Neurological diagnoses in hospitalized COVID-19 patients associated with adverse outcomes: A multinational cohort study.

Few studies examining the patient outcomes of concurrent neurological manifestations during acute COVID-19 leveraged multinational cohorts of adults and children or distinguished between central and peripheral nervous system (CNS vs. PNS) involvement. Using a federated multinational network in which local clinicians and informatics experts curated the electronic health records data, we evaluated the risk of prolonged hospitalization and mortality in hospitalized COVID-19 patients from 21 healthcare systems across 7 countries. For adults, we used a federated learning approach whereby we ran Cox proportional hazard models locally at each healthcare system and performed a meta-analysis on the aggregated results to estimate the overall risk of adverse outcomes across our geographically diverse populations. For children, we reported descriptive statistics separately due to their low frequency of neurological involvement and poor outcomes. Among the 106,229 hospitalized COVID-19 patients (104,031 patients ≥18 years; 2,198 patients <18 years, January 2020-October 2021), 15,101 (14%) had at least one CNS diagnosis, while 2,788 (3%) had at least one PNS diagnosis. After controlling for demographics and pre-existing conditions, adults with CNS involvement had longer hospital stay (11 versus 6 days) and greater risk of (Hazard Ratio = 1.78) and faster time to death (12 versus 24 days) than patients with no neurological condition (NNC) during acute COVID-19 hospitalization. Adults with PNS involvement also had longer hospital stay but lower risk of mortality than the NNC group. Although children had a low frequency of neurological involvement during COVID-19 hospitalization, a substantially higher proportion of children with CNS involvement died compared to those with NNC (6% vs 1%). Overall, patients with concurrent CNS manifestation during acute COVID-19 hospitalization faced greater risks for adverse clinical outcomes than patients without any neurological diagnosis. Our global informatics framework using a federated approach (versus a centralized data collection approach) has utility for clinical discovery beyond COVID-19.

Safety planning intervention and follow-up: A telehealth service model for suicidal individuals in emergency department settings: Study design and protocol.

BACKGROUND: The Safety Planning Intervention with follow-up services (SPI+) is a promising suicide prevention intervention, yet many Emergency Departments (EDs) lack the resources for adequate implementation. Comprehensive strategies addressing structural and organizational barriers are needed to optimize SPI+ implementation and scale-up. This protocol describes a test of one strategy in which ED staff connect at-risk patients to expert clinicians from a Suicide Prevention Consultation Center (SPCC) via telehealth. METHOD: This stepped wedge, cluster-randomized trial compares the effectiveness, implementation, cost, and cost offsets of SPI+ delivered by SPCC clinicians versus ED-based clinicians (enhanced usual care; EUC). Eight EDs will start with EUC and cross over to the SPCC phase. Blocks of two EDs will be randomly assigned to start dates 3 months apart. Approximately 13,320 adults discharged following a suicide-related ED visit will be included; EUC and SPCC samples will comprise patients from before and after SPCC crossover, respectively. Effectiveness data sources are electronic health records, administrative claims, and the National Death Index. Primary effectiveness outcomes are presence of suicidal behavior and number/type of mental healthcare visits and secondary outcomes include number/type of suicide-related acute services 6-months post-discharge. We will use the same data sources to assess cost offsets to gauge SPCC scalability and sustainability. We will examine preliminary implementation outcomes (reach, adoption, fidelity, acceptability, and feasibility) through patient, clinician, and health-system leader interviews and surveys. CONCLUSION: If the SPCC demonstrates clinical effectiveness and health system cost reduction, it may be a scalable model for evidence-based suicide prevention in the ED.

Realizing the Potential of Social Determinants Data: A Scoping Review of Approaches for Screening, Linkage, Extraction, Analysis and Interventions.

Background: Social determinants of health (SDoH) like socioeconomics and neighborhoods strongly influence outcomes, yet standardized SDoH data is lacking in electronic health records (EHR), limiting research and care quality. Methods: We searched PubMed using keywords "SDOH" and "EHR", underwent title/abstract and full-text screening. Included records were analyzed under five domains: 1) SDoH screening and assessment approaches, 2) SDoH data collection and documentation, 3) Use of natural language processing (NLP) for extracting SDoH, 4) SDoH data and health outcomes, and 5) SDoH-driven interventions. Results: We identified 685 articles, of which 324 underwent full review. Key findings include tailored screening instruments implemented across settings, census and claims data linkage providing contextual SDoH profiles, rule-based and neural network systems extracting SDoH from notes using NLP, connections found between SDoH data and healthcare utilization/chronic disease control, and integrated care management programs executed. However, considerable variability persists across data sources, tools, and outcomes. Discussion: Despite progress identifying patient social needs, further development of standards, predictive models, and coordinated interventions is critical to fulfill the potential of SDoH-EHR integration. Additional database searches could strengthen this scoping review. Ultimately widespread capture, analysis, and translation of multidimensional SDoH data into clinical care is essential for promoting health equity.

Developing a Framework to Infer Opioid Use Disorder Severity From Clinical Notes to Inform Natural Language Processing Methods: Characterization Study.

BACKGROUND: Information regarding opioid use disorder (OUD) status and severity is important for patient care. Clinical notes provide valuable information for detecting and characterizing problematic opioid use, necessitating development of natural language processing (NLP) tools, which in turn requires reliably labeled OUD-relevant text and understanding of documentation patterns. OBJECTIVE: To inform automated NLP methods, we aimed to develop and evaluate an annotation schema for characterizing OUD and its severity, and to document patterns of OUD-relevant information within clinical notes of heterogeneous patient cohorts. METHODS: We developed an annotation schema to characterize OUD severity based on criteria from the Diagnostic and Statistical Manual of Mental Disorders, 5th edition. In total, 2 annotators reviewed clinical notes from key encounters of 100 adult patients with varied evidence of OUD, including patients with and those without chronic pain, with and without medication treatment for OUD, and a control group. We completed annotations at the sentence level. We calculated severity scores based on annotation of note text with 18 classes aligned with criteria for OUD severity and determined positive predictive values for OUD severity. RESULTS: The annotation schema contained 27 classes. We annotated 1436 sentences from 82 patients; notes of 18 patients (11 of whom were controls) contained no relevant information. Interannotator agreement was above 70% for 11 of 15 batches of reviewed notes. Severity scores for control group patients were all 0. Among noncontrol patients, the mean severity score was 5.1 (SD 3.2), indicating moderate OUD, and the positive predictive value for detecting moderate or severe OUD was 0.71. Progress notes and notes from emergency department and outpatient settings contained the most and greatest diversity of information. Substance misuse and psychiatric classes were most prevalent and highly correlated across note types with high co-occurrence across patients. CONCLUSIONS: Implementation of the annotation schema demonstrated strong potential for inferring OUD severity based on key information in a small set of clinical notes and highlighting where such information is documented. These advancements will facilitate NLP tool development to improve OUD prevention, diagnosis, and treatment.

Patient Phenotyping for Atopic Dermatitis with Transformers and Machine Learning.

Background: Atopic dermatitis (AD) is a chronic skin condition that millions of people around the world live with each day. Performing research studies into identifying the causes and treatment for this disease has great potential to provide benefit for these individuals. However, AD clinical trial recruitment is a non-trivial task due to variance in diagnostic precision and phenotypic definitions leveraged by different clinicians as well as time spent finding, recruiting, and enrolling patients by clinicians to become study subjects. Thus, there is a need for automatic and effective patient phenotyping for cohort recruitment. Objective: Our study aims to present an approach for identifying patients whose electronic health records suggest that they may have AD. Methods: We created a vectorized representation of each patient and trained various supervised machine learning methods to classify when a patient has AD. Each patient is represented by a vector of either probabilities or binary values where each value indicates whether they meet a different criteria for AD diagnosis. Results: The most accurate AD classifier performed with a class-balanced accuracy of 0.8036, a precision of 0.8400, and a recall of 0.7500 when using XGBoost (Extreme Gradient Boosting). Conclusions: Creating an automated approach for identifying patient cohorts has the potential to accelerate, standardize, and automate the process of patient recruitment for AD studies; therefore, reducing clinician burden and informing knowledge discovery of better treatment options for AD.

A voice-based digital assistant for intelligent prompting of evidence-based practices during ICU rounds.

OBJECTIVE: To evaluate the technical feasibility and potential value of a digital assistant that prompts intensive care unit (ICU) rounding teams to use evidence-based practices based on analysis of their real-time discussions. METHODS: We evaluated a novel voice-based digital assistant which audio records and processes the ICU care team's rounding discussions to determine which evidence-based practices are applicable to the patient but have yet to be addressed by the team. The system would then prompt the team to consider indicated but not yet delivered practices, thereby reducing cognitive burden compared to traditional rigid rounding checklists. In a retrospective analysis, we applied automatic transcription, natural language processing, and a rule-based expert system to generate personalized prompts for each patient in 106 audio-recorded ICU rounding discussions. To assess technical feasibility, we compared the system's prompts to those created by experienced critical care nurses who directly observed rounds. To assess potential value, we also compared the system's prompts to a hypothetical paper checklist containing all evidence-based practices. RESULTS: The positive predictive value, negative predictive value, true positive rate, and true negative rate of the system's prompts were 0.45 ± 0.06, 0.83 ± 0.04, 0.68 ± 0.07, and 0.66 ± 0.04, respectively. If implemented in lieu of a paper checklist, the system would generate 56% fewer prompts per patient, with 50%±17% greater precision. CONCLUSION: A voice-based digital assistant can reduce prompts per patient compared to traditional approaches for improving evidence uptake on ICU rounds. Additional work is needed to evaluate field performance and team acceptance.

Measuring Performance on the ABCDEF Bundle During Interprofessional Rounds via a Nurse-Based Assessment Tool.

BACKGROUND: Nurse-led rounding checklists are a common strategy for facilitating evidence-based practice in the intensive care unit (ICU). To streamline checklist workflow, some ICUs have the nurse or another individual listen to the conversation and customize the checklist for each patient. Such customizations assume that individuals can reliably assess whether checklist items have been addressed. OBJECTIVE: To evaluate whether 1 critical care nurse can reliably assess checklist items on rounds. METHODS: Two nurses performed in-person observation of multidisciplinary ICU rounds. Using a standardized paper-based assessment tool, each nurse indicated whether 17 items related to the ABCDEF bundle were discussed during rounds. For each item, generalizability coefficients were used as a measure of reliability, with a single-rater value of 0.70 or greater considered sufficient to support its assessment by 1 nurse. RESULTS: The nurse observers assessed 118 patient discussions across 15 observation days. For 11 of 17 items (65%), the generalizability coefficient for a single rater met or exceeded the 0.70 threshold. The generalizability coefficients (95% CIs) of a single rater for key items were as follows: pain, 0.86 (0.74-0.97); delirium score, 0.74 (0.64-0.83); agitation score, 0.72 (0.33-1.00); spontaneous awakening trial, 0.67 (0.49-0.83); spontaneous breathing trial, 0.80 (0.70-0.89); mobility, 0.79 (0.69-0.87); and family (future/past) engagement, 0.82 (0.73-0.90). CONCLUSION: Using a paper-based assessment tool, a single trained critical care nurse can reliably assess the discussion of elements of the ABCDEF bundle during multidisciplinary rounds.

Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record?

BACKGROUND: In electronic health records, patterns of missing laboratory test results could capture patients' course of disease as well as ​​reflect clinician's concerns or worries for possible conditions. These patterns are often understudied and overlooked. This study aims to identify informative patterns of missingness among laboratory data collected across 15 healthcare system sites in three countries for COVID-19 inpatients. METHODS: We collected and analyzed demographic, diagnosis, and laboratory data for 69,939 patients with positive COVID-19 PCR tests across three countries from 1 January 2020 through 30 September 2021. We analyzed missing laboratory measurements across sites, missingness stratification by demographic variables, temporal trends of missingness, correlations between labs based on missingness indicators over time, and clustering of groups of labs based on their missingness/ordering pattern. RESULTS: With these analyses, we identified mapping issues faced in seven out of 15 sites. We also identified nuances in data collection and variable definition for the various sites. Temporal trend analyses may support the use of laboratory test result missingness patterns in identifying severe COVID-19 patients. Lastly, using missingness patterns, we determined relationships between various labs that reflect clinical behaviors. CONCLUSION: In this work, we use computational approaches to relate missingness patterns to hospital treatment capacity and highlight the heterogeneity of looking at COVID-19 over time and at multiple sites, where there might be different phases, policies, etc. Changes in missingness could suggest a change in a patient's condition, and patterns of missingness among laboratory measurements could potentially identify clinical outcomes. This allows sites to consider missing data as informative to analyses and help researchers identify which sites are better poised to study particular questions.

Toward Predicting 30-Day Readmission Among Oncology Patients: Identifying Timely and Actionable Risk Factors.

PURPOSE: Predicting 30-day readmission risk is paramount to improving the quality of patient care. In this study, we compare sets of patient-, provider-, and community-level variables that are available at two different points of a patient's inpatient encounter (first 48 hours and the full encounter) to train readmission prediction models and identify possible targets for appropriate interventions that can potentially reduce avoidable readmissions. METHODS: Using electronic health record data from a retrospective cohort of 2,460 oncology patients and a comprehensive machine learning analysis pipeline, we trained and tested models predicting 30-day readmission on the basis of data available within the first 48 hours of admission and from the entire hospital encounter. RESULTS: Leveraging all features, the light gradient boosting model produced higher, but comparable performance (area under receiver operating characteristic curve [AUROC]: 0.711) with the Epic model (AUROC: 0.697). Given features in the first 48 hours, the random forest model produces higher AUROC (0.684) than the Epic model (AUROC: 0.676). Both models flagged patients with a similar distribution of race and sex; however, our light gradient boosting and random forest models were more inclusive, flagging more patients among younger age groups. The Epic models were more sensitive to identifying patients with an average lower zip income. Our 48-hour models were powered by novel features at various levels: patient (weight change over 365 days, depression symptoms, laboratory values, and cancer type), hospital (winter discharge and hospital admission type), and community (zip income and marital status of partner). CONCLUSION: We developed and validated models comparable with the existing Epic 30-day readmission models with several novel actionable insights that could create service interventions deployed by the case management or discharge planning teams that may decrease readmission rates over time.

Acute respiratory distress syndrome after SARS-CoV-2 infection on young adult population: International observational federated study based on electronic health records through the 4CE consortium.

PURPOSE: In young adults (18 to 49 years old), investigation of the acute respiratory distress syndrome (ARDS) after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been limited. We evaluated the risk factors and outcomes of ARDS following infection with SARS-CoV-2 in a young adult population. METHODS: A retrospective cohort study was conducted between January 1st, 2020 and February 28th, 2021 using patient-level electronic health records (EHR), across 241 United States hospitals and 43 European hospitals participating in the Consortium for Clinical Characterization of COVID-19 by EHR (4CE). To identify the risk factors associated with ARDS, we compared young patients with and without ARDS through a federated analysis. We further compared the outcomes between young and old patients with ARDS. RESULTS: Among the 75,377 hospitalized patients with positive SARS-CoV-2 PCR, 1001 young adults presented with ARDS (7.8% of young hospitalized adults). Their mortality rate at 90 days was 16.2% and they presented with a similar complication rate for infection than older adults with ARDS. Peptic ulcer disease, paralysis, obesity, congestive heart failure, valvular disease, diabetes, chronic pulmonary disease and liver disease were associated with a higher risk of ARDS. We described a high prevalence of obesity (53%), hypertension (38%- although not significantly associated with ARDS), and diabetes (32%). CONCLUSION: Trough an innovative method, a large international cohort study of young adults developing ARDS after SARS-CoV-2 infection has been gather. It demonstrated the poor outcomes of this population and associated risk factor.

Long-term kidney function recovery and mortality after COVID-19-associated acute kidney injury: An international multi-centre observational cohort study.

Background: While acute kidney injury (AKI) is a common complication in COVID-19, data on post-AKI kidney function recovery and the clinical factors associated with poor kidney function recovery is lacking. Methods: A retrospective multi-centre observational cohort study comprising 12,891 hospitalized patients aged 18 years or older with a diagnosis of SARS-CoV-2 infection confirmed by polymerase chain reaction from 1 January 2020 to 10 September 2020, and with at least one serum creatinine value 1-365 days prior to admission. Mortality and serum creatinine values were obtained up to 10 September 2021. Findings: Advanced age (HR 2.77, 95%CI 2.53-3.04, p < 0.0001), severe COVID-19 (HR 2.91, 95%CI 2.03-4.17, p < 0.0001), severe AKI (KDIGO stage 3: HR 4.22, 95%CI 3.55-5.00, p < 0.0001), and ischemic heart disease (HR 1.26, 95%CI 1.14-1.39, p < 0.0001) were associated with worse mortality outcomes. AKI severity (KDIGO stage 3: HR 0.41, 95%CI 0.37-0.46, p < 0.0001) was associated with worse kidney function recovery, whereas remdesivir use (HR 1.34, 95%CI 1.17-1.54, p < 0.0001) was associated with better kidney function recovery. In a subset of patients without chronic kidney disease, advanced age (HR 1.38, 95%CI 1.20-1.58, p < 0.0001), male sex (HR 1.67, 95%CI 1.45-1.93, p < 0.0001), severe AKI (KDIGO stage 3: HR 11.68, 95%CI 9.80-13.91, p < 0.0001), and hypertension (HR 1.22, 95%CI 1.10-1.36, p = 0.0002) were associated with post-AKI kidney function impairment. Furthermore, patients with COVID-19-associated AKI had significant and persistent elevations of baseline serum creatinine 125% or more at 180 days (RR 1.49, 95%CI 1.32-1.67) and 365 days (RR 1.54, 95%CI 1.21-1.96) compared to COVID-19 patients with no AKI. Interpretation: COVID-19-associated AKI was associated with higher mortality, and severe COVID-19-associated AKI was associated with worse long-term post-AKI kidney function recovery. Funding: Authors are supported by various funders, with full details stated in the acknowledgement section.

SurvMaximin: Robust federated approach to transporting survival risk prediction models.

OBJECTIVE: For multi-center heterogeneous Real-World Data (RWD) with time-to-event outcomes and high-dimensional features, we propose the SurvMaximin algorithm to estimate Cox model feature coefficients for a target population by borrowing summary information from a set of health care centers without sharing patient-level information. MATERIALS AND METHODS: For each of the centers from which we want to borrow information to improve the prediction performance for the target population, a penalized Cox model is fitted to estimate feature coefficients for the center. Using estimated feature coefficients and the covariance matrix of the target population, we then obtain a SurvMaximin estimated set of feature coefficients for the target population. The target population can be an entire cohort comprised of all centers, corresponding to federated learning, or a single center, corresponding to transfer learning. RESULTS: Simulation studies and a real-world international electronic health records application study, with 15 participating health care centers across three countries (France, Germany, and the U.S.), show that the proposed SurvMaximin algorithm achieves comparable or higher accuracy compared with the estimator using only the information of the target site and other existing methods. The SurvMaximin estimator is robust to variations in sample sizes and estimated feature coefficients between centers, which amounts to significantly improved estimates for target sites with fewer observations. CONCLUSIONS: The SurvMaximin method is well suited for both federated and transfer learning in the high-dimensional survival analysis setting. SurvMaximin only requires a one-time summary information exchange from participating centers. Estimated regression vectors can be very heterogeneous. SurvMaximin provides robust Cox feature coefficient estimates without outcome information in the target population and is privacy-preserving.

Using Natural Language Processing to Classify Serious Illness Communication with Oncology Patients.

One core measure of healthcare quality set forth by the Institute of Medicine is whether care decisions match patient goals. High-quality "serious illness communication" about patient goals and prognosis is required to support patient-centered decision-making, however current methods are not sensitive enough to measure the quality of this communication or determine whether care delivered matches patient priorities. Natural language processing (NLP) offers an efficient method for identification and evaluation of documented serious illness communication, which could serve as the basis for future quality metrics in oncology and other forms of serious illness. In this study, we trained NLP algorithms to identify and characterize serious illness communication with oncology patients.

International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality.

Given the growing number of prediction algorithms developed to predict COVID-19 mortality, we evaluated the transportability of a mortality prediction algorithm using a multi-national network of healthcare systems. We predicted COVID-19 mortality using baseline commonly measured laboratory values and standard demographic and clinical covariates across healthcare systems, countries, and continents. Specifically, we trained a Cox regression model with nine measured laboratory test values, standard demographics at admission, and comorbidity burden pre-admission. These models were compared at site, country, and continent level. Of the 39,969 hospitalized patients with COVID-19 (68.6% male), 5717 (14.3%) died. In the Cox model, age, albumin, AST, creatine, CRP, and white blood cell count are most predictive of mortality. The baseline covariates are more predictive of mortality during the early days of COVID-19 hospitalization. Models trained at healthcare systems with larger cohort size largely retain good transportability performance when porting to different sites. The combination of routine laboratory test values at admission along with basic demographic features can predict mortality in patients hospitalized with COVID-19. Importantly, this potentially deployable model differs from prior work by demonstrating not only consistent performance but also reliable transportability across healthcare systems in the US and Europe, highlighting the generalizability of this model and the overall approach.

Changes in laboratory value improvement and mortality rates over the course of the pandemic: an international retrospective cohort study of hospitalised patients infected with SARS-CoV-2.

OBJECTIVE: To assess changes in international mortality rates and laboratory recovery rates during hospitalisation for patients hospitalised with SARS-CoV-2 between the first wave (1 March to 30 June 2020) and the second wave (1 July 2020 to 31 January 2021) of the COVID-19 pandemic. DESIGN, SETTING AND PARTICIPANTS: This is a retrospective cohort study of 83 178 hospitalised patients admitted between 7 days before or 14 days after PCR-confirmed SARS-CoV-2 infection within the Consortium for Clinical Characterization of COVID-19 by Electronic Health Record, an international multihealthcare system collaborative of 288 hospitals in the USA and Europe. The laboratory recovery rates and mortality rates over time were compared between the two waves of the pandemic. PRIMARY AND SECONDARY OUTCOME MEASURES: The primary outcome was all-cause mortality rate within 28 days after hospitalisation stratified by predicted low, medium and high mortality risk at baseline. The secondary outcome was the average rate of change in laboratory values during the first week of hospitalisation. RESULTS: Baseline Charlson Comorbidity Index and laboratory values at admission were not significantly different between the first and second waves. The improvement in laboratory values over time was faster in the second wave compared with the first. The average C reactive protein rate of change was -4.72 mg/dL vs -4.14 mg/dL per day (p=0.05). The mortality rates within each risk category significantly decreased over time, with the most substantial decrease in the high-risk group (42.3% in March-April 2020 vs 30.8% in November 2020 to January 2021, p<0.001) and a moderate decrease in the intermediate-risk group (21.5% in March-April 2020 vs 14.3% in November 2020 to January 2021, p<0.001). CONCLUSIONS: Admission profiles of patients hospitalised with SARS-CoV-2 infection did not differ greatly between the first and second waves of the pandemic, but there were notable differences in laboratory improvement rates during hospitalisation. Mortality risks among patients with similar risk profiles decreased over the course of the pandemic. The improvement in laboratory values and mortality risk was consistent across multiple countries.

Classifying Characteristics of Opioid Use Disorder From Hospital Discharge Summaries Using Natural Language Processing.

Background: Opioid use disorder (OUD) is underdiagnosed in health system settings, limiting research on OUD using electronic health records (EHRs). Medical encounter notes can enrich structured EHR data with documented signs and symptoms of OUD and social risks and behaviors. To capture this information at scale, natural language processing (NLP) tools must be developed and evaluated. We developed and applied an annotation schema to deeply characterize OUD and related clinical, behavioral, and environmental factors, and automated the annotation schema using machine learning and deep learning-based approaches. Methods: Using the MIMIC-III Critical Care Database, we queried hospital discharge summaries of patients with International Classification of Diseases (ICD-9) OUD diagnostic codes. We developed an annotation schema to characterize problematic opioid use, identify individuals with potential OUD, and provide psychosocial context. Two annotators reviewed discharge summaries from 100 patients. We randomly sampled patients with their associated annotated sentences and divided them into training (66 patients; 2,127 annotated sentences) and testing (29 patients; 1,149 annotated sentences) sets. We used the training set to generate features, employing three NLP algorithms/knowledge sources. We trained and tested prediction models for classification with a traditional machine learner (logistic regression) and deep learning approach (Autogluon based on ELECTRA's replaced token detection model). We applied a five-fold cross-validation approach to reduce bias in performance estimates. Results: The resulting annotation schema contained 32 classes. We achieved moderate inter-annotator agreement, with F1-scores across all classes increasing from 48 to 66%. Five classes had a sufficient number of annotations for automation; of these, we observed consistently high performance (F1-scores) across training and testing sets for drug screening (training: 91-96; testing: 91-94) and opioid type (training: 86-96; testing: 86-99). Performance dropped from training and to testing sets for other drug use (training: 52-65; testing: 40-48), pain management (training: 72-78; testing: 61-78) and psychiatric (training: 73-80; testing: 72). Autogluon achieved the highest performance. Conclusion: This pilot study demonstrated that rich information regarding problematic opioid use can be manually identified by annotators. However, more training samples and features would improve our ability to reliably identify less common classes from clinical text, including text from outpatient settings.

Determinants of hospital outcomes for patients with COVID-19 in the University of Pennsylvania Health System.

There is growing evidence that racial and ethnic minorities bear a disproportionate burden from COVID-19. Temporal changes in the pandemic epidemiology and diversity in the clinical course require careful study to identify determinants of poor outcomes. We analyzed 6255 hospitalized individuals with PCR-confirmed SARS-CoV-2 infection from one of 5 hospitals in the University of Pennsylvania Health System between March 2020 and March 2021, using electronic health records to assess risk factors and outcomes through 8 weeks post-admission. Discharge, readmission and mortality outcomes were analyzed in a multi-state model with multivariable Cox models for each transition. Mortality varied markedly over time, with cumulative incidence (95% CI) 30 days post-admission of 19.1% (16.9, 21.3) in March-April 2020, 5.7% (4.2, 7.5) in July-October 2020 and 10.5% (9.1,12.0) in January-March 2021; 26% of deaths occurred after discharge. Average age (SD) at admission varied from 62.7 (17.6) to 54.8 (19.9) to 60.5 (18.1); mechanical ventilation use declined from 21.3% to 9-11%. Compared to Caucasian, Black race was associated with more severe disease at admission, higher rates of co-morbidities and residing in a low-income zip code. Between-race risk differences in mortality risk diminished in multivariable models; while admitting hospital, increasing age, admission early in the pandemic, and severe disease and low blood pressure at admission were associated with increased mortality hazard. Hispanic ethnicity was associated with fewer baseline co-morbidities and lower mortality hazard (0.57, 95% CI: 0.37, .087). Multi-state modeling allows for a unified framework to analyze multiple outcomes throughout the disease course. Morbidity and mortality for hospitalized COVID-19 patients varied over time but post-discharge mortality remained non-trivial. Black race was associated with more risk factors for morbidity and with treatment at hospitals with lower mortality. Multivariable models suggest there are not between-race differences in outcomes. Future work is needed to better understand the identified between-hospital differences in mortality.

Performance of polygenic risk scores for cancer prediction in a racially diverse academic biobank.

PURPOSE: Genome-wide association studies have identified hundreds of single nucleotide variations (formerly single nucleotide polymorphisms) associated with several cancers, but the predictive ability of polygenic risk scores (PRSs) is unclear, especially among non-Whites. METHODS: PRSs were derived from genome-wide significant single-nucleotide variations for 15 cancers in 20,079 individuals in an academic biobank. We evaluated the improvement in discriminatory accuracy by including cancer-specific PRS in patients of genetically-determined African and European ancestry. RESULTS: Among the individuals of European genetic ancestry, PRSs for breast, colon, melanoma, and prostate were significantly associated with their respective cancers. Among the individuals of African genetic ancestry, PRSs for breast, colon, prostate, and thyroid were significantly associated with their respective cancers. The area under the curve of the model consisting of age, sex, and principal components was 0.621 to 0.710, and it increased by 1% to 4% with the inclusion of PRS in individuals of European genetic ancestry. In individuals of African genetic ancestry, area under the curve was overall higher in the model without the PRS (0.723-0.810) but increased by <1% with the inclusion of PRS for most cancers. CONCLUSION: PRS moderately increased the ability to discriminate the cancer status in individuals of European but not African ancestry. Further large-scale studies are needed to identify ancestry-specific genetic factors in non-White populations to incorporate PRS into cancer risk assessment.

Identifying Barriers to Post-Acute Care Referral and Characterizing Negative Patient Preferences Among Hospitalized Older Adults Using Natural Language Processing.

Our objective was to detect common barriers to post-acute care (B2PAC) among hospitalized older adults using natural language processing (NLP) of clinical notes from patients discharged home when a clinical decision support system recommended post-acute care. We annotated B2PAC sentences from discharge planning notes and developed an NLP classifier to identify the highest-value B2PAC class (negative patient preferences). Thirteen machine learning models were compared with Amazon's AutoGluon deep learning model. The study included 594 acute care notes from 100 patient encounters (1156 sentences contained 11 B2PAC) in a large academic health system. The most frequent and modifiable B2PAC class was negative patient preferences (18.3%). The best supervised model was Extreme Gradient Boosting (F1: 0.859), but the deep learning model performed better (F1: 0.916). Alerting clinicians of negative patient preferences early in the hospitalization can prompt interventions such as patient education to ensure patients receive the right level of care and avoid negative outcomes.

Initial Development of an Automated Platform for Assessing Trainee Performance on Case Presentations.

Background: Oral case presentation is a crucial skill of physicians and a key component of team-based care. However, consistent and objective assessment and feedback on presentations during training are infrequent. Objective: To determine the potential value of applying natural language processing, computer software that extracts meaning from text, to transcripts of oral case presentations as a strategy to assess their quality automatically and objectively. Methods: We transcribed a collection of simulated oral case presentations. The presentations were from eight critical care fellows and one critical care attending. They were instructed to review the medical charts of 11 real intensive care unit patient cases and to audio record themselves, presenting each case as if they were doing so on morning rounds. We then used natural language processing to convert the transcripts from human-readable text into machine-readable numbers. These numbers represent details of the presentation style and content. The distance between the numeric representation of two different transcripts negatively correlates with the similarity of those two transcripts. We ranked fellows on the basis of how similar their presentations were to the attending's presentations. Results: The 99 presentations included 260 minutes of audio (mean length: 2.6 ± 1.24 min per case). On average, 23.88 ± 2.65 sentences were spoken, and each sentence had 14.10 ± 0.67 words, 3.62 ± 0.15 medical concepts, and 0.75 ± 0.09 medical adjectives. When ranking fellows on the basis of how similar their presentations were to the attending's presentation, we found a gap between the five fellows with the most similar presentations and the three fellows with the least similar presentations (average group similarity scores of 0.62 ± 0.01 and 0.53 ± 0.01, respectively). Rankings were sensitive to whether presentation style or content information were weighted more heavily when calculating transcript similarity. Conclusion: Natural language processing enabled the ranking of case presentations on the basis of how similar they were to a reference presentation. Although additional work is needed to convert these rankings, and underlying similarity scores, into actionable feedback for trainees, these methods may support new tools for improving medical education.