features including grey and white matter voxel-based morphometry (VBM), vertex-based cortical thickness and volume, region of interest volumetric measures and wavelet-based morphometry (WBM) maps. All possible combinations of algorithms and data features were considered in pairwise classifications of matched samples of healthy controls (N = 127), patients with schizophrenia (N = 128) and patients with bipolar disorder (N = 128). Results show that the selection of feature type is important, with grey matter VBM (without data reduction) delivering the best diagnostic prediction rates (averaging over classifiers: schizophrenia vs. healthy 75%, bipolar disorder vs. healthy 63% and schizophrenia vs. bipolar disorder 62%) whereas algorithms usually yielded very similar results. Indeed, those grey matter VBM accuracy rates were not even improved by combining all feature types in a single prediction model. Further multi-class classifications considering the three groups simultaneously made evident a lack of predictive power for the bipolar group, probably due to its intermediate anatomical features, located between those observed in healthy controls and those found in patients with schizophrenia. Finally, we provide MRIPredict (https://www.nitrc.org/projects/mripredict/), a free tool for SPM, FSL and R, to easily carry out voxelwise predictions based on VBM images.
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Project description:This paper proposes to treat the jammer classification problem in the Global Navigation Satellite System bands as a black-and-white image classification problem, based on a time-frequency analysis and image mapping of a jammed signal. The paper also proposes to apply machine learning approaches in order to sort the received signal into six classes, namely five classes when the jammer is present with different jammer types and one class where the jammer is absent. The algorithms based on support vector machines show up to 94 . 90 % accuracy in classification, and the algorithms based on convolutional neural networks show up to 91 . 36 % accuracy in classification. The training and test databases generated for these tests are also provided in open access.
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Project description:BackgroundKidney disease progression rates vary among patients. Rapid and accurate prediction of kidney disease outcomes is crucial for disease management. In recent years, various prediction models using Machine Learning (ML) algorithms have been established in nephrology. However, their accuracy have been inconsistent. Therefore, we conducted a systematic review and meta-analysis to investigate the diagnostic accuracy of ML algorithms for kidney disease progression.MethodsWe searched PubMed, EMBASE, Cochrane Central Register of Controlled Trials, the Chinese Biomedicine Literature Database, Chinese National Knowledge Infrastructure, Wanfang Database, and the VIP Database for diagnostic studies on ML algorithms' accuracy in predicting kidney disease prognosis, from the establishment of these databases until October 2020. Two investigators independently evaluate study quality by QUADAS-2 tool and extracted data from single ML algorithm for data synthesis using the bivariate model and the hierarchical summary receiver operating characteristic (HSROC) model.ResultsFifteen studies were left after screening, only 6 studies were eligible for data synthesis. The sample size of these 6 studies was 12,534, and the kidney disease types could be divided into chronic kidney disease (CKD) and Immunoglobulin A Nephropathy, with 5 articles using end-stage renal diseases occurrence as the primary outcome. The main results indicated that the area under curve (AUC) of the HSROC was 0.87 (0.84-0.90) and ML algorithm exhibited a strong specificity, 95% confidence interval and heterogeneity (I2) of (0.87, 0.84-0.90, [I2 99.0%]) and a weak sensitivity of (0.68, 0.58-0.77, [I2 99.7%]) in predicting kidney disease deterioration. And the the results of subgroup analysis indicated that ML algorithm's AUC for predicting CKD prognosis was 0.82 (0.79-0.85), with the pool sensitivity of (0.64, 0.49-0.77, [I2 99.20%]) and pool specificity of (0.84, 0.74-0.91, [I2 99.84%]). The ML algorithm's AUC for predicting IgA nephropathy prognosis was 0.78 (0.74-0.81), with the pool sensitivity of (0.74, 0.71-0.77, [I2 7.10%]) and pool specificity of (0.93, 0.91-0.95, [I2 83.92%]).ConclusionTaking advantage of big data, ML algorithm-based prediction models have high accuracy in predicting kidney disease progression, we recommend ML algorithms as an auxiliary tool for clinicians to determine proper treatment and disease management strategies.
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Project description:ObjectiveThe purpose of this study was to develop an algorithm incorporating MRI metrics to classify patients with mild traumatic brain injury (mTBI) and controls.MethodsThis was an institutional review board-approved, Health Insurance Portability and Accountability Act-compliant prospective study. We recruited patients with mTBI and healthy controls through the emergency department and general population. We acquired data on a 3.0T Siemens Trio magnet including conventional brain imaging, resting-state fMRI, diffusion-weighted imaging, and magnetic field correlation (MFC), and performed multifeature analysis using the following MRI metrics: mean kurtosis (MK) of thalamus, MFC of thalamus and frontal white matter, thalamocortical resting-state networks, and 5 regional gray matter and white matter volumes including the anterior cingulum and left frontal and temporal poles. Feature selection was performed using minimal-redundancy maximal-relevance. We used classifiers including support vector machine, naive Bayesian, Bayesian network, radial basis network, and multilayer perceptron to test maximal accuracy.ResultsWe studied 24 patients with mTBI and 26 controls. Best single-feature classification uses thalamic MK yielding 74% accuracy. Multifeature analysis yields 80% accuracy using the full feature set, and up to 86% accuracy using minimal-redundancy maximal-relevance feature selection (MK thalamus, right anterior cingulate volume, thalamic thickness, thalamocortical resting-state network, thalamic microscopic MFC, and sex).ConclusionMultifeature analysis using diffusion-weighted imaging, MFC, fMRI, and volumetrics may aid in the classification of patients with mTBI compared with controls based on optimal feature selection and classification methods.Classification of evidenceThis study provides Class III evidence that classification algorithms using multiple MRI features accurately identifies patients with mTBI as defined by American Congress of Rehabilitation Medicine criteria compared with healthy controls.
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