Performance of International Classification of Disease-10 codes in detecting emergency department patients with opioid misuse.

BACKGROUND AND AIMS: Accurate case discovery is critical for disease surveillance, resource allocation and research. International Classification of Disease (ICD) diagnosis codes are commonly used for this purpose. We aimed to determine the sensitivity, specificity and positive predictive value (PPV) of ICD-10 codes for opioid misuse case discovery in the emergency department (ED) setting. DESIGN AND SETTING: Retrospective cohort study of ED encounters from January 2018 to December 2020 at an urban academic hospital in the United States. A sample of ED encounters enriched for opioid misuse was developed by oversampling ED encounters with positive urine opiate screens or pre-existing opioid-related diagnosis codes in addition to other opioid misuse risk factors. CASES: A total of 1200 randomly selected encounters were annotated by research staff for the presence of opioid misuse within health record documentation using a 5-point scale for likelihood of opioid misuse and dichotomized into cohorts of opioid misuse and no opioid misuse. MEASUREMENTS: Using manual annotation as ground truth, the sensitivity and specificity of ICD-10 codes entered during the encounter were determined with PPV adjusted for oversampled data. Metrics were also determined by disposition subgroup: discharged home or admitted. FINDINGS: There were 541 encounters annotated as opioid misuse and 617 with no opioid misuse. The majority were males (54.4%), average age was 47 years and 68.5% were discharged directly from the ED. The sensitivity of ICD-10 codes was 0.56 (95% confidence interval [CI], 0.51-0.60), specificity 0.99 (95% CI, 0.97-0.99) and adjusted PPV 0.78 (95% CI, 0.65-0.92). The sensitivity was higher for patients discharged from the ED (0.65; 95% CI, 0.60-0.69) than those admitted (0.31; 95% CI, 0.24-0.39). CONCLUSIONS: International Classification of Disease-10 codes appear to have low sensitivity but high specificity and positive predictive value in detecting opioid misuse among emergency department patients in the United States.

Multi-Task Training with In-Domain Language Models for Diagnostic Reasoning.

Generative artificial intelligence (AI) is a promising direction for augmenting clinical diagnostic decision support and reducing diagnostic errors, a leading contributor to medical errors. To further the development of clinical AI systems, the Diagnostic Reasoning Benchmark (DR.BENCH) was introduced as a comprehensive generative AI framework, comprised of six tasks representing key components in clinical reasoning. We present a comparative analysis of in-domain versus out-of-domain language models as well as multi-task versus single task training with a focus on the problem summarization task in DR.BENCH (Gao et al., 2023). We demonstrate that a multi-task, clinically-trained language model outperforms its general domain counterpart by a large margin, establishing a new state-of-the-art performance, with a ROUGE-L score of 28.55. This research underscores the value of domain-specific training for optimizing clinical diagnostic reasoning tasks.

Deployment of Real-time Natural Language Processing and Deep Learning Clinical Decision Support in the Electronic Health Record: Pipeline Implementation for an Opioid Misuse Screener in Hospitalized Adults.

BACKGROUND: The clinical narrative in electronic health records (EHRs) carries valuable information for predictive analytics; however, its free-text form is difficult to mine and analyze for clinical decision support (CDS). Large-scale clinical natural language processing (NLP) pipelines have focused on data warehouse applications for retrospective research efforts. There remains a paucity of evidence for implementing NLP pipelines at the bedside for health care delivery. OBJECTIVE: We aimed to detail a hospital-wide, operational pipeline to implement a real-time NLP-driven CDS tool and describe a protocol for an implementation framework with a user-centered design of the CDS tool. METHODS: The pipeline integrated a previously trained open-source convolutional neural network model for screening opioid misuse that leveraged EHR notes mapped to standardized medical vocabularies in the Unified Medical Language System. A sample of 100 adult encounters were reviewed by a physician informaticist for silent testing of the deep learning algorithm before deployment. An end user interview survey was developed to examine the user acceptability of a best practice alert (BPA) to provide the screening results with recommendations. The planned implementation also included a human-centered design with user feedback on the BPA, an implementation framework with cost-effectiveness, and a noninferiority patient outcome analysis plan. RESULTS: The pipeline was a reproducible workflow with a shared pseudocode for a cloud service to ingest, process, and store clinical notes as Health Level 7 messages from a major EHR vendor in an elastic cloud computing environment. Feature engineering of the notes used an open-source NLP engine, and the features were fed into the deep learning algorithm, with the results returned as a BPA in the EHR. On-site silent testing of the deep learning algorithm demonstrated a sensitivity of 93% (95% CI 66%-99%) and specificity of 92% (95% CI 84%-96%), similar to published validation studies. Before deployment, approvals were received across hospital committees for inpatient operations. Five interviews were conducted; they informed the development of an educational flyer and further modified the BPA to exclude certain patients and allow the refusal of recommendations. The longest delay in pipeline development was because of cybersecurity approvals, especially because of the exchange of protected health information between the Microsoft (Microsoft Corp) and Epic (Epic Systems Corp) cloud vendors. In silent testing, the resultant pipeline provided a BPA to the bedside within minutes of a provider entering a note in the EHR. CONCLUSIONS: The components of the real-time NLP pipeline were detailed with open-source tools and pseudocode for other health systems to benchmark. The deployment of medical artificial intelligence systems in routine clinical care presents an important yet unfulfilled opportunity, and our protocol aimed to close the gap in the implementation of artificial intelligence-driven CDS. TRIAL REGISTRATION: ClinicalTrials.gov NCT05745480; https://www.clinicaltrials.gov/ct2/show/NCT05745480.

DR.BENCH: Diagnostic Reasoning Benchmark for Clinical Natural Language Processing.

The meaningful use of electronic health records (EHR) continues to progress in the digital era with clinical decision support systems augmented by artificial intelligence. A priority in improving provider experience is to overcome information overload and reduce the cognitive burden so fewer medical errors and cognitive biases are introduced during patient care. One major type of medical error is diagnostic error due to systematic or predictable errors in judgement that rely on heuristics. The potential for clinical natural language processing (cNLP) to model diagnostic reasoning in humans with forward reasoning from data to diagnosis and potentially reduce cognitive burden and medical error has not been investigated. Existing tasks to advance the science in cNLP have largely focused on information extraction and named entity recognition through classification tasks. We introduce a novel suite of tasks coined as Diagnostic Reasoning Benchmarks, Dr.Bench, as a new benchmark for developing and evaluating cNLP models with clinical diagnostic reasoning ability. The suite includes six tasks from ten publicly available datasets addressing clinical text understanding, medical knowledge reasoning, and diagnosis generation. DR.BENCH is the first clinical suite of tasks designed to be a natural language generation framework to evaluate pre-trained language models for diagnostic reasoning. The goal of DR. BENCH is to advance the science in cNLP to support downstream applications in computerized diagnostic decision support and improve the efficiency and accuracy of healthcare providers during patient care. We fine-tune and evaluate the state-of-the-art generative models on DR.BENCH. Experiments show that with domain adaptation pre-training on medical knowledge, the model demonstrated opportunities for improvement when evaluated in DR. BENCH. We share DR. BENCH as a publicly available GitLab repository with a systematic approach to load and evaluate models for the cNLP community. We also discuss the carbon footprint produced during the experiments and encourage future work on DR.BENCH to report the carbon footprint.

The Evaluation of a Clinical Decision Support Tool Using Natural Language Processing to Screen Hospitalized Adults for Unhealthy Substance Use: Protocol for a Quasi-Experimental Design.

BACKGROUND: Automated and data-driven methods for screening using natural language processing (NLP) and machine learning may replace resource-intensive manual approaches in the usual care of patients hospitalized with conditions related to unhealthy substance use. The rigorous evaluation of tools that use artificial intelligence (AI) is necessary to demonstrate effectiveness before system-wide implementation. An NLP tool to use routinely collected data in the electronic health record was previously validated for diagnostic accuracy in a retrospective study for screening unhealthy substance use. Our next step is a noninferiority design incorporated into a research protocol for clinical implementation with prospective evaluation of clinical effectiveness in a large health system. OBJECTIVE: This study aims to provide a study protocol to evaluate health outcomes and the costs and benefits of an AI-driven automated screener compared to manual human screening for unhealthy substance use. METHODS: A pre-post design is proposed to evaluate 12 months of manual screening followed by 12 months of automated screening across surgical and medical wards at a single medical center. The preintervention period consists of usual care with manual screening by nurses and social workers and referrals to a multidisciplinary Substance Use Intervention Team (SUIT). Facilitated by a NLP pipeline in the postintervention period, clinical notes from the first 24 hours of hospitalization will be processed and scored by a machine learning model, and the SUIT will be similarly alerted to patients who flagged positive for substance misuse. Flowsheets within the electronic health record have been updated to capture rates of interventions for the primary outcome (brief intervention/motivational interviewing, medication-assisted treatment, naloxone dispensing, and referral to outpatient care). Effectiveness in terms of patient outcomes will be determined by noninferior rates of interventions (primary outcome), as well as rates of readmission within 6 months, average time to consult, and discharge rates against medical advice (secondary outcomes) in the postintervention period by a SUIT compared to the preintervention period. A separate analysis will be performed to assess the costs and benefits to the health system by using automated screening. Changes from the pre- to postintervention period will be assessed in covariate-adjusted generalized linear mixed-effects models. RESULTS: The study will begin in September 2022. Monthly data monitoring and Data Safety Monitoring Board reporting are scheduled every 6 months throughout the study period. We anticipate reporting final results by June 2025. CONCLUSIONS: The use of augmented intelligence for clinical decision support is growing with an increasing number of AI tools. We provide a research protocol for prospective evaluation of an automated NLP system for screening unhealthy substance use using a noninferiority design to demonstrate comprehensive screening that may be as effective as manual screening but less costly via automated solutions. TRIAL REGISTRATION: ClinicalTrials.gov NCT03833804; https://clinicaltrials.gov/ct2/show/NCT03833804. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/42971.

Machine Learning Techniques to Explore Clinical Presentations of COVID-19 Severity and to Test the Association With Unhealthy Opioid Use: Retrospective Cross-sectional Cohort Study.

BACKGROUND: The COVID-19 pandemic has exacerbated health inequities in the United States. People with unhealthy opioid use (UOU) may face disproportionate challenges with COVID-19 precautions, and the pandemic has disrupted access to opioids and UOU treatments. UOU impairs the immunological, cardiovascular, pulmonary, renal, and neurological systems and may increase severity of outcomes for COVID-19. OBJECTIVE: We applied machine learning techniques to explore clinical presentations of hospitalized patients with UOU and COVID-19 and to test the association between UOU and COVID-19 disease severity. METHODS: This retrospective, cross-sectional cohort study was conducted based on data from 4110 electronic health record patient encounters at an academic health center in Chicago between January 1, 2020, and December 31, 2020. The inclusion criterion was an unplanned admission of a patient aged ≥18 years; encounters were counted as COVID-19-positive if there was a positive test for COVID-19 or 2 COVID-19 International Classification of Disease, Tenth Revision codes. Using a predefined cutoff with optimal sensitivity and specificity to identify UOU, we ran a machine learning UOU classifier on the data for patients with COVID-19 to estimate the subcohort of patients with UOU. Topic modeling was used to explore and compare the clinical presentations documented for 2 subgroups: encounters with UOU and COVID-19 and those with no UOU and COVID-19. Mixed effects logistic regression accounted for multiple encounters for some patients and tested the association between UOU and COVID-19 outcome severity. Severity was measured with 3 utilization metrics: low-severity unplanned admission, medium-severity unplanned admission and receiving mechanical ventilation, and high-severity unplanned admission with in-hospital death. All models controlled for age, sex, race/ethnicity, insurance status, and BMI. RESULTS: Topic modeling yielded 10 topics per subgroup and highlighted unique comorbidities associated with UOU and COVID-19 (eg, HIV) and no UOU and COVID-19 (eg, diabetes). In the regression analysis, each incremental increase in the classifier's predicted probability of UOU was associated with 1.16 higher odds of COVID-19 outcome severity (odds ratio 1.16, 95% CI 1.04-1.29; P=.009). CONCLUSIONS: Among patients hospitalized with COVID-19, UOU is an independent risk factor associated with greater outcome severity, including in-hospital death. Social determinants of health and opioid-related overdose are unique comorbidities in the clinical presentation of the UOU patient subgroup. Additional research is needed on the role of COVID-19 therapeutics and inpatient management of acute COVID-19 pneumonia for patients with UOU. Further research is needed to test associations between expanded evidence-based harm reduction strategies for UOU and vaccination rates, hospitalizations, and risks for overdose and death among people with UOU and COVID-19. Machine learning techniques may offer more exhaustive means for cohort discovery and a novel mixed methods approach to population health.

The Identification of Subphenotypes and Associations with Health Outcomes in Patients with Opioid-Related Emergency Department Encounters Using Latent Class Analysis.

The emergency department (ED) is a critical setting for the treatment of patients with opioid misuse. Detecting relevant clinical profiles allows for tailored treatment approaches. We sought to identify and characterize subphenotypes of ED patients with opioid-related encounters. A latent class analysis was conducted using 14,057,302 opioid-related encounters from 2016 through 2017 using the National Emergency Department Sample (NEDS), the largest all-payer ED database in the United States. The optimal model was determined by face validity and information criteria-based metrics. A three-step approach assessed class structure, assigned individuals to classes, and examined characteristics between classes. Class associations were determined for hospitalization, in-hospital death, and ED charges. The final five-class model consisted of the following subphenotypes: Chronic pain (class 1); Alcohol use (class 2); Depression and pain (class 3); Psychosis, liver disease, and polysubstance use (class 4); and Pregnancy (class 5). Using class 1 as the reference, the greatest odds for hospitalization occurred in classes 3 and 4 (Ors 5.24 and 5.33, p < 0.001) and for in-hospital death in class 4 (OR 3.44, p < 0.001). Median ED charges ranged from USD 2177 (class 1) to USD 2881 (class 4). These subphenotypes provide a basis for examining patient-tailored approaches for this patient population.

Development and multimodal validation of a substance misuse algorithm for referral to treatment using artificial intelligence (SMART-AI): a retrospective deep learning study.

BACKGROUND: Substance misuse is a heterogeneous and complex set of behavioural conditions that are highly prevalent in hospital settings and frequently co-occur. Few hospital-wide solutions exist to comprehensively and reliably identify these conditions to prioritise care and guide treatment. The aim of this study was to apply natural language processing (NLP) to clinical notes collected in the electronic health record (EHR) to accurately screen for substance misuse. METHODS: The model was trained and developed on a reference dataset derived from a hospital-wide programme at Rush University Medical Center (RUMC), Chicago, IL, USA, that used structured diagnostic interviews to manually screen admitted patients over 27 months (between Oct 1, 2017, and Dec 31, 2019; n=54 915). The Alcohol Use Disorder Identification Test and Drug Abuse Screening Tool served as reference standards. The first 24 h of notes in the EHR were mapped to standardised medical vocabulary and fed into single-label, multilabel, and multilabel with auxillary-task neural network models. Temporal validation of the model was done using data from the subsequent 12 months on a subset of RUMC patients (n=16 917). External validation was done using data from Loyola University Medical Center, Chicago, IL, USA between Jan 1, 2007, and Sept 30, 2017 (n=1991 adult patients). The primary outcome was discrimination for alcohol misuse, opioid misuse, or non-opioid drug misuse. Discrimination was assessed by the area under the receiver operating characteristic curve (AUROC). Calibration slope and intercept were measured with the unreliability index. Bias assessments were performed across demographic subgroups. FINDINGS: The model was trained on a cohort that had 3·5% misuse (n=1 921) with any type of substance. 220 (11%) of 1921 patients with substance misuse had more than one type of misuse. The multilabel convolutional neural network classifier had a mean AUROC of 0·97 (95% CI 0·96-0·98) during temporal validation for all types of substance misuse. The model was well calibrated and showed good face validity with model features containing explicit mentions of aberrant drug-taking behaviour. A false-negative rate of 0·18-0·19 and a false-positive rate of 0·03 between non-Hispanic Black and non-Hispanic White groups occurred. In external validation, the AUROCs for alcohol and opioid misuse were 0·88 (95% CI 0·86-0·90) and 0·94 (0·92-0·95), respectively. INTERPRETATION: We developed a novel and accurate approach to leveraging the first 24 h of EHR notes for screening multiple types of substance misuse. FUNDING: National Institute On Drug Abuse, National Institutes of Health.

External validation of a machine learning classifier to identify unhealthy alcohol use in hospitalized patients.

BACKGROUND AND AIMS: Unhealthy alcohol use (UAU) is one of the leading causes of global morbidity. A machine learning approach to alcohol screening could accelerate best practices when integrated into electronic health record (EHR) systems. This study aimed to validate externally a natural language processing (NLP) classifier developed at an independent medical center. DESIGN: Retrospective cohort study. SETTING: The site for validation was a midwestern United States tertiary-care, urban medical center that has an inpatient structured universal screening model for unhealthy substance use and an active addiction consult service. PARTICIPANTS/CASES: Unplanned admissions of adult patients between October 23, 2017 and December 31, 2019, with EHR documentation of manual alcohol screening were included in the cohort (n = 57 605). MEASUREMENTS: The Alcohol Use Disorders Identification Test (AUDIT) served as the reference standard. AUDIT scores ≥5 for females and ≥8 for males served as cases for UAU. To examine error in manual screening or under-reporting, a post hoc error analysis was conducted, reviewing discordance between the NLP classifier and AUDIT-derived reference. All clinical notes excluding the manual screening and AUDIT documentation from the EHR were included in the NLP analysis. FINDINGS: Using clinical notes from the first 24 hours of each encounter, the NLP classifier demonstrated an area under the receiver operating characteristic curve (AUCROC) and precision-recall area under the curve (PRAUC) of 0.91 (95% CI = 0.89-0.92) and 0.56 (95% CI = 0.53-0.60), respectively. At the optimal cut point of 0.5, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 0.66 (95% CI = 0.62-0.69), 0.98 (95% CI = 0.98-0.98), 0.35 (95% CI = 0.33-0.38), and 1.0 (95% CI = 1.0-1.0), respectively. CONCLUSIONS: External validation of a publicly available alcohol misuse classifier demonstrates adequate sensitivity and specificity for routine clinical use as an automated screening tool for identifying at-risk patients.

Investigating Unhealthy Alcohol Use As an Independent Risk Factor for Increased COVID-19 Disease Severity: Observational Cross-sectional Study.

BACKGROUND: Unhealthy alcohol use (UAU) is known to disrupt pulmonary immune mechanisms and increase the risk of acute respiratory distress syndrome in patients with pneumonia; however, little is known about the effects of UAU on outcomes in patients with COVID-19 pneumonia. To our knowledge, this is the first observational cross-sectional study that aims to understand the effect of UAU on the severity of COVID-19. OBJECTIVE: We aim to determine if UAU is associated with more severe clinical presentation and worse health outcomes related to COVID-19 and if socioeconomic status, smoking, age, BMI, race/ethnicity, and pattern of alcohol use modify the risk. METHODS: In this observational cross-sectional study that took place between January 1, 2020, and December 31, 2020, we ran a digital machine learning classifier on the electronic health record of patients who tested positive for SARS-CoV-2 via nasopharyngeal swab or had two COVID-19 International Classification of Disease, 10th Revision (ICD-10) codes to identify patients with UAU. After controlling for age, sex, ethnicity, BMI, smoking status, insurance status, and presence of ICD-10 codes for cancer, cardiovascular disease, and diabetes, we then performed a multivariable regression to examine the relationship between UAU and COVID-19 severity as measured by hospital care level (ie, emergency department admission, emergency department admission with ventilator, or death). We used a predefined cutoff with optimal sensitivity and specificity on the digital classifier to compare disease severity in patients with and without UAU. Models were adjusted for age, sex, race/ethnicity, BMI, smoking status, and insurance status. RESULTS: Each incremental increase in the predicted probability from the digital alcohol classifier was associated with a greater odds risk for more severe COVID-19 disease (odds ratio 1.15, 95% CI 1.10-1.20). We found that patients in the unhealthy alcohol group had a greater odds risk to develop more severe disease (odds ratio 1.89, 95% CI 1.17-3.06), suggesting that UAU was associated with an 89% increase in the odds of being in a higher severity category. CONCLUSIONS: In patients infected with SARS-CoV-2, UAU is an independent risk factor associated with greater disease severity and/or death.

Bias and fairness assessment of a natural language processing opioid misuse classifier: detection and mitigation of electronic health record data disadvantages across racial subgroups.

OBJECTIVES: To assess fairness and bias of a previously validated machine learning opioid misuse classifier. MATERIALS & METHODS: Two experiments were conducted with the classifier's original (n = 1000) and external validation (n = 53 974) datasets from 2 health systems. Bias was assessed via testing for differences in type II error rates across racial/ethnic subgroups (Black, Hispanic/Latinx, White, Other) using bootstrapped 95% confidence intervals. A local surrogate model was estimated to interpret the classifier's predictions by race and averaged globally from the datasets. Subgroup analyses and post-hoc recalibrations were conducted to attempt to mitigate biased metrics. RESULTS: We identified bias in the false negative rate (FNR = 0.32) of the Black subgroup compared to the FNR (0.17) of the White subgroup. Top features included "heroin" and "substance abuse" across subgroups. Post-hoc recalibrations eliminated bias in FNR with minimal changes in other subgroup error metrics. The Black FNR subgroup had higher risk scores for readmission and mortality than the White FNR subgroup, and a higher mortality risk score than the Black true positive subgroup (P < .05). DISCUSSION: The Black FNR subgroup had the greatest severity of disease and risk for poor outcomes. Similar features were present between subgroups for predicting opioid misuse, but inequities were present. Post-hoc mitigation techniques mitigated bias in type II error rate without creating substantial type I error rates. From model design through deployment, bias and data disadvantages should be systematically addressed. CONCLUSION: Standardized, transparent bias assessments are needed to improve trustworthiness in clinical machine learning models.

External validation of an opioid misuse machine learning classifier in hospitalized adult patients.

BACKGROUND: Opioid misuse screening in hospitals is resource-intensive and rarely done. Many hospitalized patients are never offered opioid treatment. An automated approach leveraging routinely captured electronic health record (EHR) data may be easier for hospitals to institute. We previously derived and internally validated an opioid classifier in a separate hospital setting. The aim is to externally validate our previously published and open-source machine-learning classifier at a different hospital for identifying cases of opioid misuse. METHODS: An observational cohort of 56,227 adult hospitalizations was examined between October 2017 and December 2019 during a hospital-wide substance use screening program with manual screening. Manually completed Drug Abuse Screening Test served as the reference standard to validate a convolutional neural network (CNN) classifier with coded word embedding features from the clinical notes of the EHR. The opioid classifier utilized all notes in the EHR and sensitivity analysis was also performed on the first 24 h of notes. Calibration was performed to account for the lower prevalence than in the original cohort. RESULTS: Manual screening for substance misuse was completed in 67.8% (n = 56,227) with 1.1% (n = 628) identified with opioid misuse. The data for external validation included 2,482,900 notes with 67,969 unique clinical concept features. The opioid classifier had an AUC of 0.99 (95% CI 0.99-0.99) across the encounter and 0.98 (95% CI 0.98-0.99) using only the first 24 h of notes. In the calibrated classifier, the sensitivity and positive predictive value were 0.81 (95% CI 0.77-0.84) and 0.72 (95% CI 0.68-0.75). For the first 24 h, they were 0.75 (95% CI 0.71-0.78) and 0.61 (95% CI 0.57-0.64). CONCLUSIONS: Our opioid misuse classifier had good discrimination during external validation. Our model may provide a comprehensive and automated approach to opioid misuse identification that augments current workflows and overcomes manual screening barriers.

The Addition of United States Census-Tract Data Does Not Improve the Prediction of Substance Misuse.

Predictors from the structured data in the electronic health record (EHR) have previously been used for case-identification in substance misuse. We aim to examine the added benefit from census-tract data, a proxy for socioeconomic status, to improve identification. A cohort of 186,611 hospitalizations was derived between 2007 and 2017. Reference labels included alcohol misuse only, opioid misuse only, and both alcohol and opioid misuse. Baseline models were created using 24 EHR variables, and enhanced models were created with the addition of 48 census-tract variables from the United States American Community Survey. The absolute net reclassification index (NRI) was applied to measure the benefit in adding census-tract variables to baseline models. The baseline models already had good calibration and discrimination. Adding census-tract variables provided negligible improvement to sensitivity and specificity and NRI was less than 1% across substance groups. Our results show the census-tract added minimal value to prediction models.

Differences in length of stay and discharge destination among patients with substance use disorders: The effect of Substance Use Intervention Team (SUIT) consultation service.

BACKGROUND: Addiction medicine consultation services (ACS) may improve outcomes of hospitalized patients with substance use disorders (SUD). Our aim was to examine the difference in length of stay and the hazard ratio for a routine hospital discharge between SUD patients receiving and not receiving ACS. METHODS: Structured EHR data from 2018 of 1,900 adult patients with a SUD-related diagnostic code at an urban academic health center were examined among 35,541 total encounters. Cox proportional hazards regression models were fit using a cause-specific approach to examine differences in hospital outcome (i.e., routine discharge, leaving against medical advice, in-hospital death, or transfer to another level of care). Models were adjusted for age, sex, race, ethnicity, insurance status, and comorbidities. RESULTS: Length of stay was shorter among encounters with a SUD that received a SUIT consultation versus those admissions that did not receive one (5.77 v. 6.54 days, p<0.01). In adjusted analyses, admissions that received a SUIT consultation had a higher hazard of a routine discharge [hazard ratio (95% confidence interval): 1.16 (1.03-1.30)] compared to those not receiving a SUIT consultation. CONCLUSIONS: The SUIT consultation service was associated with a reduced length of stay and an increased hazard of a routine discharge. The SUIT model may serve as a benchmark and inform other health systems attempting to improve outcomes in SUD patient cohorts.

Publicly available machine learning models for identifying opioid misuse from the clinical notes of hospitalized patients.

BACKGROUND: Automated de-identification methods for removing protected health information (PHI) from the source notes of the electronic health record (EHR) rely on building systems to recognize mentions of PHI in text, but they remain inadequate at ensuring perfect PHI removal. As an alternative to relying on de-identification systems, we propose the following solutions: (1) Mapping the corpus of documents to standardized medical vocabulary (concept unique identifier [CUI] codes mapped from the Unified Medical Language System) thus eliminating PHI as inputs to a machine learning model; and (2) training character-based machine learning models that obviate the need for a dictionary containing input words/n-grams. We aim to test the performance of models with and without PHI in a use-case for an opioid misuse classifier. METHODS: An observational cohort sampled from adult hospital inpatient encounters at a health system between 2007 and 2017. A case-control stratified sampling (n = 1000) was performed to build an annotated dataset for a reference standard of cases and non-cases of opioid misuse. Models for training and testing included CUI codes, character-based, and n-gram features. Models applied were machine learning with neural network and logistic regression as well as expert consensus with a rule-based model for opioid misuse. The area under the receiver operating characteristic curves (AUROC) were compared between models for discrimination. The Hosmer-Lemeshow test and visual plots measured model fit and calibration. RESULTS: Machine learning models with CUI codes performed similarly to n-gram models with PHI. The top performing models with AUROCs > 0.90 included CUI codes as inputs to a convolutional neural network, max pooling network, and logistic regression model. The top calibrated models with the best model fit were the CUI-based convolutional neural network and max pooling network. The top weighted CUI codes in logistic regression has the related terms 'Heroin' and 'Victim of abuse'. CONCLUSIONS: We demonstrate good test characteristics for an opioid misuse computable phenotype that is void of any PHI and performs similarly to models that use PHI. Herein we share a PHI-free, trained opioid misuse classifier for other researchers and health systems to use and benchmark to overcome privacy and security concerns.

Validation of an alcohol misuse classifier in hospitalized patients.

BACKGROUND: Current modes of identifying alcohol misuse in hospitalized patients rely on self-report questionnaires and diagnostic codes that have limitations, including low sensitivity. Information in the clinical notes of the electronic health record (EHR) may further augment the identification of alcohol misuse. Natural language processing (NLP) with supervised machine learning has been successful at analyzing clinical notes and identifying cases of alcohol misuse in trauma patients. METHODS: An alcohol misuse NLP classifier, previously developed on trauma patients who completed the Alcohol Use Disorders Identification Test, was validated in a cohort of 1000 hospitalized patients at a large, tertiary health system between January 1, 2007 and September 1, 2017. The clinical notes were processed using the clinical Text Analysis and Knowledge Extraction System. The National Institute on Alcohol Abuse and Alcoholism (NIAAA) guidelines for alcohol misuse were used during annotation of the medical records in our validation dataset. RESULTS: The alcohol misuse classifier had an area under the receiver operating characteristic curve of 0.91 (95% CI 0.90-0.93) in the cohort of hospitalized patients. The sensitivity, specificity, positive predictive value, and negative predictive value were 0.88 (95% CI 0.85-0.90), 0.78 (95% CI 0.74-0.82), 0.85 (95% CI 0.82-0.87), and 0.82 (95% CI 0.78-0.86), respectively. The Hosmer-Lemeshow Test (p = 0.13) demonstrates good model fit. Additionally, there was a dose-dependent response in alcohol consumption behaviors across increasing strata of predicted probabilities for alcohol misuse. CONCLUSION: The alcohol misuse NLP classifier had good discrimination and test characteristics in hospitalized patients. An approach using the clinical notes with NLP and supervised machine learning may better identify alcohol misuse cases than conventional methods solely relying on billing diagnostic codes.

Subtypes in patients with opioid misuse: A prognostic enrichment strategy using electronic health record data in hospitalized patients.

BACKGROUND: Approaches are needed to better delineate the continuum of opioid misuse that occurs in hospitalized patients. A prognostic enrichment strategy with latent class analysis (LCA) may facilitate treatment strategies in subtypes of opioid misuse. We aim to identify subtypes of patients with opioid misuse and examine the distinctions between the subtypes by examining patient characteristics, topic models from clinical notes, and clinical outcomes. METHODS: This was an observational study of inpatient hospitalizations at a tertiary care center between 2007 and 2017. Patients with opioid misuse were identified using an operational definition applied to all inpatient encounters. LCA with eight class-defining variables from the electronic health record (EHR) was applied to identify subtypes in the cohort of patients with opioid misuse. Comparisons between subtypes were made using the following approaches: (1) descriptive statistics on patient characteristics and healthcare utilization using EHR data and census-level data; (2) topic models with natural language processing (NLP) from clinical notes; (3) association with hospital outcomes. FINDINGS: The analysis cohort was 6,224 (2.7% of all hospitalizations) patient encounters with opioid misuse with a data corpus of 422,147 clinical notes. LCA identified four subtypes with differing patient characteristics, topics from the clinical notes, and hospital outcomes. Class 1 was categorized by high hospital utilization with known opioid-related conditions (36.5%); Class 2 included patients with illicit use, low socioeconomic status, and psychoses (12.8%); Class 3 contained patients with alcohol use disorders with complications (39.2%); and class 4 consisted of those with low hospital utilization and incidental opioid misuse (11.5%). The following hospital outcomes were the highest for each subtype when compared against the other subtypes: readmission for class 1 (13.9% vs. 10.5%, p<0.01); discharge against medical advice for class 2 (12.3% vs. 5.3%, p<0.01); and in-hospital death for classes 3 and 4 (3.2% vs. 1.9%, p<0.01). CONCLUSIONS: A 4-class latent model was the most parsimonious model that defined clinically interpretable and relevant subtypes for opioid misuse. Distinct subtypes were delineated after examining multiple domains of EHR data and applying methods in artificial intelligence. The approach with LCA and readily available class-defining substance use variables from the EHR may be applied as a prognostic enrichment strategy for targeted interventions.

Development and application of a high throughput natural language processing architecture to convert all clinical documents in a clinical data warehouse into standardized medical vocabularies.

OBJECTIVE: Natural language processing (NLP) engines such as the clinical Text Analysis and Knowledge Extraction System are a solution for processing notes for research, but optimizing their performance for a clinical data warehouse remains a challenge. We aim to develop a high throughput NLP architecture using the clinical Text Analysis and Knowledge Extraction System and present a predictive model use case. MATERIALS AND METHODS: The CDW was comprised of 1 103 038 patients across 10 years. The architecture was constructed using the Hadoop data repository for source data and 3 large-scale symmetric processing servers for NLP. Each named entity mention in a clinical document was mapped to the Unified Medical Language System concept unique identifier (CUI). RESULTS: The NLP architecture processed 83 867 802 clinical documents in 13.33 days and produced 37 721 886 606 CUIs across 8 standardized medical vocabularies. Performance of the architecture exceeded 500 000 documents per hour across 30 parallel instances of the clinical Text Analysis and Knowledge Extraction System including 10 instances dedicated to documents greater than 20 000 bytes. In a use-case example for predicting 30-day hospital readmission, a CUI-based model had similar discrimination to n-grams with an area under the curve receiver operating characteristic of 0.75 (95% CI, 0.74-0.76). DISCUSSION AND CONCLUSION: Our health system's high throughput NLP architecture may serve as a benchmark for large-scale clinical research using a CUI-based approach.