Spot the difference: comparing results of analyses from real patient data and synthetic derivatives

Foraker, Randi E.; Yu, Sean; Gupta, Aditi; Michelson, Andrew P.; Soto, José A.; Colvin, Ryan; Loh, Francis E.; Kollef, Marin H.; Maddox, Thomas M.; Evanoff, Bradley; Dror, Hovav; Zamstein, Noa; Lai, Albert M.; Payne, Philip R. O.

doi:10.1093/jamiaopen/ooaa060

Cited by 45 publications

(45 citation statements)

References 15 publications

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“…There have been limited replications of clinical studies using synthetic data, with only a handful of examples in the context of observational research 42 43 and larger clinical trial data. 44 The current study adds to this body of work and contributes to the evidence base for enabling more access to clinical trial data through synthesis.…”

Section: Introductionmentioning

confidence: 99%

Can synthetic data be a proxy for real clinical trial data? A validation study

Azizi

Zheng²,

Mosquera³

et al. 2021

BMJ Open

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ObjectivesThere are increasing requirements to make research data, especially clinical trial data, more broadly available for secondary analyses. However, data availability remains a challenge due to complex privacy requirements. This challenge can potentially be addressed using synthetic data.SettingReplication of a published stage III colon cancer trial secondary analysis using synthetic data generated by a machine learning method.ParticipantsThere were 1543 patients in the control arm that were included in our analysis.Primary and secondary outcome measuresAnalyses from a study published on the real dataset were replicated on synthetic data to investigate the relationship between bowel obstruction and event-free survival. Information theoretic metrics were used to compare the univariate distributions between real and synthetic data. Percentage CI overlap was used to assess the similarity in the size of the bivariate relationships, and similarly for the multivariate Cox models derived from the two datasets.ResultsAnalysis results were similar between the real and synthetic datasets. The univariate distributions were within 1% of difference on an information theoretic metric. All of the bivariate relationships had CI overlap on the tau statistic above 50%. The main conclusion from the published study, that lack of bowel obstruction has a strong impact on survival, was replicated directionally and the HR CI overlap between the real and synthetic data was 61% for overall survival (real data: HR 1.56, 95% CI 1.11 to 2.2; synthetic data: HR 2.03, 95% CI 1.44 to 2.87) and 86% for disease-free survival (real data: HR 1.51, 95% CI 1.18 to 1.95; synthetic data: HR 1.63, 95% CI 1.26 to 2.1).ConclusionsThe high concordance between the analytical results and conclusions from synthetic and real data suggests that synthetic data can be used as a reasonable proxy for real clinical trial datasets.Trial registration numberNCT00079274.

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Section: Introductionmentioning

confidence: 99%

Can synthetic data be a proxy for real clinical trial data? A validation study

Azizi

Zheng²,

Mosquera³

et al. 2021

BMJ Open

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“…The synthetic data generation platform creates a computationally derived data set which is statistically identical to that of the original patients. The computationally-derived variables and their pairwise correlations had the same or very similar distributions as the relationships among variables in the original data ( 20 ). We included a Spearman's correlation comparison between the variables in the original compared to the variables derived from the MDClone synthetic data platform ( Supplementary Figure 1 ).…”

Section: Methodsmentioning

confidence: 96%

The Use of Synthetic Electronic Health Record Data and Deep Learning to Improve Timing of High-Risk Heart Failure Surgical Intervention by Predicting Proximity to Catastrophic Decompensation

Guo

Foraker

MacGregor

et al. 2020

Front. Digit. Health

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Objective: Although many clinical metrics are associated with proximity to decompensation in heart failure (HF), none are individually accurate enough to risk-stratify HF patients on a patient-by-patient basis. The dire consequences of this inaccuracy in risk stratification have profoundly lowered the clinical threshold for application of high-risk surgical intervention, such as ventricular assist device placement. Machine learning can detect non-intuitive classifier patterns that allow for innovative combination of patient feature predictive capability. A machine learning-based clinical tool to identify proximity to catastrophic HF deterioration on a patient-specific basis would enable more efficient direction of high-risk surgical intervention to those patients who have the most to gain from it, while sparing others. Synthetic electronic health record (EHR) data are statistically indistinguishable from the original protected health information, and can be analyzed as if they were original data but without any privacy concerns. We demonstrate that synthetic EHR data can be easily accessed and analyzed and are amenable to machine learning analyses.Methods: We developed synthetic data from EHR data of 26,575 HF patients admitted to a single institution during the decade ending on 12/31/2018. Twenty-seven clinically-relevant features were synthesized and utilized in supervised deep learning and machine learning algorithms (i.e., deep neural networks [DNN], random forest [RF], and logistic regression [LR]) to explore their ability to predict 1-year mortality by five-fold cross validation methods. We conducted analyses leveraging features from prior to/at and after/at the time of HF diagnosis.Results: The area under the receiver operating curve (AUC) was used to evaluate the performance of the three models: the mean AUC was 0.80 for DNN, 0.72 for RF, and 0.74 for LR. Age, creatinine, body mass index, and blood pressure levels were especially important features in predicting death within 1-year among HF patients.Conclusions: Machine learning models have considerable potential to improve accuracy in mortality prediction, such that high-risk surgical intervention can be applied only in those patients who stand to benefit from it. Access to EHR-based synthetic data derivatives eliminates risk of exposure of EHR data, speeds time-to-insight, and facilitates data sharing. As more clinical, imaging, and contractile features with proven predictive capability are added to these models, the development of a clinical tool to assist in timing of intervention in surgical candidates may be possible.

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“…In this study, we utilized electronic health record (EHR) data from a large academic liver transplant center. Our institution partnered with MDClone [ 18 , 19 ] (Beer Sheva, Israel) for the data storage and retrieval. MDClone platform is a data engine by storing EHR medical events in a time order for each patient.…”

Section: Methodsmentioning

confidence: 99%

Predicting mortality among patients with liver cirrhosis in electronic health records with machine learning

et al. 2021

Self Cite

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Objective Liver cirrhosis is a leading cause of death and effects millions of people in the United States. Early mortality prediction among patients with cirrhosis might give healthcare providers more opportunity to effectively treat the condition. We hypothesized that laboratory test results and other related diagnoses would be associated with mortality in this population. Our another assumption was that a deep learning model could outperform the current Model for End Stage Liver disease (MELD) score in predicting mortality. Materials and methods We utilized electronic health record data from 34,575 patients with a diagnosis of cirrhosis from a large medical center to study associations with mortality. Three time-windows of mortality (365 days, 180 days and 90 days) and two cases with different number of variables (all 41 available variables and 4 variables in MELD-NA) were studied. Missing values were imputed using multiple imputation for continuous variables and mode for categorical variables. Deep learning and machine learning algorithms, i.e., deep neural networks (DNN), random forest (RF) and logistic regression (LR) were employed to study the associations between baseline features such as laboratory measurements and diagnoses for each time window by 5-fold cross validation method. Metrics such as area under the receiver operating curve (AUC), overall accuracy, sensitivity, and specificity were used to evaluate models. Results Performance of models comprising all variables outperformed those with 4 MELD-NA variables for all prediction cases and the DNN model outperformed the LR and RF models. For example, the DNN model achieved an AUC of 0.88, 0.86, and 0.85 for 90, 180, and 365-day mortality respectively as compared to the MELD score, which resulted in corresponding AUCs of 0.81, 0.79, and 0.76 for the same instances. The DNN and LR models had a significantly better f1 score compared to MELD at all time points examined. Conclusion Other variables such as alkaline phosphatase, alanine aminotransferase, and hemoglobin were also top informative features besides the 4 MELD-Na variables. Machine learning and deep learning models outperformed the current standard of risk prediction among patients with cirrhosis. Advanced informatics techniques showed promise for risk prediction in patients with cirrhosis.

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Spot the difference: comparing results of analyses from real patient data and synthetic derivatives

Cited by 45 publications

References 15 publications

Can synthetic data be a proxy for real clinical trial data? A validation study

Can synthetic data be a proxy for real clinical trial data? A validation study

The Use of Synthetic Electronic Health Record Data and Deep Learning to Improve Timing of High-Risk Heart Failure Surgical Intervention by Predicting Proximity to Catastrophic Decompensation

Predicting mortality among patients with liver cirrhosis in electronic health records with machine learning

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