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.

In contrast, transformers employ a "Scaled Dot-Product Attention" mechanism that is parallelizable. This unique attention mechanism allows for large-scale pretraining. Additionally, self-supervised pretraining paradigm such as masked language modeling onlarge unlabeled datasets enabled transformers to be trained without costly annotations. Transformer model, although originally designed for the NLP [3] domain, Transformers have witnessed adaptations in various domains such as computer vision [5, 6], remote sensing [7], time series [8], speech processing [9] and multimodal learning [10]. Consequently, modality specific surveys emerged, focusing on medical imaging [11-13] and biomedical language models [14] in the medical domain. This paper aims to provide comprehensive overview of Transformer models utilized across multiple modalities of data to address healthcare objectives. We discuss pre-training strategies to manage the lack of robust and annotated healthcare datasets. The rest of the paper is organized as follows: Section 2 discusses the strategy to search for relevant citations; Section 3 describes the architecture of the original transformer; Section 4 describes the two primary Transformer variants: the Bidirectional Encoder Representations from Transformers (BERT) and the Vision Transformer (ViT). Section 5 describes advancements in large language models (LLM), and section 6 through 12 provides a review of Transformers in healthcare.

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.

The intensive care unit (ICU) is a specialized hospital space where critically ill patients receive intensive care and monitoring. Comprehensive monitoring is imperative in assessing patients conditions, in particular acuity, and ultimately the quality of care. However, the extent of patient monitoring in the ICU is limited due to time constraints and the workload on healthcare providers. Currently, visual assessments for acuity, including fine details such as facial expressions, posture, and mobility, are sporadically captured, or not captured at all. These manual observations are subjective to the individual, prone to documentation errors, and overburden care providers with the additional workload. Artificial Intelligence (AI) enabled systems has the potential to augment the patient visual monitoring and assessment due to their exceptional learning capabilities. Such systems require robust annotated data to train. To this end, we have developed pervasive sensing and data processing system which collects data from multiple modalities depth images, color RGB images, accelerometry, electromyography, sound pressure, and light levels in ICU for developing intelligent monitoring systems for continuous and granular acuity, delirium risk, pain, and mobility assessment. This paper presents the Intelligent Intensive Care Unit (I2CU) system architecture we developed for real-time patient monitoring and visual assessment.

Existing Intensive Care Unit (ICU) delirium prediction models do not consider environmental factors despite strong evidence of their influence on delirium. This study reports the first deep-learning based delirium prediction model for ICU patients using only ambient noise and light information. Ambient light and noise intensities were measured from ICU rooms of 102 patients from May 2021 to September 2022 using Thunderboard, ActiGraph sensors and an iPod with AudioTools application. These measurements were divided into daytime (0700 to 1859) and nighttime (1900 to 0659). Deep learning models were trained using this data to predict the incidence of delirium during ICU stay or within 4 days of discharge. Finally, outcome scores were analyzed to evaluate the importance and directionality of every feature. Daytime noise levels were significantly higher than nighttime noise levels. When using only noise features or a combination of noise and light features 1-D convolutional neural networks (CNN) achieved the strongest performance: AUC=0.77, 0.74; Sensitivity=0.60, 0.56; Specificity=0.74, 0.74; Precision=0.46, 0.40 respectively. Using only light features, Long Short-Term Memory (LSTM) networks performed best: AUC=0.80, Sensitivity=0.60, Specificity=0.77, Precision=0.37. Maximum nighttime and minimum daytime noise levels were the strongest positive and negative predictors of delirium respectively. Nighttime light level was a stronger predictor of delirium than daytime light level. Total influence of light features outweighed that of noise features on the second and fourth day of ICU stay. This study shows that ambient light and noise intensities are strong predictors of long-term delirium incidence in the ICU. It reveals that daytime and nighttime environmental factors might influence delirium differently and that the importance of light and noise levels vary over the course of an ICU stay.

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.

Reprints will not be available from the author(s). ABSTRACT Objectives: We hypothesize that multistate models are beneficial in analyzing transitions through kidney states and understanding the underlying processes influencing the course of kidney health. Specifically, we aim to quantify longitudinal acute kidney injury (AKI) trajectories and to describe transitions through progressing and recovery states and outcomes among hospitalized patients. Methods: In this large, longitudinal cohort study, 138,449 adult patients admitted to a quaternary care hospital between January 2012 and August 2019 were staged based on Kidney Disease: Improving Global Outcomes (KDIGO) serum creatinine criteria as No AKI, Stage 1, Stage 2, Stage 3, and Stage 3 with renal replacement therapy (RRT) AKI for the first 14 days of their hospital stay. We fit and examined 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 age, sex, race, admission comorbidities, and prolonged intensive care unit (ICU) stay 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% (n = 32,739) had Stage 1 AKI, 18% (n = 8,670) had Stage 2 AKI, and 17% (n = 7,916) had AKI Stage 3 with or without RRT.

Accurate prediction of postoperative complications can inform shared decisions regarding prognosis, preoperative risk-reduction, and postoperative resource use. We hypothesized that multi-task deep learning models would outperform random forest models in predicting postoperative complications, and that integrating high-resolution intraoperative physiological time series would result in more granular and personalized health representations that would improve prognostication compared to preoperative predictions. In a longitudinal cohort study of 56,242 patients undergoing 67,481 inpatient surgical procedures at a university medical center, we compared deep learning models with random forests for predicting nine common postoperative complications using preoperative, intraoperative, and perioperative patient data. Our study indicated several significant results across experimental settings that suggest the utility of deep learning for capturing more precise representations of patient health for augmented surgical decision support. Multi-task learning improved efficiency by reducing computational resources without compromising predictive performance. Integrated gradients interpretability mechanisms identified potentially modifiable risk factors for each complication. Monte Carlo dropout methods provided a quantitative measure of prediction uncertainty that has the potential to enhance clinical trust. Multi-task learning, interpretability mechanisms, and uncertainty metrics demonstrated potential to facilitate effective clinical implementation.

Recent deep learning research based on Transformer model architectures has demonstrated state-of-the-art performance across a variety of domains and tasks, mostly within the computer vision and natural language processing domains. While some recent studies have implemented Transformers for clinical tasks using electronic health records data, they are limited in scope, flexibility, and comprehensiveness. In this study, we propose a flexible Transformer-based EHR embedding pipeline and predictive model framework that introduces several novel modifications of existing workflows that capitalize on data attributes unique to the healthcare domain. We showcase the feasibility of our flexible design in a case study in the intensive care unit, where our models accurately predict seven clinical outcomes pertaining to readmission and patient mortality over multiple future time horizons.

-- In cognitive psychology, automatic and self-reinforcing irrational thought patterns are known as cognitive distortions. Left unchecked, patients exhibiting these types of thoughts can become stuck in negative feedback loops of unhealthy thinking, leading to inaccurate perceptions of reality commonly associated with anxiety and depression. In this paper, we present a machine learning framework for the automatic detection and classification of 15 common cognitive distortions in two novel mental health free text datasets collected from both crowdsourcing and a real-world online therapy program. When differentiating between distorted and non-distorted passages, our model achieved a weighted F1 score of 0.88. For classifying distorted passages into one of 15 distortion categories, our model yielded weighted F1 scores of 0.68 in the larger crowdsourced dataset and 0.45 in the smaller online counseling dataset, both of which outperformed random baseline metrics by a large margin. For both tasks, we also identified the most discriminative words and phrases between classes to highlight common thematic elements for improving targeted and therapist-guided mental health treatment. Furthermore, we performed an exploratory analysis using unsupervised content-based clustering and topic modeling algorithms as first efforts towards a data-driven perspective on the thematic relationship between similar cognitive distortions traditionally deemed unique. Finally, we highlight the difficulties in applying mental health-based machine learning in a real-world setting and comment on the implications and benefits of our framework for improving automated delivery of therapeutic treatment in conjunction with traditional cognitive-behavioral therapy. CCORDING to the National Institute of Mental Health, anxiety disorders affect more than 18% of the U.S. adult population every year [1]. Additionally, the National Survey of Drug Use and Health reports that 6.7% of the U.S. adult population experienced at least one major depressive disorder episode in the past year [2]. This work was supported by NSF-IIP 1631871 from the National Science Foundation (NSF), Division of Industrial Innovation and Partnerships (IIP). Rashidi are with the University of Florida, Gainesville, FL 32611 USA (email: shickelb@ufl.edu; S. Benton is with T AO Connect, Inc., St. Petersburg, FL 33701 USA (email: sherry .benton@taoconnect.org).