Predictive analytics framework for electronic health records with machine learning advancements : optimising hospital resources utilisation with predictive and epidemiological models

The primary aim of this thesis was to investigate the feasibility and robustness of predictive machine-learning models in the context of improving hospital resources’ utilisation with data- driven approaches and predicting hospitalisation with hospital quality assessment metrics such as length of stay. The length of stay predictions includes the validity of the proposed methodological predictive framework on each hospital’s electronic health records data source. In this thesis, we relied on electronic health records (EHRs) to drive a data-driven predictive inpatient length of stay (LOS) research framework that suits the most demanding hospital facilities for hospital resources’ utilisation context. The thesis focused on the viability of the methodological predictive length of stay approaches on dynamic and demanding healthcare facilities and hospital settings such as the intensive care units and the emergency departments. While the hospital length of stay predictions are (internal) healthcare inpatients outcomes assessment at the time of admission to discharge, the thesis also considered (external) factors outside hospital control, such as forecasting future hospitalisations from the spread of infectious communicable disease during pandemics. The internal and external splits are the thesis’ main contributions. Therefore, the thesis evaluated the public health measures during events of uncertainty (e.g. pandemics) and measured the effect of non-pharmaceutical intervention during outbreaks on future hospitalised cases. This approach is the first contribution in the literature to examine the epidemiological curves’ effect using simulation models to project the future hospitalisations on their strong potential to impact hospital beds’ availability and stress hospital workflow and workers, to the best of our knowledge. The main research commonalities between chapters are the usefulness of ensembles learning models in the context of LOS for hospital resources utilisation. The ensembles learning models anticipate better predictive performance by combining several base models to produce an optimal predictive model. These predictive models explored the internal LOS for various chronic and acute conditions using data-driven approaches to determine the most accurate and powerful predicted outcomes. This eventually helps to achieve desired outcomes for hospital professionals who are working in hospital settings

Applications of Machine Learning in Medical Prognosis Using Electronic Medical Records

Approximately 84 % of hospitals are adopting electronic medical records (EMR) In the United States. EMR is a vital resource to help clinicians diagnose the onset or predict the future condition of a specific disease. With machine learning advances, many research projects attempt to extract medically relevant and actionable data from massive EMR databases using machine learning algorithms. However, collecting patients\u27 prognosis factors from Electronic EMR is challenging due to privacy, sensitivity, and confidentiality. In this study, we developed medical generative adversarial networks (GANs) to generate synthetic EMR prognosis factors using minimal information collected during routine care in specialized healthcare facilities. The generated prognosis variables used in developing predictive models for (1) chronic wound healing in patients diagnosed with Venous Leg Ulcers (VLUs) and (2) antibiotic resistance in patients diagnosed with Skin and soft tissue infections (SSTIs). Our proposed medical GANs, EMR-TCWGAN and DermaGAN, can produce both continuous and categorical features from EMR. We utilized conditional training strategies to enhance training and generate classified data regarding healing vs. non-healing in EMR-TCWGAN and susceptibility vs. resistance in DermGAN. The ability of the proposed GAN models to generate realistic EMR data was evaluated by TSTR (test on the synthetic, train on the real), discriminative accuracy, and visualization. We analyzed the synthetic data augmentation technique\u27s practicality in improving the wound healing prognostic model and antibiotic resistance classifier. We achieved the area under the curve (AUC) of 0.875 in the wound healing prognosis model and an average AUC of 0.830 in the antibiotic resistance classifier by using the synthetic samples generated by GANs in the training process. These results suggest that GANs can be considered a data augmentation method to generate realistic EMR data

Detection of Patients at Risk of Multidrug-Resistant Enterobacteriaceae Infection Using Graph Neural Networks: A Retrospective Study

Funding: This research was funded by the Joint Swiss–Portuguese Academic Program from the University of Applied Sciences and Arts Western Switzerland (HES-SO) and the Fundação para a Ciência e Tecnologia (FCT). S.G.P. also acknowledges FCT for her direct funding (CEECINST/00051/2018) and her research unit (UIDB/05704/2020). Funders were not involved in the study design, data pre-processing, data analysis, interpretation, or report writing. Author contributions: R.G. and A.B. designed and implemented the models, and ran the experiments and analyses. R.G. and D.T. wrote the manuscript draft. D.T. and S.G.P. conceptualized the experiments and acquired funding. R.G., D.P., and S.G.P. curated the data. R.G., A.B., D.P., and D.T. analyzed the data. All authors reviewed and approved the manuscript. Competing interests: The authors declare that they have no competing interests.Background: While Enterobacteriaceae bacteria are commonly found in the healthy human gut, their colonization of other body parts can potentially evolve into serious infections and health threats. We investigate a graph-based machine learning model to predict risks of inpatient colonization by multidrug-resistant (MDR) Enterobacteriaceae. Methods: Colonization prediction was defined as a binary task, where the goal is to predict whether a patient is colonized by MDR Enterobacteriaceae in an undesirable body part during their hospital stay. To capture topological features, interactions among patients and healthcare workers were modeled using a graph structure, where patients are described by nodes and their interactions are described by edges. Then, a graph neural network (GNN) model was trained to learn colonization patterns from the patient network enriched with clinical and spatiotemporal features. Results: The GNN model achieves performance between 0.91 and 0.96 area under the receiver operating characteristic curve (AUROC) when trained in inductive and transductive settings, respectively, up to 8% above a logistic regression baseline (0.88). Comparing network topologies, the configuration considering ward-related edges (0.91 inductive, 0.96 transductive) outperforms the configurations considering caregiver-related edges (0.88, 0.89) and both types of edges (0.90, 0.94). For the top 3 most prevalent MDR Enterobacteriaceae, the AUROC varies from 0.94 for Citrobacter freundii up to 0.98 for Enterobacter cloacae using the best-performing GNN model. Conclusion: Topological features via graph modeling improve the performance of machine learning models for Enterobacteriaceae colonization prediction. GNNs could be used to support infection prevention and control programs to detect patients at risk of colonization by MDR Enterobacteriaceae and other bacteria families.info:eu-repo/semantics/publishedVersio

Dimensionality reduction and ensemble of LSTMs for antimicrobial resistance prediction

Bacterial resistance to antibiotics has been rapidly increasing, resulting in a low antibiotic effectiveness even treating common infections. The presence of resistant pathogens in environments such as a hospital Intensive Care Unit (ICU) exacerbates the critical admission-acquired infections. This work focuses on the prediction of antibiotic resistance in Pseudomonas aeruginosa nosocomial infections at the ICU, using Long Short-Term Memory (LSTM) artificial neural networks as predictive method. The analyzed data were extracted from the Electronic Health Records (EHR) of patients admitted in the University Hospital of Fuenlabrada from 2004 to 2019, and were modeled as Multivariate Time Series. A data-driven dimensionality reduction method is built by adapting three feature importance techniques from the literature to the considered data, and proposing an algorithm for selecting the most appropriate number of features. This is done using LSTM sequential capabilities so that the temporal aspect of features is taken into account. Furthermore, an ensemble of LSTMs is used to reduce the performance variance. Our results indicate that the patient's admission information, the antibiotics administered during the ICU stay, and the previous antimicrobial resistance are the most important features. The proposed dimensionality reduction method dramatically reduces the number of features while considerably increasing the prediction performance. The variance in the performance is reduced by considering the ensemble of classifiers. In essence, the proposed framework achieve, in a computationally cost efficient manner, promising results for supporting decisions in this clinical task, characterized by high dimensionality, data scarcity and concept drift.This work has been partly supported by the Spanish Research Agency, grant numbers PID2019-106623RB-C41, AEI/10.13039/501100011033 (BigTheory), PID2019-107768RA-I00 (AAVis-BMR), by funding action by the Community of Madrid in the framework of the Multiannual Agreement with Rey Juan Carlos University in line of action 1 ‘‘Encouragement of Young Phd students investigation’’ Project Mapping-UCI (Ref F661), by the IDEAI-UPC Consolidated Research Group Grant from Catalan Agency of University and Research Grants (AGAUR, Generalitat de Catalunya) (2017 SGR 574) and by the Secretariat for Universities and Research of the Ministry of Research and Universities of the Government of Catalonia and the European Social Fund (2021 FI-B 00965).Peer ReviewedPostprint (published version

ICU Patients’ Pattern Recognition and Correlation Identification of Vital Parameters Using Optimized Machine Learning Models

Early detection of patient deterioration in the Intensive Care Unit (ICU) can play a crucial role in improving patient outcomes. Conventional severity scales currently used to predict patient deterioration are based on a number of factors, the majority of which consist of multiple investigations. Recent advancements in machine learning (ML) within the healthcare domain offer the potential to alleviate the burden of continuous patient monitoring. In this study, we propose an optimized ML model designed to leverage variations in vital signs observed during the final 24 hours of an ICU stay for outcome predictions. Further, we elucidate the relative contributions of distinct vital parameters to these outcomes The dataset compiled in real-time encompasses six pivotal vital parameters: systolic (0) and diastolic (1) blood pressure, pulse rate (2), respiratory rate (3), oxygen saturation (SpO2) (4), and temperature (5). Of these vital parameters, systolic blood pressure emerges as the most significant predictor associated with mortality prediction. Using a fivefold cross-validation method, several ML classifiers are used to categorize the last 24 hours of time series data after ICU admission into three groups: recovery, death, and intubation. Notably, the optimized Gradient Boosting classifier exhibited the highest performance in detecting mortality, achieving an area under the receiver-operator curve (AUC) of 0.95. Through the integration of electronic health records with this ML software, there is the promise of early notifications regarding adverse outcomes, potentially several hours before the onset of hemodynamic instability

On the Use of Time Series Kernel and Dimensionality Reduction to Identify the Acquisition of Antimicrobial Multidrug Resistance in the Intensive Care Unit

Presentation at the 2021 KDD Workshop on Applied Data Science for Healthcare, 15.08.21 - 16.08.21. https://dshealthkdd.github.io/dshealth-2021/The acquisition of Antimicrobial Multidrug Resistance (AMR) in patients admitted to the Intensive Care Units (ICU) is a major global concern. This study analyses data in the form of multivariate time series (MTS) from 3476 patients recorded at the ICU of University Hospital of Fuenlabrada (Madrid) from 2004 to 2020. 18% of the patients acquired AMR during their stay in the ICU. The goal of this paper is an early prediction of the development of AMR. Towards that end, we leverage the time-series cluster kernel (TCK) to learn similarities between MTS. To evaluate the effectiveness of TCK as a kernel, we applied several dimensionality reduction techniques for visualization and classification tasks. The experimental results show that TCK allows identifying a group of patients that acquire the AMR during the first 48 hours of their ICU stay, and it also provides good classification capabilities

Towards developing a reliable medical device for automated epileptic seizure detection in the ICU

Abstract. Epilepsy is a prevalent neurological disorder that affects millions of people globally, and its diagnosis typically involves laborious manual inspection of electroencephalography (EEG) data. Automated detection of epileptic seizures in EEG signals could potentially improve diagnostic accuracy and reduce diagnosis time, but there should be special attention to the number of false alarms to reduce unnecessary treatments and costs. This research presents a study on the use of machine learning techniques for EEG seizure detection with the aim of investigating the effectiveness of different algorithms in terms of high sensitivity and low false alarm rates for feature extraction, selection, pre-processing, classification, and post-processing in designing a medical device for detecting seizure activity in EEG data. The current state-of-the-art methods which are validated clinically using large amounts of data are introduced. The study focuses on finding potential machine learning methods, considering KNN, SVM, decision trees and, Random forests, and compares their performance on the task of seizure detection using features introduced in the literature. Also using ensemble methods namely, bootstrapping and majority voting techniques we achieved a sensitivity of 0.80 and FAR/h of 2.10, accuracy of 97.1% and specificity of 98.2%. Overall, the findings of this study can be useful for developing more accurate and efficient algorithms for EEG seizure detection medical device, which can contribute to the early diagnosis and treatment of epilepsy in the intensive care unit for critically ill patients

Antimicrobial Resistance Prediction in Intensive Care Unit for Pseudomonas Aeruginosa using Temporal Data-Driven Models

One threatening medical problem for human beings is the increasing antimicrobial resistance of some microorganisms. This problem is especially difficult in Intensive Care Units (ICUs) of hospitals due to the vulnerable state of patients. Knowing in advance whether a concrete bacterium is resistant or susceptible to an antibiotic is a crux step for clinicians to determine an effective antibiotic treatment. This usual clinical procedure takes approximately 48 hours and it is named antibiogram. It tests the bacterium resistance to one or more antimicrobial families (six of them considered in this work). This article focuses on cultures of the Pseudomonas Aeruginosa bacterium because is one of the most dangerous in the ICU. Several temporal data-driven models are proposed and analyzed to predict the resistance or susceptibility to a determined antibiotic family previously to know the antibiogram result and only using the available past information from a data set. This data set is formed by anonymized electronic health records data from more than 3300 ICU patients during 15 years. Several data-driven classifier methods are used in combination with several temporal modeling approaches. The results show that our predictions are reasonably accurate for some antimicrobial families, and could be used by clinicians to determine the best antibiotic therapy in advance. This early prediction can save valuable time to start the adequate treatment for an ICU patient. This study corroborates the results of a previous work pointing that the antimicrobial resistance of bacteria in the ICU is related to other recent resistance tests of ICU patients. This information is very valuable for making accurate antimicrobial resistance predictions