Dataset Information

Estimating Rates of Progression and Predicting Future Visual Fields in Glaucoma Using a Deep Variational Autoencoder.

ABSTRACT: In this manuscript we develop a deep learning algorithm to improve estimation of rates of progression and prediction of future patterns of visual field loss in glaucoma. A generalized variational auto-encoder (VAE) was trained to learn a low-dimensional representation of standard automated perimetry (SAP) visual fields using 29,161 fields from 3,832 patients. The VAE was trained on a 90% sample of the data, with randomization at the patient level. Using the remaining 10%, rates of progression and predictions were generated, with comparisons to SAP mean deviation (MD) rates and point-wise (PW) regression predictions, respectively. The longitudinal rate of change through the VAE latent space (e.g., with eight dimensions) detected a significantly higher proportion of progression than MD at two (25% vs. 9%) and four (35% vs 15%) years from baseline. Early on, VAE improved prediction over PW, with significantly smaller mean absolute error in predicting the 4th, 6th and 8th visits from the first three (e.g., visit eight: VAE8: 5.14?dB vs. PW: 8.07?dB; P?

SUBMITTER: Berchuck SI

PROVIDER: S-EPMC6888896 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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Estimating Rates of Progression and Predicting Future Visual Fields in Glaucoma Using a Deep Variational Autoencoder.

Berchuck Samuel I SI Mukherjee Sayan S Medeiros Felipe A FA

Scientific reports 20191202 1

In this manuscript we develop a deep learning algorithm to improve estimation of rates of progression and prediction of future patterns of visual field loss in glaucoma. A generalized variational auto-encoder (VAE) was trained to learn a low-dimensional representation of standard automated perimetry (SAP) visual fields using 29,161 fields from 3,832 patients. The VAE was trained on a 90% sample of the data, with randomization at the patient level. Using the remaining 10%, rates of progression an ...[more]

PMID: 31792321

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Project description:BackgroundMultiple studies have shown the utility of transcriptome-wide RNA-seq profiles as features for machine learning-based prediction of response to chemotherapy in cancer. While tumor transcriptome profiles are publicly available for thousands of tumors for many cancer types, a relatively modest number of tumor profiles are clinically annotated for response to chemotherapy. The paucity of labeled examples and the high dimension of the feature data limit performance for predicting therapeutic response using fully-supervised classification methods. Recently, multiple studies have established the utility of a deep neural network approach, the variational autoencoder (VAE), for generating meaningful latent features from original data. Here, we report the first study of a semi-supervised approach using VAE-encoded tumor transcriptome features and regularized gradient boosted decision trees (XGBoost) to predict chemotherapy drug response for five cancer types: colon, pancreatic, bladder, breast, and sarcoma.ResultsWe found: (1) VAE-encoding of the tumor transcriptome preserves the cancer type identity of the tumor, suggesting preservation of biologically relevant information; and (2) as a feature-set for supervised classification to predict response-to-chemotherapy, the unsupervised VAE encoding of the tumor's gene expression profile leads to better area under the receiver operating characteristic curve and area under the precision-recall curve classification performance than the original gene expression profile or the PCA principal components or the ICA components of the gene expression profile, in four out of five cancer types that we tested.ConclusionsGiven high-dimensional "omics" data, the VAE is a powerful tool for obtaining a nonlinear low-dimensional embedding; it yields features that retain biological patterns that distinguish between different types of cancer and that enable more accurate tumor transcriptome-based prediction of response to chemotherapy than would be possible using the original data or their principal components.

Project description:PurposeTo model the global test-retest variability of visual fields (VFs) in glaucoma.DesignRetrospective cohort study.ParticipantsTest-retest VFs from 4044 eyes of 4044 participants.MethodsWe selected 2 reliable VFs per eye measured with the Humphrey Field Analyzer (Swedish interactive threshold algorithm 24-2) within 30 days of each other. Each VF had fixation losses (FLs) of 33% or less, false-negative results (FNRs) of 20% or less, and false-positive results (FPRs) of 20% or less. Stepwise linear regression was applied to select the model best predicting the global test-retest variability from 3 categories of features of the first VF: (1) base parameters (age, mean deviation, pattern standard deviation, glaucoma hemifield test results, FPR, FNR, and FL); (2) total deviation (TD) at each location; and (3) computationally derived archetype VF loss patterns. The global test-retest variability was defined as root mean square deviation (RMSD) of TD values at all 52 VF locations.Main outcome measuresArchetype models to predict the global test-retest variability.ResultsThe mean ± standard deviation of the root mean square deviation was 4.39 ± 2.55 dB. Between the 2 VF tests, TD values were correlated more strongly in central than in peripheral VF locations (intraclass coefficient, 0.66-0.89; P < 0.001). Compared with the model using base parameters alone (adjusted R2 = 0.45), adding TD values improved prediction accuracy of the global variability (adjusted R2 = 0.53; P < 0.001; Bayesian information criterion [BIC] decrease of 527; change of >6 represents strong improvement). Lower TD sensitivity in the outermost peripheral VF locations was predictive of higher global variability. Adding archetypes to the base model improved model performance with an adjusted R2 of 0.53 (P < 0.001) and lowering of BIC by 583. Greater variability was associated with concentric peripheral defect, temporal hemianopia, inferotemporal defect, near total loss, superior peripheral defect, and central scotoma (listed in order of decreasing statistical significance), and less normal VF results and superior paracentral defect.ConclusionsInclusion of archetype VF loss patterns and TD values based on first VF improved the prediction of the global test-retest variability than using traditional global VF indices alone.

Dataset Information

Estimating Rates of Progression and Predicting Future Visual Fields in Glaucoma Using a Deep Variational Autoencoder.

Publications

Estimating Rates of Progression and Predicting Future Visual Fields in Glaucoma Using a Deep Variational Autoencoder.

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