| Literature DB >> 35677186 |
Robert P Hirten1, Lewis Tomalin2, Matteo Danieletto3, Eddye Golden3, Micol Zweig3, Sparshdeep Kaur3, Drew Helmus1, Anthony Biello1, Renata Pyzik4, Erwin P Bottinger3, Laurie Keefer1, Dennis Charney5, Girish N Nadkarni3, Mayte Suarez-Farinas2, Zahi A Fayad4.
Abstract
Objective: To determine whether a machine learning model can detect SARS-CoV-2 infection from physiological metrics collected from wearable devices. Materials andEntities:
Keywords: COVID-19; apple watch; coronavirus; machine learning; wearable device
Year: 2022 PMID: 35677186 PMCID: PMC9129173 DOI: 10.1093/jamiaopen/ooac041
Source DB: PubMed Journal: JAMIA Open ISSN: 2574-2531
Figure 1.General Strategy for training and testing statistical classifiers. Diagram illustrating the general strategy for developing the statistical classifier. (A) Subjects wore smartwatches that collect measurements of HRV and RHR. Subjects answer daily surveys to provide health outcomes including COVID test results. (B) Each day each subject is labeled as either; COVID+ if observation was made within ±7 days of the patients first positive COVID-19 test, otherwise the observation is labeled COVID−. (C) HRV measurements were too sparse to estimate HRV COSINOR parameters (MESOR, Amplitude, and Acrophase) for each day, thus, we estimated smoothed parameters using a 7-day sliding window. RHR (mean, standard deviation, minimum, and maximum) was also estimated over this window. (D) The data were split into 100 training and testing sets, models were fit to the training data and performance was estimated using 10-fold CV. 10-CV predictions were used define a decision rule that increases sensitivity, this decision rule was applied to the predictions in the testing data to get the final performance. COVID-19: Coronavirus Disease 2019; CV: cross-validation; HRV: heart rate variability; RHR: resting heart rate.
Baseline characteristics of study participants
| Total cohort ( | Never COVID-19 positive ( | COVID-19 positive ( |
| |
|---|---|---|---|---|
| Age, mean (SD) | 37.9 (9.82) | 37.9 (9.73) | 37.3 (10.55) | .65 |
| Body Mass Index, mean (SD) | 25.7 (5.47) | 25.7 (5.50) | 25.8 (5.31) | .91 |
| Male gender (%) | 139 (34.2) | 128 (35.8) | 11 (22.4) | .09 |
| Race (%) | .07 | |||
| Asian | 111 (27.3) | 104 (29.1) | 7 (14.3) | |
| Black | 43 (10.6) | 40 (11.2) | 3 (6.1) | |
| Hispanic/Latino | 71 (17.4) | 58 (16.2) | 13 (26.5) | |
| Other | 23 (5.7) | 21 (5.9) | 2 (4.1) | |
| White | 159 (39.1) | 135 (37.7) | 24 (49.0) | |
| Baseline negative SARS-CoV-2 Nasal PCR (%) | 382 (93.9) | 346 (96.6) | 36 (73.5) | <.001 |
| Baseline negative SARS-CoV-2 serum antibody (%) | 367 (90.2) | 325 (90.8) | 42 (85.7) | .39 |
| Baseline smoking status (%) | .61 | |||
| Never/rarely smoker | 343 (84.3) | 300 (83.8) | 43 (87.8) | |
| Current/past smoker | 64 (15.7) | 58 (16.2) | 6 (12.2) |
COVID-19, coronavirus disease 2019; PCR, polymerase chain reaction; SD, standard deviation.
Validation performance of GBM and Elastic Net machine learning methods
| Machine learning method | Area under receiver operating characteristic | Area under partial receiver operating characteristic (sensitivity > 0.75) | Area under precision recall curve |
|---|---|---|---|
| Gradient boosting machines | 0.85 | 0.79 | 0.19 |
| Elastic net regularization | 0.60 | 0.60 | 0.03 |
Figure 2.Model performance in training and testing data. (A) ROC curve and AUC over all training and validation samples. (B) Boxplots show distribution of validation performance metrics in over all 100 training sets. (C) Plot shows specificity (red, upward sloping line) and sensitivity (blue, downward sloping line) at different response thresholds for all validation samples, a threshold ∼0.21 achieved a sensitivity of 77% and a specificity of 78%. (D) Boxplots show distribution of performance metrics over all 100 training and test sets using the 0.21 threshold decision rule. (E) ROC curve and AUC over all testing samples. AUC: area under the curve; ROC: receiver operating characteristic.
Performance summary of the gradient boosting machine learning model in validation and testing sets before and after calibration
| 10-fold cross-validation before calibration ( | 10-fold cross-validation after calibration ( | Testing sets ( | |
|---|---|---|---|
| AUC | 84.7% (CI ±∼0.1%) | 84.7% (CI ±∼0.1%) | 86.4% (CI ±∼3%) |
| AUC partial | 78.5% (CI ±∼1%) | 78.5% (CI ±∼1%) | 79.6% (CI ±∼3%) |
| Accuracy | 95.4% (CI ±∼0.1%) | 78% (CI ±∼1%) | 77.2% (CI ±∼1%) |
| Sensitivity | 57.4% (CI ±∼1%) | 76.8% (CI ±∼1%) | 81.7% (CI ±∼4%) |
| Specificity | 95.7% (CI ±∼0.1%) | 78.0% (CI ±∼1%) | 77.2% (CI ±∼1%) |
| Balanced accuracy | 76.5% (CI ±∼0.1%) | 77.4% (CI ±∼1%) | 79.5% (CI ±∼2%) |
| auPRC | 19.3% (CI ±∼1%) | 19.3% (CI ±∼0.1%) | 18.0% (CI ±∼3%) |
AUC, area under the curve; auPRC, area under the precision recall curve; CI: confidence interval.
Figure 3.Changes in HRV parameters and model predictions over time. (A) Box plots show the importance of each variable selected by the GBM models over all 100 training sets. (B) Line plots show daily measurements of HRV parameters (Acrophase, MESOR, and Amplitude), and Maximum resting heart rate, as well as the probability of infection (black, solid line) predicted by the model. Feature values are centered, scaled and smoothed to facilitate comparison. Daily measurements for 9 subjects are shown, predictions for each of these 9 subjects all had AUC > 65% in validation. Vertical red-dashed lines indicate the infection window for each patient, horizontal gray solid line indicates the .18 probability threshold used for the decision rule. AUC: area under the curve; GBM: gradient-boosting machines; HRV: heart rate variability.