PreprintCited by 253Machine Learning in HealthcarePrivacy-Preserving Technologies in DataCOVID-19 Clinical Research Studies

Federated Learning of Electronic Health Records Improves Mortality Prediction in Patients Hospitalized with COVID-19

Open access
Vaid, Akhil, Jaladanki, Suraj K, Xu, Jie, Teng, Shelly, Kumar, Arvind, Lee, Samuel, Somani, Sulaiman, Paranjpe, Ishan +15 more·2020·JMIR Medical Informatics

Published version of a preprint

Abstract

Machine learning (ML) models require large datasets which may be siloed across different healthcare institutions. Using federated learning, a ML technique that avoids locally aggregating raw clinical data across multiple institutions, we predict mortality within seven days in hospitalized COVID-19 patients. Patient data was collected from Electronic Health Records (EHRs) from five hospitals within the Mount Sinai Health System (MSHS). Logistic Regression with L1 regularization (LASSO) and Multilayer Perceptron (MLP) models were trained using local data at each site, a pooled model with combined data from all five sites, and a federated model that only shared parameters with a central aggregator. Both the federated LASSO and federated MLP models performed better than their local model counterparts at four hospitals. The federated MLP model also outperformed the federated LASSO model at all hospitals. Federated learning shows promise in COVID-19 EHR data to develop robust predictive models without compromising patient privacy.

AI snapshot

Written from the paper’s full text.

TL;DR

This study used federated learning to predict 7-day mortality among 4,029 hospitalized COVID-19 patients across five Mount Sinai Health System hospitals, comparing local, pooled, and federated LASSO and MLP models. Federated models generally improved on local models, and federated MLP often performed best, while pooled LASSO remained stronger than federated LASSO.

Key findings

  • In 4,029 COVID-19-positive patients, 7-day mortality prevalence differed significantly across hospitals (p<0.001), ranging from 5.6% to 24.2%.
  • Federated LASSO outperformed local LASSO at all sites except MSQ, with AUC-ROC 0.693–0.805; pooled LASSO outperformed federated LASSO at all five sites, with AUC-ROC 0.736–0.822.
  • Federated MLP surpassed federated LASSO at all sites and consistently outperformed all other tested models at all hospitals except MSB; local MLP outperformed local LASSO at all hospitals.
  • Adding Gaussian noise to federated MLP decreased performance at all sites except MSQ; AUC-ROC ranged 0.796–0.834 without noise and 0.767–0.830 with noise.

Methods

  • Data came from Epic EHRs of five MSHS hospitals in NYC: MSB (n=611), MSH (n=1644), MSM (n=749), MSQ (n=540), and MSW (n=485); primary outcome was mortality within seven days of admission.
  • LASSO and MLP models were trained locally at each site, pooled across all sites, and federated via parameter sharing with a central aggregator using federated averaging; no raw data were shared.
  • Models were evaluated with 10-fold stratified cross-validation, using AUC-ROC averaged across folds; Gaussian noise experiments simulated federated learning in practice.

Limitations

  • Stated: data were limited to MSHS hospitals in NYC, which may limit generalizability; the work focused on principle rather than an operational deployment and did not address load balancing, convergence, or scaling; only clinical data and two classifiers were used; identical MLP architectures were used across strategies for comparison but could have been further optimized.
  • Evident from the text: there was no external validation outside the same health system, and some sites had small samples and marked differences in mortality prevalence (e.g., MSQ n=540, 23.0%; MSW n=485, 5.6%), which may affect site-level comparisons.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1101/2020.08.11.20172809

Cites

22 of 22 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 1 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    There were significant differences across hospitals in the proportion of mortality within seven days, which ranged from 5.6% to 24.2%.

    “We found significant differences across hospitals in the proportion of outcome, specifically mortality within seven days (p<0.001), which ranged from 5.6% to 24.2% (Table 1).”
    Quote in the paperNot a substantial claim
  • Findingown data

    There were significant differences across hospitals in gender, age, ethnicity, and race.

    “There were also significant differences in gender (p=0.004), age (p<0.001), ethnicity (p<0.001), and race (p<0.001).”
    Quote in the paperNot a substantial claim
  • Findingown data

    There were significant differences across hospitals in the majority of key clinical features, such as asthma and white blood cell counts.

    “We found significant differences in the majority of key clinical features such as past medical history like asthma (p<0.001) and relevant lab tests including white blood cell counts (p<0.001; Supplementary Table 1).”
    Quote in the paperNot a substantial claim
  • Findingreasoning

    MSQ was the only hospital where federated LASSO performed slightly worse than the local model, with a difference of 0.04 in AUC-ROC.

    “MSQ was the only hospital where federated LASSO performed slightly worse than the local model with a difference of 0.04 in AUC-ROC, which may be attributed to a low sample size of 540 patients and a high mortality prevalence of 23.0% compared to other sites.”
    Quote in the paperNot a substantial claim
  • Findingreasoning

    Federated MLP outperformed pooled MLP at all sites.

    “Federated MLP also outperformed pooled MLP at all sites which might be due to the experimental condition where the same underlying architecture was used for all MLP models.”
    Quote in the paperSubstantial claim
  • May combine two claims. 6
  • Classified as probably not a substantial claim. 8
  • May combine two claims.

    Findingown data

    Both federated LASSO and federated MLP models performed better than their local model counterparts at four hospitals.

    “Both the federated LASSO and federated MLP models performed better than their local model counterparts at four hospitals.”
    • Also stated in: § DISCUSSION · plain
      “The primary findings of this study demonstrate that federated MLP and LASSO models outperformed their respective local models at most sites.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Federated LASSO outperformed local LASSO at all sites except MSQ, with AUC-ROC ranging from 0.693 to 0.805.

    “Federated LASSO outperformed the site’s local LASSO at all sites except MSQ, with AUC-ROC ranging from 0.693 to 0.805.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    LASSO pooled outperformed federated LASSO at all five sites, with AUC-ROC ranging from 0.736 to 0.822.

    “LASSO pooled outperformed federated LASSO at all five sites and had AUC-ROCs ranging from 0.736 to 0.822.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    MSW had the lowest sample size of all hospitals at 485 and the lowest COVID-19 mortality prevalence of 5.6%.

    “MSW had the lowest sample size of all hospitals at 485 and the lowest COVID-19 mortality prevalence of 5.6%.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim.

    Study design and conductnone given

    All models were trained and evaluated using 10-fold stratified cross validation.

    “All models were trained and evaluated using 10-fold stratified cross validation.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    Experiments with the addition of Gaussian noise were performed to simulate federated learning in practice.

    “To simulate federated learning in practice, we also performed experiments with the addition of Gaussian noise (see Supplementary Materials).”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Interpretationreasoning

    Data collection was limited to MSHS hospitals in NYC, which may limit model generalizability to hospitals in other regions.

    “First, data collection was limited to MSHS hospitals in NYC. This may limit model generalizability to hospitals in other regions.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductreasoning

    The study was placed within TRIPOD guidelines and code was released under GPLv3 to promote replicability.

    “To promote replicability, we placed our study within the Transparent Reporting of a Multivariable Prediction Model for Individual Prognosis or Diagnosis (TRIPOD) guidelines (Supplementary Table 3) and released our code under the GPLv3 license (Supplementary Materials).”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S4 (based).

    Interpretationnone given

    Federated learning is an effective method to share ML models without jeopardizing patient privacy.

    “Federated learning is an effective method to share ML models without jeopardizing patient privacy.”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim.

    Study design and conductreasoning

    Federated models did not receive any raw data.

    “Through this technique, federated models did not receive any raw data.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductreasoning

    Each MLP model was built with the same architecture for consistency and direct comparisons.

    “For consistency and to enable direct comparisons, each MLP model was built with the same architecture.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductreasoning

    Multiple class balancing techniques were assessed due to varying prevalence across hospitals.

    “Due to varying prevalence across hospitals, we assessed multiple class balancing techniques (Supplementary Table 2).”
    Quote in the paperNot a substantial claim
12 of 12
  • The paper relies on this without support.

    Adding Gaussian noise to federated model parameters increases data security.

    “An average difference of 0.013 in AUC-ROC across all hospitals in these two models demonstrates that noise may be inserted to increase data security without severely compromising federated model performance.”
  • The paper relies on this without support.

    The pooled model, trained on combined data from all sites, represents an ideal framework for comparison.

    “Although the pooled model is not practically feasible, it represents an ideal framework.”
2 of 2

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Authors
Vaid, A., Jaladanki, S. K., Xu, J., Teng, S., Kumar, A., Lee, S., Somani, S., Paranjpe, I., Freitas, J. K. D., Wanyan, T., Johnson, K. W., Bicak, M., Klang, E., Kwon, Y. J., Costa, A., Zhao, S., Miotto, R., Charney, A. W., Böttinger, E., Fayad, Z. A., Nadkarni, G. N., Wang, F., & Glicksberg, B. S.
Affiliations
  • Icahn School of Medicine at Mount Sinai (US)
  • Weill Cornell Medicine (US)
  • Indiana University Bloomington (US)
  • Hasso Plattner Institute (DE)
Corresponding author
Glicksberg, Benjamin S
Venue
JMIR Medical Informatics
Publisher
openRxiv
Published
2020-08-14
Volume
9
Issue
1
Pages
e24207-e24207
ISSN
2291-9694 (ISSN-L)
OpenAlex
W3118996476
Cited by
253
References
20
Citations by year
2026: 33 · 2025: 40 · 2024: 43 · 2023: 54 · 2022: 47 · 2021: 32 · 2020: 4
FWCI
15.49
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • JMIR Medical Informatics (publishedVersion, cc-by)
  • medRxiv (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by-nc-nd)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • publish.UP (University of Potsdam) (submittedVersion, cc-by)
Funders
  • National Institutes of Health (UL1TR001433)
  • National Center for Advancing Translational Sciences (U54 TR001433-05)
Topics
  • Physical Sciences › Computer Science › Artificial Intelligence › Machine Learning in Healthcare
  • Physical Sciences › Computer Science › Artificial Intelligence › Privacy-Preserving Technologies in Data
  • Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
Keywords
federated learning, COVID-19 pandemic, mortality prediction, hospitalized patients, electronic health records, data privacy, model generalization, LASSO, multilayer perceptron

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