Angier Allen

Mr. Angier Allen

Dascena, Inc.
orcid

Research Focus & Metrics

Academic Career Length

7Years (2020-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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19 January 2022 in BMJ Open Diabetes Research & Care
Verified
Journal Article
Open access
PDF file
AAAngier Allen
Angier Allen
ZIZohora Iqbal
Zohora Iqbal
AGAbigail Green-Saxena
Abigail Green-Saxena
MHMyrna Hurtado
Myrna Hurtado
JHjana hoffman
jana hoffman
RDRitankar Das
Ritankar Das
Introduction Diabetic kidney disease (DKD) accounts for the majority of increased risk of mortality for patients with diabetes, and eventually manifests in approximately half of those patients diagnosed with type 2 diabetes mellitus (T2DM). Although increased screening frequency can avoid delayed diagnoses, this is not uniformly implemented. The purpose of this study was to develop and retrospectively validate a machine learning algorithm (MLA) that predicts stages of DKD within 5 years upon diagnosis of T2DM. Research design and methods Two MLAs were trained to predict stages of DKD severity, and compared with the Centers for Disease Control and Prevention (CDC) risk score to evaluate performance. The models were validated on a hold-out test set as well as an external dataset sourced from separate facilities. Results The MLAs outperformed the CDC risk score in both the hold-out test and external datasets. Our algorithms achieved an area under the receiver operating characteristic curve (AUROC) of 0.75 on the hold-out set for prediction of any-stage DKD and an AUROC of over 0.82 for more severe endpoints, compared with the CDC risk score with an AUROC <0.70 on all test sets and endpoints. Conclusion This retrospective study shows that an MLA can provide timely predictions of DKD among patients with recently diagnosed T2DM.

1 November 2020 in Annals of Medicine & Surgery
Verified
Journal Article
Open access
LRLogan Ryan
Logan Ryan
CLCarson Lam
Carson Lam
SMSamson Mataraso
Samson Mataraso
AAAngier Allen
Angier Allen
AGAbigail Green-Saxena
Abigail Green-Saxena
RDRitankar Das
Ritankar Das
Prediction of patients at risk for mortality can help triage patients and assist in resource allocation. Develop and evaluate a machine learning-based algorithm which accurately predicts mortality in COVID-19, pneumonia, and mechanically ventilated patients. Retrospective study of 53,001 total ICU patients, including 9166 patients with pneumonia and 25,895 mechanically ventilated patients, performed on the MIMIC dataset. An additional retrospective analysis was performed on a community hospital dataset containing 114 patients positive for SARS-COV-2 by PCR test. The outcome of interest was in-hospital patient mortality. When trained and tested on the MIMIC dataset, the XGBoost predictor obtained area under the receiver operating characteristic (AUROC) values of 0.82, 0.81, 0.77, and 0.75 for mortality prediction on mechanically ventilated patients at 12-, 24-, 48-, and 72- hour windows, respectively, and AUROCs of 0.87, 0.78, 0.77, and 0.734 for mortality prediction on pneumonia patients at 12-, 24-, 48-, and 72- hour windows, respectively. The predictor outperformed the qSOFA, MEWS and CURB-65 risk scores at all prediction windows. When tested on the community hospital dataset, the predictor obtained AUROCs of 0.91, 0.90, 0.86, and 0.87 for mortality prediction on COVID-19 patients at 12-, 24-, 48-, and 72- hour windows, respectively, outperforming the qSOFA, MEWS and CURB-65 risk scores at all prediction windows. This machine learning-based algorithm is a useful predictive tool for anticipating patient mortality at clinically useful timepoints, and is capable of accurate mortality prediction for mechanically ventilated patients as well as those diagnosed with pneumonia and COVID-19.

16 June 2021 in Applied Sciences
Verified
Journal Article
Open access
PDF file
AAAngier Allen
Angier Allen
ASAnna Siefkas
Anna Siefkas
EPEmily Pellegrini
Emily Pellegrini
HBHoyt Burdick
Hoyt Burdick
GBGina Barnes
Gina Barnes
RDRitankar Das
Ritankar Das
Background: Machine learning methods have been developed to predict the likelihood of a given event or classify patients into two or more diagnostic categories. Digital twin models, which forecast entire trajectories of patient health data, have potential applications in clinical trials and patient management. Methods: In this study, we apply a digital twin model based on a variational autoencoder to a population of patients who went on to experience an ischemic stroke. The digital twin’s ability to model patient clinical features was assessed with regard to its ability to forecast clinical measurement trajectories leading up to the onset of the acute medical event and beyond using International Classification of Diseases (ICD) codes for ischemic stroke and lab values as inputs. Results: The simulated patient trajectories were virtually indistinguishable from real patient data, with similar feature means, standard deviations, inter-feature correlations, and covariance structures on a withheld test set. A logistic regression adversary model was unable to distinguish between the real and simulated data area under the receiver operating characteristic (ROC) curve (AUCadversary = 0.51). Conclusion: Through accurate projection of patient trajectories, this model may help inform clinical decision making or provide virtual control arms for efficient clinical trials.

22 October 2020 in JMIR Public Health and Surveillance
Verified
Journal Article
Open access
AAAngier Allen
Angier Allen
SMSamson Mataraso
Samson Mataraso
ASAnna Siefkas
Anna Siefkas
HBHoyt Burdick
Hoyt Burdick
GBGregory Braden
Gregory Braden
RDRitankar Das
Ritankar Das
Background: Racial disparities in health care are well documented in the United States. As machine learning methods become more common in health care settings, it is important to ensure that these methods do not contribute to racial disparities through biased predictions or differential accuracy across racial groups. Objective: The goal of the research was to assess a machine learning algorithm intentionally developed to minimize bias in in-hospital mortality predictions between white and nonwhite patient groups. Methods: Bias was minimized through preprocessing of algorithm training data. We performed a retrospective analysis of electronic health record data from patients admitted to the intensive care unit (ICU) at a large academic health center between 2001 and 2012, drawing data from the Medical Information Mart for Intensive Care–III database. Patients were included if they had at least 10 hours of available measurements after ICU admission, had at least one of every measurement used for model prediction, and had recorded race/ethnicity data. Bias was assessed through the equal opportunity difference. Model performance in terms of bias and accuracy was compared with the Modified Early Warning Score (MEWS), the Simplified Acute Physiology Score II (SAPS II), and the Acute Physiologic Assessment and Chronic Health Evaluation (APACHE). Results: The machine learning algorithm was found to be more accurate than all comparators, with a higher sensitivity, specificity, and area under the receiver operating characteristic. The machine learning algorithm was found to be unbiased (equal opportunity difference 0.016, P=.20). APACHE was also found to be unbiased (equal opportunity difference 0.019, P=.11), while SAPS II and MEWS were found to have significant bias (equal opportunity difference 0.038, P=.006 and equal opportunity difference 0.074, P<.001, respectively). Conclusions: This study indicates there may be significant racial bias in commonly used severity scoring systems and that machine learning algorithms may reduce bias while improving on the accuracy of these methods.

4 October 2023 in JAMIA Open
Verified
Journal Article
Open access
PDF file
NHNicholas Hirons
Nicholas Hirons
AAAngier Allen
Angier Allen
NMNoah Matsuyoshi
Noah Matsuyoshi
JSJason Su
Jason Su
LKLeanne Kaye
Leanne Kaye
MBMeredith A Barrett
Meredith A Barrett
Objective: Changes in short-acting beta-agonist (SABA) use are an important signal of asthma control and risk of asthma exacerbations. Inhaler sensors passively capture SABA use and may provide longitudinal data to identify at-riskpatients. We evaluate the performance of several ML models in predicting daily SABA use for participants with asthma and determine relevant features for predictive accuracy. Methods: Participants with self-reported asthma enrolled in a digital health platform (Propeller Health, WI), which included a smartphone application and inhaler sensors that collected the date and time of SABA use. Linear regression, random forests, and temporal convolutional networks (TCN) were applied to predict expected SABA puffs/person/day from SABA usage and environmental triggers. The models were compared with a simple baseline model using explained variance (R2), as well as using average precision (AP) and area under the receiving operator characteristic curve (ROC AUC) for predicting days with ≥1–10 puffs. Results: Data included 1.2 million days of data from 13 202 participants. A TCN outperformed other models in predicting puff count (R2 = 0.562) and day-over-day change in puff count (R2 = 0.344). The TCN predicted days with ≥10 puffs with an ROC AUC score of 0.952 and an AP of 0.762 for predicting a day with ≥1 puffs. SABA use over the preceding 7 days had the highest feature importance, with a smaller but meaningful contribution from air pollutant features. Conclusion: Predicted SABA use may serve as a valuable forward-looking signal to inform early clinical intervention and self-management. Further validation with known exacerbation events is needed.

10 July 2020 in JMIR Preprints
Verified
Preprint
Open access
AAAngier Allen
Angier Allen
SMSamson Mataraso
Samson Mataraso
ASAnna Siefkas
Anna Siefkas
HBHoyt Burdick
Hoyt Burdick
GBGregory Braden
Gregory Braden
RDRitankar Das
Ritankar Das
BACKGROUND Racial disparities in health care are well documented in the United States. As machine learning methods become more common in health care settings, it is important to ensure that these methods do not contribute to racial disparities through biased predictions or differential accuracy across racial groups. OBJECTIVE The goal of the research was to assess a machine learning algorithm intentionally developed to minimize bias in in-hospital mortality predictions between white and nonwhite patient groups. METHODS Bias was minimized through preprocessing of algorithm training data. We performed a retrospective analysis of electronic health record data from patients admitted to the intensive care unit (ICU) at a large academic health center between 2001 and 2012, drawing data from the Medical Information Mart for Intensive Care–III database. Patients were included if they had at least 10 hours of available measurements after ICU admission, had at least one of every measurement used for model prediction, and had recorded race/ethnicity data. Bias was assessed through the equal opportunity difference. Model performance in terms of bias and accuracy was compared with the Modified Early Warning Score (MEWS), the Simplified Acute Physiology Score II (SAPS II), and the Acute Physiologic Assessment and Chronic Health Evaluation (APACHE). RESULTS The machine learning algorithm was found to be more accurate than all comparators, with a higher sensitivity, specificity, and area under the receiver operating characteristic. The machine learning algorithm was found to be unbiased (equal opportunity difference 0.016, P=.20). APACHE was also found to be unbiased (equal opportunity difference 0.019, P=.11), while SAPS II and MEWS were found to have significant bias (equal opportunity difference 0.038, P=.006 and equal opportunity difference 0.074, P<.001, respectively). CONCLUSIONS This study indicates there may be significant racial bias in commonly used severity scoring systems and that machine learning algorithms may reduce bias while improving on the accuracy of these methods.