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Deep learning has recently demonstrated the ability to predict long-term patient risk and its stratification when trained on imaging data such as chest radiographs. However, existing methods formulate estimating patient risk as a binary classification, typically ignoring or limiting the use of temporal information, and not accounting for the loss of patient follow-up, which reduces the fidelity of estimation and limits the prediction to a certain time horizon. In this paper, we demonstrate that deep survival and time-to-event prediction models can outperform binary classifiers at predicting mortality and risk of adverse health events. In our study, deep survival models were trained to predict risk scores from chest radiographs and patient demographic information in the Prostate, Lung, Colorectal, and Ovarian (PLCO) cancer screening trial (25,433 patient data points used in this paper) for 2-, 5-, and 10-year time horizons. Binary classification models that predict mortality at these time horizons were built as baselines. Compared to the considered alternative, deep survival models improve the Brier score (5-year: 0.0455 [95% CI, 0.0427–0.0482] vs. 0.0555 [95% CI, (0.0535–0.0575)], p < 0.05) and expected calibration error (ECE) (5-year: 0.0110 [95% CI, 0.0080–0.0141] vs. 0.0747 [95% CI, 0.0718–0.0776], p < 0.05) for those fixed time horizons and are able to generate predictions for any time horizon, without the need to retrain the models. Our study suggests that deep survival analysis tools can outperform binary classification in terms of both discriminative performance and calibration, offering a potentially plausible solution for forecasting risk in clinical practice.

Abstract We tested the ability of a physiologically driven minimally invasive closed-loop algorithm, called Resuscitation based on Functional Hemodynamic Monitoring (ReFit), to stabilize for up to 3 h a porcine model of noncompressible hemorrhage induced by severe liver injury and do so during both ground and air transport. Twelve animals were resuscitated using ReFit to drive fluid and vasopressor infusion to a mean arterial pressure (MAP) > 60 mmHg and heart rate

Abstract In this article, we introduce a novel type of spatio-temporal sequential patterns called Constricted Spatio-Temporal Sequential (CSTS) patterns and thoroughly analyze their properties. We demonstrate that the set of CSTS patterns is a concise representation of all spatio-temporal sequential patterns that can be discovered in a given dataset. To measure significance of the discovered CSTS patterns we adapt the participation index measure. We also provide CSTS-Miner: an algorithm that discovers all participation index strong CSTS patterns in event data. We experimentally evaluate the proposed algorithms using two crime-related datasets: Pittsburgh Police Incident Blotter Dataset and Boston Crime Incident Reports Dataset. In the experiments, the CSTS-Miner algorithm is compared with the other four state-of-the-art algorithms: STS-Miner, CSTPM, STBFM and CST-SPMiner. As the results of the experiments suggest, the proposed algorithm discovers much fewer patterns than the other selected algorithms. Finally, we provide the examples of interesting crime-related patterns discovered by the proposed CSTS-Miner algorithm.

Summary: Background: Healthcare-associated bacterial pathogens frequently carry plasmids that contribute to antibiotic resistance and virulence. The horizontal transfer of plasmids in healthcare settings has been previously documented, but genomic and epidemiologic methods to study this phenomenon remain underdeveloped. The objectives of this study were to apply whole-genome sequencing to systematically resolve and track plasmids carried by nosocomial pathogens in a single hospital, and to identify epidemiologic links that indicated likely horizontal plasmid transfer. Methods: We performed an observational study of plasmids circulating among bacterial isolates infecting patients at a large hospital. We first examined plasmids carried by isolates sampled from the same patient over time and isolates that caused clonal outbreaks in the same hospital to develop thresholds with which horizontal plasmid transfer within a tertiary hospital could be inferred. We then applied those sequence similarity thresholds to perform a systematic screen of 3074 genomes of nosocomial bacterial isolates from a single hospital for the presence of 89 plasmids. We also collected and reviewed data from electronic health records for evidence of geotemporal links between patients infected with bacteria encoding plasmids of interest. Findings: Our analyses determined that 95% of analyzed genomes maintained roughly 95% of their plasmid genetic content and accumulated fewer than 15 SNPs per 100 kb of plasmid sequence. Applying these similarity thresholds to identify horizontal plasmid transfer identified 45 plasmids that potentially circulated among clinical isolates. Ten highly preserved plasmids met criteria for geotemporal links associated with horizontal transfer. Several plasmids with shared backbones also encoded different additional mobile genetic element content, and these elements were variably present among the sampled clinical isolate genomes. Interpretation: Evidence suggests that the horizontal transfer of plasmids among nosocomial bacterial pathogens appears to be frequent within hospitals and can be monitored with whole genome sequencing and comparative genomics approaches. These approaches should incorporate both nucleotide identity and reference sequence coverage to study the dynamics of plasmid transfer in the hospital. Funding: This research was supported by the US National Institute of Allergy and Infectious Disease (NIAID) and the University of Pittsburgh School of Medicine.

Abstract Background: Whole-genome sequencing (WGS) has traditionally been used in infection prevention to confirm or refute the presence of an outbreak after it has occurred. Due to decreasing costs of WGS, an increasing number of institutions have been utilizing WGS-based surveillance. Additionally, machine learning or statistical modeling to supplement infection prevention practice have also been used. We systematically reviewed the use of WGS surveillance and machine learning to detect and investigate outbreaks in healthcare settings. Methods: We performed a PubMed search using separate terms for WGS surveillance and/or machine-learning technologies for infection prevention through March 15, 2021. Results: Of 767 studies returned using the WGS search terms, 42 articles were included for review. Only 2 studies (4.8%) were performed in real time, and 39 (92.9%) studied only 1 pathogen. Nearly all studies (n = 41, 97.6%) found genetic relatedness between some isolates collected. Across all studies, 525 outbreaks were detected among 2,837 related isolates (average, 5.4 isolates per outbreak). Also, 35 studies (83.3%) only utilized geotemporal clustering to identify outbreak transmission routes. Of 21 studies identified using the machine-learning search terms, 4 were included for review. In each study, machine learning aided outbreak investigations by complementing methods to gather epidemiologic data and automating identification of transmission pathways. Conclusions: WGS surveillance is an emerging method that can enhance outbreak detection. Machine learning has the potential to identify novel routes of pathogen transmission. Broader incorporation of WGS surveillance into infection prevention practice has the potential to transform the detection and control of healthcare outbreaks.

We consider whether one can forecast the emergence of variants of concern in the SARS-CoV-2 outbreak and similar pandemics. We explore methods of population genetics and identify key relevant principles in both deterministic and stochastic models of spread of infectious disease. Finally, we demonstrate that fitness variation, defined as a trait for which an increase in its value is associated with an increase in net Darwinian fitness if the value of other traits are held constant, is a strong indicator of imminent transition in the viral population.

Background: We explored sex-based differences in discharge location after resuscitation from cardiac arrest. Methods: We performed a single-center retrospective cohort study including patients hospitalized after resuscitation from cardiac arrest from January 2010 to May 2020. We identified patients from a prospective registry, from which we extracted standard demographic and clinical variables. We explored favorable discharge location, defined as discharge to home or acute rehabilitation for survivors to hospital discharge. We tested the association of sex with the residuals of a multivariable logistic regression built using bidirectional selection to control for clinically relevant covariates. Results: We included 2,278 patients. Mean age was 59 (SD 16), 40% were women, and 77% were admitted after out-of-hospital cardiac arrest. A total of 970 patients (43%) survived to discharge; of those, 607 (63% of survivors) had a favorable discharge location. Female sex showed a weak independent association with unfavorable discharge location (adjusted OR 0.94 (95%CI 0.89–0.99)). Conclusions: Our results suggest a possible sex-based disparity in discharge location after cardiac arrest.

Risk models have historically displayed only moderate predictive performance in estimating mortality risk in left ventricular assist device therapy. This study evaluated whether machine learning can improve risk prediction for left ventricular assist devices. Primary durable left ventricular assist devices reported in the Interagency Registry for Mechanically Assisted Circulatory Support between March 1, 2006 and December 31, 2016 were included. The study cohort was randomly divided 3:1 into training and testing sets. Logistic regression and machine learning models (extreme gradient boosting) were created in the training set for 90-day and 1-year mortality and their performance was evaluated after bootstrapping with 1000 replications in the testing set. Differences in model performance were also evaluated in cases of concordance versus discordance in predicted risk between logistic regression and extreme gradient boosting as defined by equal size patient tertiles. A total of 16,120 patients were included. Calibration metrics were comparable between logistic regression and extreme gradient boosting. C-index was improved with extreme gradient boosting (90-day: 0.707 [0.683-0.730] versus 0.740 [0.717-0.762] and 1-year: 0.691 [0.673-0.710] versus 0.714 [0.695-0.734]; each p

Early recognition of pathologic cardiorespiratory stress and forecasting cardiorespiratory decompensation in the critically ill is difficult even in highly monitored patients in the Intensive Care Unit (ICU). Instability can be intuitively defined as the overt manifestation of the failure of the host to adequately respond to cardiorespiratory stress. The enormous volume of patient data available in ICU environments, both of high-frequency numeric and waveform data accessible from bedside monitors, plus Electronic Health Record (EHR) data, presents a platform ripe for Artificial Intelligence (AI) approaches for the detection and forecasting of instability, and data-driven intelligent clinical decision support (CDS). Building unbiased, reliable, and usable AI-based systems across health care sites is rapidly becoming a high priority, specifically as these systems relate to diagnostics, forecasting, and bedside clinical decision support. The ICU environment is particularly well-positioned to demonstrate the value of AI in saving lives. The goal is to create AI models embedded in a real-time CDS for forecasting and mitigation of critical instability in ICU patients of sufficient readiness to be deployed at the bedside. Such a system must leverage multi-source patient data, machine learning, systems engineering, and human action expertise, the latter being key to successful CDS implementation in the clinical workflow and evaluation of bias. We present one approach to create an operationally relevant AI-based forecasting CDS system.

For fluid resuscitation of critically ill individuals to be effective, it must be well calibrated in terms of timing and dosages of treatments. In current practice, the cardiovascular sufficiency of patients during fluid resuscitation is determined using primarily invasively measured vital signs, including Arterial Pressure and Mixed Venous Oxygen Saturation (SvO2), which may not be available in outside-of-hospital settings, particularly in the field when treating subjects injured in traffic accidents or wounded in combat where only non-invasive monitoring is available to drive care. In this paper, we propose (1) a Machine Learning (ML) approach to estimate the sufficiency utilizing features extracted from non-invasive vital signs and (2) a novel framework to address the detrimental impact of inter-patient diversity on the ability of ML models to generalize well to unseen subjects. Through comprehensive evaluation on the physiological data collected in laboratory animal experiments, we demonstrate that the proposed approaches can achieve competitive performance on new patients using only non-invasive measurements. These characteristics enable effective monitoring of fluid resuscitation in real-world acute settings with limited monitoring resources and can help facilitate broader adoption of ML in this important subfield of healthcare.

Introduction About 42 million surgeries are performed annually in the USA. While the postoperative mortality is less than 2%, 12% of all patients in the high-risk surgery group account for 80% of postoperative deaths. New onset of haemodynamic instability is common in surgical patients and its delayed treatment leads to increased morbidity and mortality. The goal of this proposal is to develop, validate and test real-time intraoperative risk prediction tools based on clinical data and high-fidelity physiological waveforms to predict haemodynamic instability during surgery.Methods and analysis We will initiate our work using an existing annotated intraoperative database from the University of California Irvine, including clinical and high-fidelity waveform data. These data will be used for the training and development of the machine learning model (Carnegie Mellon University) that will then be tested on prospectively collected database (University of California Los Angeles). Simultaneously, we will use existing knowledge of haemodynamic instability patterns derived from our intensive care unit cohorts, medical information mart for intensive care II data, University of California Irvine data and animal studies to create smart alarms and graphical user interface for a clinical decision support. Using machine learning, we will extract a core dataset, which characterises the signatures of normal intraoperative variability, various haemodynamic instability aetiologies and variable responses to resuscitation. We will then employ clinician-driven iterative design to create a clinical decision support user interface, and evaluate its effect in simulated high-risk surgeries.Ethics and dissemination We will publish the results in a peer-reviewed publication and will present this work at professional conferences for the anaesthesiology and computer science communities. Patient-level data will be made available within 6 months after publication of the primary manuscript. The study has been approved by University of California, Los Angeles Institutional review board. (IRB #19–0 00 354).

Early prediction of the potential for neurological recovery after resuscitation from cardiac arrest is difficult but important. Currently, no clinical finding or combination of findings are sufficient to accurately predict or preclude favorable recovery of comatose patients in the first 24 to 48 hours after resuscitation. Thus, life-sustaining therapy is often continued for several days in patients whose irrecoverable injury is not yet recognized. Conversely, early withdrawal of life-sustaining therapy increases mortality among patients who otherwise might have gone on to recover. In this work, we present Canonical Autocorrelation Analysis (CAA) and Canonical Autocorrelation Embeddings (CAE), novel methods suitable for identifying complex patterns in high-resolution multivariate data often collected in highly monitored clinical environments such as intensive care units. CAE embeds sets of datapoints onto a space that characterizes their latent correlation structures and allows direct comparison of these structures through the use of a distance metric. The methodology may be particularly suitable when the unit of analysis is not just an individual datapoint but a dataset, as for instance in patients for whom physiological measures are recorded over time, and where changes of correlation patterns in these datasets are informative for the task at hand. We present a proof of concept to illustrate the potential utility of CAE by applying it to characterize electroencephalographic recordings from 80 comatose survivors of cardiac arrest, aiming to identify patients who will survive to hospital discharge with favorable functional recovery. Our results show that with very low probability of making a Type 1 error, we are able to identify 32.5% of patients who are likely to have a good neurological outcome, some of whom have otherwise unfavorable clinical characteristics. Importantly, some of these had 5% predicted chance of favorable recovery based on initial illness severity measures alone. Providing this information to support clinical decision-making could motivate the continuation of life-sustaining therapies for these patients.