arXiv subjects

Yuanfang Ren

Publications and source records attributed to Yuanfang Ren.

27 records · Page 2Linked to original sources

arXiv2024

APRICOT-Mamba: Acuity Prediction in Intensive Care Unit (ICU): Development and Validation of a Stability, Transitions, and Life-Sustaining Therapies Prediction Model

The acuity state of patients in the intensive care unit (ICU) can quickly change from stable to unstable. Early detection of deteriorating conditions can result in providing timely interventions and improved survival rates. In this study, we propose APRICOT-M (Acuity Prediction in Intensive Care Unit-Mamba), a 150k-parameter state space-based neural network to predict acuity state, transitions, and the need for life-sustaining therapies in real-time in ICU patients. The model uses data obtained in the prior four hours in the ICU and patient information obtained at admission to predict the acuity outcomes in the next four hours. We validated APRICOT-M externally on data from hospitals not used in development (75,668 patients from 147 hospitals), temporally on data from a period not used in development (12,927 patients from one hospital from 2018-2019), and prospectively on data collected in real-time (215 patients from one hospital from 2021-2023) using three large datasets: the University of Florida Health (UFH) dataset, the electronic ICU Collaborative Research Database (eICU), and the Medical Information Mart for Intensive Care (MIMIC)-IV. The area under the receiver operating characteristic curve (AUROC) of APRICOT-M for mortality (external 0.94-0.95, temporal 0.97-0.98, prospective 0.96-1.00) and acuity (external 0.95-0.95, temporal 0.97-0.97, prospective 0.96-0.96) shows comparable results to state-of-the-art models. Furthermore, APRICOT-M can predict transitions to instability (external 0.81-0.82, temporal 0.77-0.78, prospective 0.68-0.75) and need for life-sustaining therapies, including mechanical ventilation (external 0.82-0.83, temporal 0.87-0.88, prospective 0.67-0.76), and vasopressors (external 0.81-0.82, temporal 0.73-0.75, prospective 0.66-0.74). This tool allows for real-time acuity monitoring in critically ill patients and can help clinicians make timely interventions.

cs.AI↗

arXiv2024

Acute kidney injury prediction for non-critical care patients: a retrospective external and internal validation study

Background: Acute kidney injury (AKI), the decline of kidney excretory function, occurs in up to 18% of hospitalized admissions. Progression of AKI may lead to irreversible kidney damage. Methods: This retrospective cohort study includes adult patients admitted to a non-intensive care unit at the University of Pittsburgh Medical Center (UPMC) (n = 46,815) and University of Florida Health (UFH) (n = 127,202). We developed and compared deep learning and conventional machine learning models to predict progression to Stage 2 or higher AKI within the next 48 hours. We trained local models for each site (UFH Model trained on UFH, UPMC Model trained on UPMC) and a separate model with a development cohort of patients from both sites (UFH-UPMC Model). We internally and externally validated the models on each site and performed subgroup analyses across sex and race. Results: Stage 2 or higher AKI occurred in 3% (n=3,257) and 8% (n=2,296) of UFH and UPMC patients, respectively. Area under the receiver operating curve values (AUROC) for the UFH test cohort ranged between 0.77 (UPMC Model) and 0.81 (UFH Model), while AUROC values ranged between 0.79 (UFH Model) and 0.83 (UPMC Model) for the UPMC test cohort. UFH-UPMC Model achieved an AUROC of 0.81 (95% confidence interval [CI] [0.80, 0.83]) for UFH and 0.82 (95% CI [0.81,0.84]) for UPMC test cohorts; an area under the precision recall curve values (AUPRC) of 0.6 (95% CI, [0.05, 0.06]) for UFH and 0.13 (95% CI, [0.11,0.15]) for UPMC test cohorts. Kinetic estimated glomerular filtration rate, nephrotoxic drug burden and blood urea nitrogen remained the top three features with the highest influence across the models and health centers. Conclusion: Locally developed models displayed marginally reduced discrimination when tested on another institution, while the top set of influencing features remained the same across the models and sites.

cs.LG↗

arXiv2023

Computable Phenotypes of Patient Acuity in the Intensive Care Unit

Continuous monitoring and patient acuity assessments are key aspects of Intensive Care Unit (ICU) practice, but both are limited by time constraints imposed on healthcare providers. Moreover, anticipating clinical trajectories remains imprecise. The objectives of this study are to (1) develop an electronic phenotype of acuity using automated variable retrieval within the electronic health records and (2) describe transitions between acuity states that illustrate the clinical trajectories of ICU patients. We gathered two single-center, longitudinal electronic health record datasets for 51,372 adult ICU patients admitted to the University of Florida Health (UFH) Gainesville (GNV) and Jacksonville (JAX). We developed algorithms to quantify acuity status at four-hour intervals for each ICU admission and identify acuity phenotypes using continuous acuity status and k-means clustering approach. 51,073 admissions for 38,749 patients in the UFH GNV dataset and 22,219 admissions for 12,623 patients in the UFH JAX dataset had at least one ICU stay lasting more than four hours. There were three phenotypes: persistently stable, persistently unstable, and transitioning from unstable to stable. For stable patients, approximately 0.7%-1.7% would transition to unstable, 0.02%-0.1% would expire, 1.2%-3.4% would be discharged, and the remaining 96%-97% would remain stable in the ICU every four hours. For unstable patients, approximately 6%-10% would transition to stable, 0.4%-0.5% would expire, and the remaining 89%-93% would remain unstable in the ICU in the next four hours. We developed phenotyping algorithms for patient acuity status every four hours while admitted to the ICU. This approach may be useful in developing prognostic and clinical decision-support tools to aid patients, caregivers, and providers in shared decision-making processes regarding escalation of care and patient values.

q-bio.QM↗

arXiv2023

Identifying acute illness phenotypes via deep temporal interpolation and clustering network on physiologic signatures

Initial hours of hospital admission impact clinical trajectory, but early clinical decisions often suffer due to data paucity. With clustering analysis for vital signs within six hours of admission, patient phenotypes with distinct pathophysiological signatures and outcomes may support early clinical decisions. We created a single-center, longitudinal EHR dataset for 75,762 adults admitted to a tertiary care center for 6+ hours. We proposed a deep temporal interpolation and clustering network to extract latent representations from sparse, irregularly sampled vital sign data and derived distinct patient phenotypes in a training cohort (n=41,502). Model and hyper-parameters were chosen based on a validation cohort (n=17,415). Test cohort (n=16,845) was used to analyze reproducibility and correlation with biomarkers. The training, validation, and testing cohorts had similar distributions of age (54-55 yrs), sex (55% female), race, comorbidities, and illness severity. Four clusters were identified. Phenotype A (18%) had most comorbid disease with higher rate of prolonged respiratory insufficiency, acute kidney injury, sepsis, and three-year mortality. Phenotypes B (33%) and C (31%) had diffuse patterns of mild organ dysfunction. Phenotype B had favorable short-term outcomes but second-highest three-year mortality. Phenotype C had favorable clinical outcomes. Phenotype D (17%) had early/persistent hypotension, high rate of early surgery, and substantial biomarker rate of inflammation but second-lowest three-year mortality. After comparing phenotypes' SOFA scores, clustering results did not simply repeat other acuity assessments. In a heterogeneous cohort, four phenotypes with distinct categories of disease and outcomes were identified by a deep temporal interpolation and clustering network. This tool may impact triage decisions and clinical decision-support under time constraints.

cs.LG↗

arXiv2023

Transformer Models for Acute Brain Dysfunction Prediction

Acute brain dysfunctions (ABD), which include coma and delirium, are prevalent in the ICU, especially among older patients. The current approach in manual assessment of ABD by care providers may be sporadic and subjective. Hence, there exists a need for a data-driven robust system automating the assessment and prediction of ABD. In this work, we develop a machine learning system for real-time prediction of ADB using Electronic Health Record (HER) data. Our data processing pipeline enables integration of static and temporal data, and extraction of features relevant to ABD. We train several state-of-the-art transformer models and baseline machine learning models including CatBoost and XGB on the data that was collected from patients admitted to the ICU at UF Shands Hospital. We demonstrate the efficacy of our system for tasks related to acute brain dysfunction including binary classification of brain acuity and multi-class classification (i.e., coma, delirium, death, or normal), achieving a mean AUROC of 0.953 on our Long-former implementation. Our system can then be deployed for real-time prediction of ADB in ICUs to reduce the number of incidents caused by ABD. Moreover, the real-time system has the potential to reduce costs, duration of patients stays in the ICU, and mortality among those afflicted.

cs.LG↗

arXiv2023

Computable Phenotypes to Characterize Changing Patient Brain Dysfunction in the Intensive Care Unit

In the United States, more than 5 million patients are admitted annually to ICUs, with ICU mortality of 10%-29% and costs over $82 billion. Acute brain dysfunction status, delirium, is often underdiagnosed or undervalued. This study's objective was to develop automated computable phenotypes for acute brain dysfunction states and describe transitions among brain dysfunction states to illustrate the clinical trajectories of ICU patients. We created two single-center, longitudinal EHR datasets for 48,817 adult patients admitted to an ICU at UFH Gainesville (GNV) and Jacksonville (JAX). We developed algorithms to quantify acute brain dysfunction status including coma, delirium, normal, or death at 12-hour intervals of each ICU admission and to identify acute brain dysfunction phenotypes using continuous acute brain dysfunction status and k-means clustering approach. There were 49,770 admissions for 37,835 patients in UFH GNV dataset and 18,472 admissions for 10,982 patients in UFH JAX dataset. In total, 18% of patients had coma as the worst brain dysfunction status; every 12 hours, around 4%-7% would transit to delirium, 22%-25% would recover, 3%-4% would expire, and 67%-68% would remain in a coma in the ICU. Additionally, 7% of patients had delirium as the worst brain dysfunction status; around 6%-7% would transit to coma, 40%-42% would be no delirium, 1% would expire, and 51%-52% would remain delirium in the ICU. There were three phenotypes: persistent coma/delirium, persistently normal, and transition from coma/delirium to normal almost exclusively in first 48 hours after ICU admission. We developed phenotyping scoring algorithms that determined acute brain dysfunction status every 12 hours while admitted to the ICU. This approach may be useful in developing prognostic and decision-support tools to aid patients and clinicians in decision-making on resource use and escalation of care.

q-bio.QM↗

arXiv2023

Clinical Courses of Acute Kidney Injury in Hospitalized Patients: A Multistate Analysis

Objectives: We aim to quantify longitudinal acute kidney injury (AKI) trajectories and to describe transitions through progressing and recovery states and outcomes among hospitalized patients using multistate models. Methods: In this large, longitudinal cohort study, 138,449 adult patients admitted to a quaternary care hospital between 2012 and 2019 were staged based on Kidney Disease: Improving Global Outcomes serum creatinine criteria for the first 14 days of their hospital stay. We fit multistate models to estimate probability of being in a certain clinical state at a given time after entering each one of the AKI stages. We investigated the effects of selected variables on transition rates via Cox proportional hazards regression models. Results: Twenty percent of hospitalized encounters (49,325/246,964) had AKI; among patients with AKI, 66% had Stage 1 AKI, 18% had Stage 2 AKI, and 17% had AKI Stage 3 with or without RRT. At seven days following Stage 1 AKI, 69% (95% confidence interval [CI]: 68.8%-70.5%) were either resolved to No AKI or discharged, while smaller proportions of recovery (26.8%, 95% CI: 26.1%-27.5%) and discharge (17.4%, 95% CI: 16.8%-18.0%) were observed following AKI Stage 2. At 14 days following Stage 1 AKI, patients with more frail conditions (Charlson comorbidity index greater than or equal to 3 and had prolonged ICU stay) had lower proportion of transitioning to No AKI or discharge states. Discussion: Multistate analyses showed that the majority of Stage 2 and higher severity AKI patients could not resolve within seven days; therefore, strategies preventing the persistence or progression of AKI would contribute to the patients' life quality. Conclusions: We demonstrate multistate modeling framework's utility as a mechanism for a better understanding of the clinical course of AKI with the potential to facilitate treatment and resource planning.

q-bio.QM↗

arXiv2020

Application of Deep Interpolation Network for Clustering of Physiologic Time Series

Background: During the early stages of hospital admission, clinicians must use limited information to make diagnostic and treatment decisions as patient acuity evolves. However, it is common that the time series vital sign information from patients to be both sparse and irregularly collected, which poses a significant challenge for machine / deep learning techniques to analyze and facilitate the clinicians to improve the human health outcome. To deal with this problem, We propose a novel deep interpolation network to extract latent representations from sparse and irregularly sampled time-series vital signs measured within six hours of hospital admission. Methods: We created a single-center longitudinal dataset of electronic health record data for all (n=75,762) adult patient admissions to a tertiary care center lasting six hours or longer, using 55% of the dataset for training, 23% for validation, and 22% for testing. All raw time series within six hours of hospital admission were extracted for six vital signs (systolic blood pressure, diastolic blood pressure, heart rate, temperature, blood oxygen saturation, and respiratory rate). A deep interpolation network is proposed to learn from such irregular and sparse multivariate time series data to extract the fixed low-dimensional latent patterns. We use k-means clustering algorithm to clusters the patient admissions resulting into 7 clusters. Findings: Training, validation, and testing cohorts had similar age (55-57 years), sex (55% female), and admission vital signs. Seven distinct clusters were identified. M Interpretation: In a heterogeneous cohort of hospitalized patients, a deep interpolation network extracted representations from vital sign data measured within six hours of hospital admission. This approach may have important implications for clinical decision-support under time constraints and uncertainty.

cs.LG↗

arXiv2019

Added Value of Intraoperative Data for Predicting Postoperative Complications: Development and Validation of a MySurgeryRisk Extension

To test the hypothesis that accuracy, discrimination, and precision in predicting postoperative complications improve when using both preoperative and intraoperative data input features versus preoperative data alone. Models that predict postoperative complications often ignore important intraoperative physiological changes. Incorporation of intraoperative physiological data may improve model performance. This retrospective cohort analysis included 52,529 inpatient surgeries at a single institution during a 5 year period. Random forest machine learning models in the validated MySurgeryRisk platform made patient-level predictions for three postoperative complications and mortality during hospital admission using electronic health record data and patient neighborhood characteristics. For each outcome, one model trained with preoperative data alone and one model trained with both preoperative and intraoperative data. Models were compared by accuracy, discrimination (expressed as AUROC), precision (expressed as AUPRC), and reclassification indices (NRI). Machine learning models incorporating both preoperative and intraoperative data had greater accuracy, discrimination, and precision than models using preoperative data alone for predicting all three postoperative complications (intensive care unit length of stay >48 hours, mechanical ventilation >48 hours, and neurological complications including delirium) and in-hospital mortality (accuracy: 88% vs. 77%, AUROC: 0.93 vs. 0.87, AUPRC: 0.21 vs. 0.15). Overall reclassification improvement was 2.9-10.0% for complications and 11.2% for in-hospital mortality. Incorporating both preoperative and intraoperative data significantly increased accuracy, discrimination, and precision for machine learning models predicting postoperative complications.

cs.CY↗