Critical Transitions in Intensive Care Units: A Sepsis Case Study

The progression of complex human diseases is associated with critical transitions across dynamical regimes. These transitions often spawn early-warning signals and provide insights into the underlying disease-driving mechanisms. In this paper, we propose a computational method based on surprise loss (SL) to discover data-driven indicators of such transitions in a multivariate time series dataset of septic shock and non-sepsis patient cohorts (MIMIC-III database). The core idea of SL is to train a mathematical model on time series in an unsupervised fashion and to quantify the deterioration of the model's forecast (out-of-sample) performance relative to its past (in-sample) performance. Considering the highest value of the moving average of SL as a critical transition, our retrospective analysis revealed that critical transitions occurred at a median of over 35 hours before the onset of septic shock, which suggests the applicability of our method as an early-warning indicator. Furthermore, we show that clinical variables at critical-transition regions are significantly different between septic shock and non-sepsis cohorts. Therefore, our paper contributes a critical-transition-based data-sampling strategy that can be utilized for further analysis, such as patient classification. Moreover, our method outperformed other indicators of critical transition in complex systems, such as temporal autocorrelation and variance.Comment: 16 pages, 8 figures, 2 table

Multitask learning and benchmarking with clinical time series data

Health care is one of the most exciting frontiers in data mining and machine learning. Successful adoption of electronic health records (EHRs) created an explosion in digital clinical data available for analysis, but progress in machine learning for healthcare research has been difficult to measure because of the absence of publicly available benchmark data sets. To address this problem, we propose four clinical prediction benchmarks using data derived from the publicly available Medical Information Mart for Intensive Care (MIMIC-III) database. These tasks cover a range of clinical problems including modeling risk of mortality, forecasting length of stay, detecting physiologic decline, and phenotype classification. We propose strong linear and neural baselines for all four tasks and evaluate the effect of deep supervision, multitask training and data-specific architectural modifications on the performance of neural models.Comment: This version of the paper adds details about the generation of the benchmark tasks and describes improved neural baseline

Machine learning for early prediction of circulatory failure in the intensive care unit

Intensive care clinicians are presented with large quantities of patient information and measurements from a multitude of monitoring systems. The limited ability of humans to process such complex information hinders physicians to readily recognize and act on early signs of patient deterioration. We used machine learning to develop an early warning system for circulatory failure based on a high-resolution ICU database with 240 patient years of data. This automatic system predicts 90.0% of circulatory failure events (prevalence 3.1%), with 81.8% identified more than two hours in advance, resulting in an area under the receiver operating characteristic curve of 94.0% and area under the precision-recall curve of 63.0%. The model was externally validated in a large independent patient cohort.Comment: 5 main figures, 1 main table, 13 supplementary figures, 5 supplementary tables; 250ppi image

SLEEPNET: Automated Sleep Staging System via Deep Learning

Sleep disorders, such as sleep apnea, parasomnias, and hypersomnia, affect 50-70 million adults in the United States (Hillman et al., 2006). Overnight polysomnography (PSG), including brain monitoring using electroencephalography (EEG), is a central component of the diagnostic evaluation for sleep disorders. While PSG is conventionally performed by trained technologists, the recent rise of powerful neural network learning algorithms combined with large physiological datasets offers the possibility of automation, potentially making expert-level sleep analysis more widely available. We propose SLEEPNET (Sleep EEG neural network), a deployed annotation tool for sleep staging. SLEEPNET uses a deep recurrent neural network trained on the largest sleep physiology database assembled to date, consisting of PSGs from over 10,000 patients from the Massachusetts General Hospital (MGH) Sleep Laboratory. SLEEPNET achieves human-level annotation performance on an independent test set of 1,000 EEGs, with an average accuracy of 85.76% and algorithm-expert inter-rater agreement (IRA) of kappa = 79.46%, comparable to expert-expert IRA

Riemannian geometry applied to detection of respiratory states from EEG signals: the basis for a brain-ventilator interface

During mechanical ventilation, patient-ventilator disharmony is frequently observed and may result in increased breathing effort, compromising the patient's comfort and recovery. This circumstance requires clinical intervention and becomes challenging when verbal communication is difficult. In this work, we propose a brain computer interface (BCI) to automatically and non-invasively detect patient-ventilator disharmony from electroencephalographic (EEG) signals: a brain-ventilator interface (BVI). Our framework exploits the cortical activation provoked by the inspiratory compensation when the subject and the ventilator are desynchronized. Use of a one-class approach and Riemannian geometry of EEG covariance matrices allows effective classification of respiratory states. The BVI is validated on nine healthy subjects that performed different respiratory tasks that mimic a patient-ventilator disharmony. Classification performances, in terms of areas under ROC curves, are significantly improved using EEG signals compared to detection based on air flow. Reduction in the number of electrodes that can achieve discrimination can often be desirable (e.g. for portable BCI systems). By using an iterative channel selection technique, the Common Highest Order Ranking (CHOrRa), we find that a reduced set of electrodes (n=6) can slightly improve for an intra-subject configuration, and it still provides fairly good performances for a general inter-subject setting. Results support the discriminant capacity of our approach to identify anomalous respiratory states, by learning from a training set containing only normal respiratory epochs. The proposed framework opens the door to brain-ventilator interfaces for monitoring patient's breathing comfort and adapting ventilator parameters to patient respiratory needs.Comment: 14 pages, 7 figure

Discovering shared and individual latent structure in multiple time series

This paper proposes a nonparametric Bayesian method for exploratory data analysis and feature construction in continuous time series. Our method focuses on understanding shared features in a set of time series that exhibit significant individual variability. Our method builds on the framework of latent Diricihlet allocation (LDA) and its extension to hierarchical Dirichlet processes, which allows us to characterize each series as switching between latent ``topics'', where each topic is characterized as a distribution over ``words'' that specify the series dynamics. However, unlike standard applications of LDA, we discover the words as we learn the model. We apply this model to the task of tracking the physiological signals of premature infants; our model obtains clinically significant insights as well as useful features for supervised learning tasks.Comment: Additional supplementary section in tex fil

A Deep Q-learning/genetic Algorithms Based Novel Methodology For Optimizing Covid-19 Pandemic Government Actions

Whenever countries are threatened by a pandemic, as is the case with the COVID-19 virus, governments should take the right actions to safeguard public health as well as to mitigate the negative effects on the economy. In this regard, there are two completely different approaches governments can take: a restrictive one, in which drastic measures such as self-isolation can seriously damage the economy, and a more liberal one, where more relaxed restrictions may put at risk a high percentage of the population. The optimal approach could be somewhere in between, and, in order to make the right decisions, it is necessary to accurately estimate the future effects of taking one or other measures. In this paper, we use the SEIR epidemiological model (Susceptible - Exposed - Infected - Recovered) for infectious diseases to represent the evolution of the virus COVID-19 over time in the population. To optimize the best sequences of actions governments can take, we propose a methodology with two approaches, one based on Deep Q-Learning and another one based on Genetic Algorithms. The sequences of actions (confinement, self-isolation, two-meter distance or not taking restrictions) are evaluated according to a reward system focused on meeting two objectives: firstly, getting few people infected so that hospitals are not overwhelmed with critical patients, and secondly, avoiding taking drastic measures for too long which can potentially cause serious damage to the economy. The conducted experiments prove that our methodology is a valid tool to discover actions governments can take to reduce the negative effects of a pandemic in both senses. We also prove that the approach based on Deep Q-Learning overcomes the one based on Genetic Algorithms for optimizing the sequences of actions

Patient Similarity Analysis with Longitudinal Health Data

Healthcare professionals have long envisioned using the enormous processing powers of computers to discover new facts and medical knowledge locked inside electronic health records. These vast medical archives contain time-resolved information about medical visits, tests and procedures, as well as outcomes, which together form individual patient journeys. By assessing the similarities among these journeys, it is possible to uncover clusters of common disease trajectories with shared health outcomes. The assignment of patient journeys to specific clusters may in turn serve as the basis for personalized outcome prediction and treatment selection. This procedure is a non-trivial computational problem, as it requires the comparison of patient data with multi-dimensional and multi-modal features that are captured at different times and resolutions. In this review, we provide a comprehensive overview of the tools and methods that are used in patient similarity analysis with longitudinal data and discuss its potential for improving clinical decision making

Probabilistic Machine Learning for Healthcare

Machine learning can be used to make sense of healthcare data. Probabilistic machine learning models help provide a complete picture of observed data in healthcare. In this review, we examine how probabilistic machine learning can advance healthcare. We consider challenges in the predictive model building pipeline where probabilistic models can be beneficial including calibration and missing data. Beyond predictive models, we also investigate the utility of probabilistic machine learning models in phenotyping, in generative models for clinical use cases, and in reinforcement learning.Comment: Annual Reviews of Biomedical Data Science 202

AI-oriented Medical Workload Allocation for Hierarchical Cloud/Edge/Device Computing

In a hierarchically-structured cloud/edge/device computing environment, workload allocation can greatly affect the overall system performance. This paper deals with AI-oriented medical workload generated in emergency rooms (ER) or intensive care units (ICU) in metropolitan areas. The goal is to optimize AI-workload allocation to cloud clusters, edge servers, and end devices so that minimum response time can be achieved in life-saving emergency applications. In particular, we developed a new workload allocation method for the AI workload in distributed cloud/edge/device computing systems. An efficient scheduling and allocation strategy is developed in order to reduce the overall response time to satisfy multi-patient demands. We apply several ICU AI workloads from a comprehensive edge computing benchmark Edge AIBench. The healthcare AI applications involved are short-of-breath alerts, patient phenotype classification, and life-death threats. Our experimental results demonstrate the high efficiency and effectiveness in real-life health-care and emergency applications