Evaluation of Digital Well being Data (EHR) has an amazing potential for enhancing affected person care, quantitatively measuring efficiency of medical practices, and facilitating medical analysis. Statistical estimation and machine studying (ML) fashions skilled on EHR information can be utilized to foretell the likelihood of assorted illnesses (akin to diabetes), monitor affected person wellness, and predict how sufferers reply to particular medicine. For such fashions, researchers and practitioners want entry to EHR information. Nonetheless, it may be difficult to leverage EHR information whereas guaranteeing information privateness and conforming to affected person confidentiality laws (akin to HIPAA).

Typical strategies to anonymize information (e.g., de-identification) are sometimes tedious and expensive. Furthermore, they will distort essential options from the unique dataset, lowering the utility of the information considerably; they can be prone to privateness assaults. Alternatively, an strategy based mostly on producing artificial information can preserve each essential dataset options and privateness.

To that finish, we suggest a novel generative modeling framework in “EHR-Secure: Producing Excessive-Constancy and Privateness-Preserving Artificial Digital Well being Data“. With the revolutionary methodology in EHR-Secure, we present that artificial information can fulfill two key properties: (i) excessive constancy (i.e., they’re helpful for the duty of curiosity, akin to having related downstream efficiency when a diagnostic mannequin is skilled on them), (ii) meet sure privateness measures (i.e., they don’t reveal any actual affected person’s id). Our state-of-the-art outcomes stem from novel approaches for encoding/decoding options, normalizing complicated distributions, conditioning adversarial coaching, and representing lacking information.

Producing artificial information from the unique information with EHR-Secure.

Challenges of Producing Practical Artificial EHR Information

There are a number of elementary challenges to producing artificial EHR information. EHR information include heterogeneous options with totally different traits and distributions. There may be numerical options (e.g., blood strain) and categorical options with many or two classes (e.g., medical codes, mortality final result). A few of these could also be static (i.e., not various in the course of the modeling window), whereas others are time-varying, akin to common or sporadic lab measurements. Distributions may come from totally different households — categorical distributions may be extremely non-uniform (e.g., for under-represented teams) and numerical distributions may be extremely skewed (e.g., a small proportion of values being very massive whereas the overwhelming majority are small). Relying on a affected person’s situation, the variety of visits may differ drastically — some sufferers go to a clinic solely as soon as whereas some go to tons of of occasions, resulting in a variance in sequence lengths that’s sometimes a lot greater in comparison with different time-series information. There could be a excessive ratio of lacking options throughout totally different sufferers and time steps, as not all lab measurements or different enter information are collected.

Examples of actual EHR information: temporal numerical options (higher) and temporal categorical options (decrease).

EHR-Secure: Artificial EHR Information Era Framework

EHR-Secure consists of sequential encoder-decoder structure and generative adversarial networks (GANs), depicted within the determine beneath. As a result of EHR information are heterogeneous (as described above), direct modeling of uncooked EHR information is difficult for GANs. To bypass this, we suggest using a sequential encoder-decoder structure, to be taught the mapping from the uncooked EHR information to the latent representations, and vice versa.

Block diagram of EHR-Secure framework.

Whereas studying the mapping, esoteric distributions of numerical and categorical options pose an awesome problem. For instance, some values or numerical ranges may dominate the distribution, however the functionality of modeling uncommon instances is important. The proposed characteristic mapping and stochastic normalization (remodeling authentic characteristic distributions into uniform distributions with out info loss) are key to dealing with such information by changing to distributions for which the coaching of encoder-decoder and GAN are extra secure (particulars may be discovered within the paper). The mapped latent representations, generated by the encoder, are then used for GAN coaching. After coaching each the encoder-decoder framework and GANs, EHR-Secure can generate artificial heterogeneous EHR information from any enter, for which we feed randomly sampled vectors. Observe that solely the skilled generator and decoders are used for producing artificial information.


We concentrate on two real-world EHR datasets to showcase the EHR-Secure framework, MIMIC-III and eICU. Each are inpatient datasets that include various lengths of sequences and embrace a number of numerical and categorical options with lacking elements.

Constancy Outcomes

The constancy metrics concentrate on the standard of synthetically generated information by measuring the realisticness of the artificial information. Larger constancy implies that it’s harder to distinguish between artificial and actual information. We consider the constancy of artificial information by way of a number of quantitative and qualitative analyses.


Having related protection and avoiding under-representation of sure information regimes are each essential for artificial information technology. Because the beneath t-SNE analyses present, the protection of the artificial information (blue) may be very related with the unique information (purple). With membership inference metrics (will likely be launched within the privateness part), we additionally confirm that EHR-Secure doesn’t simply memorize the unique prepare information.

t-SNE analyses on temporal and static information on MIMIC-III (higher) and eICU (decrease) datasets.

Statistical Similarity

We offer quantitative comparisons of statistical similarity between authentic and artificial information for every characteristic. Most statistics are well-aligned between authentic and artificial information — for instance a measure of the KS statistics, i.e,. the utmost distinction within the cumulative distribution perform (CDF) between the unique and the artificial information, are principally decrease than 0.03. Extra detailed tables may be discovered within the paper. The determine beneath exemplifies the CDF graphs for authentic vs. artificial information for 3 options — general they appear very shut generally.

CDF graphs of two options between authentic and artificial EHR information. Left: Imply Airway Stress. Proper: Minute Quantity Alarm.


As a result of some of the essential use instances of artificial information is enabling ML improvements, we concentrate on the constancy metric that measures the flexibility of fashions skilled on artificial information to make correct predictions on actual information. We evaluate such mannequin efficiency to an equal mannequin skilled with actual information. Related mannequin efficiency would point out that the artificial information captures the related informative content material for the duty. As one of many essential potential use instances of EHR, we concentrate on the mortality prediction job. We contemplate 4 totally different predictive fashions: Gradient Boosting Tree Ensemble (GBDT), Random Forest (RF), Logistic Regression (LR), Gated Recurrent Items (GRU).

Mortality prediction efficiency with the mannequin skilled on actual vs. artificial information. Left: MIMIC-III. Proper: eICU.

Within the determine above we see that in most eventualities, coaching on artificial vs. actual information are extremely related by way of Space Beneath Receiver Working Traits Curve (AUC). On MIMIC-III, the very best mannequin (GBDT) on artificial information is simply 2.6% worse than the very best mannequin on actual information; whereas on eICU, the very best mannequin (RF) on artificial information is simply 0.9% worse.

Privateness Outcomes

We contemplate three totally different privateness assaults to quantify the robustness of the artificial information with respect to privateness.

  • Membership inference assault: An adversary predicts whether or not a recognized topic was a gift within the coaching information used for coaching the artificial information mannequin.
  • Re-identification assault: The adversary explores the likelihood of some options being re-identified utilizing artificial information and matching to the coaching information.
  • Attribute inference assault: The adversary predicts the worth of delicate options utilizing artificial information.
Privateness danger analysis throughout three privateness metrics: membership-inference (top-left), re-identification (top-right), and attribute inference (backside). The perfect worth of privateness danger for membership inference is random guessing (0.5). For re-identification, the best case is to switch the artificial information with disjoint holdout authentic information.

The determine above summarizes the outcomes together with the best achievable worth for every metric. We observe that the privateness metrics are very near the best in all instances. The chance of understanding whether or not a pattern of the unique information is a member used for coaching the mannequin may be very near random guessing; it additionally verifies that EHR-Secure doesn’t simply memorize the unique prepare information. For the attribute inference assault, we concentrate on the prediction job of inferring particular attributes (e.g., gender, faith, and marital standing) from different attributes. We evaluate prediction accuracy when coaching a classifier with actual information in opposition to the identical classifier skilled with artificial information. As a result of the EHR-Secure bars are all decrease, the outcomes display that entry to artificial information doesn’t result in greater prediction efficiency on particular options as in comparison with entry to the unique information.

Comparability to Different Strategies

We evaluate EHR-Secure to alternate options (TimeGAN, RC-GAN, C-RNN-GAN) proposed for time-series artificial information technology. As proven beneath, EHR-Secure considerably outperforms every.

Downstream job efficiency (AUC) compared to alternate options.


We suggest a novel generative modeling framework, EHR-Secure, that may generate extremely sensible artificial EHR information which might be strong to privateness assaults. EHR-Secure is predicated on generative adversarial networks utilized to the encoded uncooked information. We introduce a number of improvements within the structure and coaching mechanisms which might be motivated by the important thing challenges of EHR information. These improvements are key to our outcomes that present almost-identical properties with actual information (when desired downstream capabilities are thought-about) with almost-ideal privateness preservation. An essential future course is generative modeling functionality for multimodal information, together with textual content and picture, as fashionable EHR information may include each.


We gratefully acknowledge the contributions of Michel Mizrahi, Nahid Farhady Ghalaty, Thomas Jarvinen, Ashwin S. Ravi, Peter Brune, Fanyu Kong, Dave Anderson, George Lee, Arie Meir, Farhana Bandukwala, Elli Kanal, and Tomas Pfister.

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