Dataset Information

MethylNet: an automated and modular deep learning approach for DNA methylation analysis.

ABSTRACT: BACKGROUND:DNA methylation (DNAm) is an epigenetic regulator of gene expression programs that can be altered by environmental exposures, aging, and in pathogenesis. Traditional analyses that associate DNAm alterations with phenotypes suffer from multiple hypothesis testing and multi-collinearity due to the high-dimensional, continuous, interacting and non-linear nature of the data. Deep learning analyses have shown much promise to study disease heterogeneity. DNAm deep learning approaches have not yet been formalized into user-friendly frameworks for execution, training, and interpreting models. Here, we describe MethylNet, a DNAm deep learning method that can construct embeddings, make predictions, generate new data, and uncover unknown heterogeneity with minimal user supervision. RESULTS:The results of our experiments indicate that MethylNet can study cellular differences, grasp higher order information of cancer sub-types, estimate age and capture factors associated with smoking in concordance with known differences. CONCLUSION:The ability of MethylNet to capture nonlinear interactions presents an opportunity for further study of unknown disease, cellular heterogeneity and aging processes.

SUBMITTER: Levy JJ

PROVIDER: S-EPMC7076991 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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MethylNet: an automated and modular deep learning approach for DNA methylation analysis.

Levy Joshua J JJ Titus Alexander J AJ Petersen Curtis L CL Chen Youdinghuan Y Salas Lucas A LA Christensen Brock C BC

BMC bioinformatics 20200317 1

<h4>Background</h4>DNA methylation (DNAm) is an epigenetic regulator of gene expression programs that can be altered by environmental exposures, aging, and in pathogenesis. Traditional analyses that associate DNAm alterations with phenotypes suffer from multiple hypothesis testing and multi-collinearity due to the high-dimensional, continuous, interacting and non-linear nature of the data. Deep learning analyses have shown much promise to study disease heterogeneity. DNAm deep learning approache ...[more]

PMID: 32183722

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Project description:The neurological ailment known as Parkinson's disease (PD) affects people throughout the globe. The neurodegenerative PD-related disorder primarily affects people in middle to late life. Motor symptoms such as tremors, muscle rigidity, and sluggish, clumsy movement are common in patients with this disorder. Genetic and environmental variables play significant roles in the development of PD. Despite much investigation, the root cause of this neurodegenerative disease is still unidentified. Clinical diagnostics rely heavily on promptly detecting such irregularities to slow or stop the progression of illnesses successfully. Because of its direct correlation with brain activity, electroencephalography (EEG) is an essential PD diagnostic technique. Electroencephalography, or EEG, data are biomarkers of brain activity changes. However, these signals are non-linear, non-stationary, and complicated, making analysis difficult. One must often resort to a lengthy human labor process to accomplish results using traditional machine-learning approaches. The breakdown, feature extraction, and classification processes are typical examples of these stages. To overcome these obstacles, we present a novel deep-learning model for the automated identification of Parkinson's disease (PD). The Gabor transform, a standard method in EEG signal processing, was used to turn the raw data from the EEG recordings into spectrograms. In this research, we propose densely linked bidirectional long short-term memory (DLBLSTM), which first represents each layer as the sum of its hidden state plus the hidden states of all layers above it, then recursively transmits that representation to all layers below it. This study's suggested deep learning model was trained using these spectrograms as input data. Using a robust sixfold cross-validation method, the proposed model showed excellent accuracy with a classification accuracy of 99.6%. The results indicate that the suggested algorithm can automatically identify PD.

Project description:Purpose: To assess the accuracy and efficacy of a semi-automated deep learning algorithm (DLA) assisted approach to detect vision-threatening diabetic retinopathy (DR). Methods: We developed a two-step semi-automated DLA-assisted approach to grade fundus photographs for vision-threatening referable DR. Study images were obtained from the Lingtou Cohort Study, and captured at participant enrollment in 2009-2010 ("baseline images") and annual follow-up between 2011 and 2017. To begin, a validated DLA automatically graded baseline images for referable DR and classified them as positive, negative, or ungradable. Following, each positive image, all other available images from patients who had a positive image, and a 5% random sample of all negative images were selected and regraded by trained human graders. A reference standard diagnosis was assigned once all graders achieved consistent grading outcomes or with a senior ophthalmologist's final diagnosis. The semi-automated DLA assisted approach combined initial DLA screening and subsequent human grading for images identified as high-risk. This approach was further validated within the follow-up image datasets and its time and economic costs evaluated against fully human grading. Results: For evaluation of baseline images, a total of 33,115 images were included and automatically graded by the DLA. 2,604 images (480 positive results, 624 available other images from participants with a positive result, and 1500 random negative samples) were selected and regraded by graders. The DLA achieved an area under the receiver operating characteristic curve (AUC), sensitivity, specificity, and accuracy of 0.953, 0.970, 0.879, and 88.6%, respectively. In further validation within the follow-up image datasets, a total of 88,363 images were graded using this semi-automated approach and human grading was performed on 8975 selected images. The DLA achieved an AUC, sensitivity, and specificity of 0.914, 0.852, 0.853, respectively. Compared against fully human grading, the semi-automated DLA-assisted approach achieved an estimated 75.6% time and 90.1% economic cost saving. Conclusions: The DLA described in this study was able to achieve high accuracy, sensitivity, and specificity in grading fundus images for referable DR. Validated against long-term follow-up datasets, a semi-automated DLA-assisted approach was able to accurately identify suspect cases, and minimize misdiagnosis whilst balancing safety, time, and economic cost.

Dataset Information

MethylNet: an automated and modular deep learning approach for DNA methylation analysis.

Publications

MethylNet: an automated and modular deep learning approach for DNA methylation analysis.

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