Predicting sepsis onset using a machine learned causal probabilistic network algorithm based on electronic health records data

Advancing sepsis diagnosis and immunotherapy machine learning-driven identification of stable molecular biomarkers and therapeutic targets

Sepsis represents a significant global health challenge, necessitating early detection and effective treatment for improved outcomes. While traditional inflammatory markers facilitate the diagnosis of sepsis, the aspect of immune suppression remains poorly addressed. This study aimed to identify critical immune-related genes (IIRGs) associated with sepsis through genomic analysis and machine learning techniques, thereby enhancing diagnostic and treatment response predictions. Analyses of two extensive datasets were conducted, identifying significant immune genes using the ESTIMATE algorithm, Weighted Gene Correlation Network Analysis (WGCNA), and five machine learning methods. Prediction models were constructed and validated using six machine learning algorithms, achieving high accuracy (AUC > 0.75). Eleven key IIRGs were identified as active in immune pathways, such as the JAK-STAT signaling pathway, and were significantly correlated with immune cell infiltration in sepsis. Additionally, drug sensitivity analysis indicated that IIRGs correlated with responses to anticancer drugs. These results underscore the potential of these genes in enhancing sepsis diagnosis and treatment, highlighting the imperative for further validation across diverse populations.

EMR-LIP: A lightweight framework for standardizing the preprocessing of longitudinal irregular data in electronic medical records

OBJECTIVE

Longitudinal data from Electronic Medical Records (EMRs) are increasingly utilized to construct predictive models for various clinical tasks, offering enhanced insights into patient health. However, significant discrepancies exist in preprocessing the irregular and intricate EMR data across studies due to the absence of universally accepted tools and standardization methods. This study introduces the Electronic Medical Record Longitudinal Irregular Data Preprocessing (EMR-LIP) framework, a lightweight approach for optimizing the preprocessing of longitudinal, irregular EMR data, aiming to enhance research efficiency, consistency, reproducibility, and comparability.

MATERIALS AND METHODS

EMR-LIP modularizes the preprocessing of longitudinal irregular EMR data, offering tools with a low level of encapsulation. Compared to other pipelines, EMR-LIP categorizes variables in a more granular manner, designing specific preprocessing techniques for each type. To demonstrate its versatility, EMR-LIP was applied in an empirical study to two public EMR databases, MIMIC-IV and eICU-CRD. Data processed with EMR-LIP was then used to test several renowned deep learning models on a range of commonly used benchmark tasks.

RESULTS

In both the MIMIC-IV and eICU-CRD databases, models based on EMR-LIP showed superior baseline performance compared to previous studies. Interestingly, using data preprocessed by EMR-LIP, traditional models such as LSTM and GRU outperformed more complex models, achieving an AUROC of up to 0.94 for in-hospital death prediction. Additionally, models based on EMR-LIP showed stable performance across various resampling intervals and exhibited better fairness in performance across different ethnic groups.

CONCLUSION

EMR-LIP streamlines the preprocessing of irregular longitudinal EMR data, offering an end-to-end solution for model-ready data creation, and has been open-sourced for collaborative refinement by the research community.

Advances in diagnosis and prognosis of bacteraemia, bloodstream infection, and sepsis using machine learning: A comprehensive living literature review

BACKGROUND

Blood-related infections are a significant concern in healthcare. They can lead to serious medical complications and even death if not promptly diagnosed and treated. Throughout time, medical research has sought to identify clinical factors and strategies to improve the management of these conditions. The increasing adoption of electronic health records has led to a wealth of electronically available medical information and predictive models have emerged as invaluable tools. This manuscript offers a detailed survey of machine-learning techniques used for the diagnosis and prognosis of bacteraemia, bloodstream infections, and sepsis shedding light on their efficacy, potential limitations, and the intricacies of their integration into clinical practice.

METHODS

This study presents a comprehensive analysis derived from a thorough search across prominent databases, namely EMBASE, Google Scholar, PubMed, Scopus, and Web of Science, spanning from their inception dates to October 25, 2023. Eligibility assessment was conducted independently by investigators, with inclusion criteria encompassing peer-reviewed articles and pertinent non-peer-reviewed literature. Clinical and technical data were meticulously extracted and integrated into a registry, facilitating a holistic examination of the subject matter. To maintain currency and comprehensiveness, readers are encouraged to contribute manuscript suggestions and/or reports for integration into this living registry.

RESULTS

While machine learning (ML) models exhibit promise in advanced disease stages such as sepsis, early stages remain underexplored due to data limitations. Biochemical markers emerge as pivotal predictors during early stages such as bacteraemia, or bloodstream infections, while vital signs assume significance in sepsis prognosis. Integrating temporal trend information into conventional machine learning models appears to enhance performance. Unfortunately, sequential deep learning models face challenges, showing minimal performance improvements and significant drops in external datasets, potentially due to learning missing patterns within the scarce data available rather than understanding disease dynamics. Real-life implementation receives limited attention, as meeting design requirements proves challenging within existing healthcare infrastructure. The data collected in an event-based fashion during clinical practice is insufficient to fully harness the potential of these data-hungry models. Despite limitations, opportunities abound in leveraging flexible models and exploiting real-time non-invasive data collection technologies such as wearable devices or microneedles. Addressing research gaps in early disease stages, harnessing patient history data often underused, and embracing continual diagnostics beyond treatment initiation are crucial for improving healthcare decision-making support and adoption across the entire management pathway.

CONCLUSIONS

This comprehensive survey illuminates the landscape of ML applications in blood-related infection management, offering insights for future research and clinical practice. Implementing clinical ML-based clinical decision support systems requires balancing research with practical considerations. Current methodologies often lead to complex models lacking transparency and practical validation. Integration into healthcare systems faces regulatory, privacy, and trust challenges. Clear presentations and adherence to standards are essential to boost confidence in machine learning models for real-world healthcare applications.

Expanding the diagnostic toolbox for complex genetic immune disorders

Laboratory-based immunology evaluation is essential to the diagnostic workup of patients with complex immune disorders, and is as essential, if not more so, depending on the context, as genetic testing, because it enables identification of aberrant pathways amenable to therapeutic intervention and clarifies variants of uncertain significance. There have been considerable advances in techniques and instrumentation in the clinical laboratory in the past 2 decades, although there are still "miles to go." One of the goals of the clinical laboratory is to ensure advanced diagnostic testing is widely accessible to physicians and thus patients, through reference laboratories, particularly in the context of academic medical centers. This ensures a greater likelihood of translating research discoveries into the diagnostic laboratory, on the basis of patient care needs rather than a sole emphasis on commercial utility. However, these advances are under threat from burdensome regulatory oversight that can compromise, at best, and curtail, at worst, the ability to rapidly diagnose rare immune disorders and ensure delivery of precision medicine. This review discusses the clinical utility of diagnostic immunology tools, beyond cellular immunophenotyping of lymphocyte subsets, which can be used in conjunction with clinical and other laboratory data for diagnosis as well as monitoring of therapeutic response in patients with genetic immunologic diseases.

Harnessing artificial intelligence in sepsis care: advances in early detection, personalized treatment, and real-time monitoring

Sepsis remains a leading cause of morbidity and mortality worldwide due to its rapid progression and heterogeneous nature. This review explores the potential of Artificial Intelligence (AI) to transform sepsis management, from early detection to personalized treatment and real-time monitoring. AI, particularly through machine learning (ML) techniques such as random forest models and deep learning algorithms, has shown promise in analyzing electronic health record (EHR) data to identify patterns that enable early sepsis detection. For instance, random forest models have demonstrated high accuracy in predicting sepsis onset in intensive care unit (ICU) patients, while deep learning approaches have been applied to recognize complications such as sepsis-associated acute respiratory distress syndrome (ARDS). Personalized treatment plans developed through AI algorithms predict patient-specific responses to therapies, optimizing therapeutic efficacy and minimizing adverse effects. AI-driven continuous monitoring systems, including wearable devices, provide real-time predictions of sepsis-related complications, enabling timely interventions. Beyond these advancements, AI enhances diagnostic accuracy, predicts long-term outcomes, and supports dynamic risk assessment in clinical settings. However, ethical challenges, including data privacy concerns and algorithmic biases, must be addressed to ensure fair and effective implementation. The significance of this review lies in addressing the current limitations in sepsis management and highlighting how AI can overcome these hurdles. By leveraging AI, healthcare providers can significantly enhance diagnostic accuracy, optimize treatment protocols, and improve overall patient outcomes. Future research should focus on refining AI algorithms with diverse datasets, integrating emerging technologies, and fostering interdisciplinary collaboration to address these challenges and realize AI's transformative potential in sepsis care.

Artificial Intelligence in Sepsis Management: An Overview for Clinicians

Sepsis is one of the leading causes of mortality in hospital settings, and early diagnosis is a crucial challenge to improve clinical outcomes. Artificial intelligence (AI) is emerging as a valuable resource to address this challenge, with numerous investigations exploring its application to predict and diagnose sepsis early, as well as personalizing its treatment. Machine learning (ML) models are able to use clinical data collected from hospital Electronic Health Records or continuous monitoring to predict patients at risk of sepsis hours before the onset of symptoms. Background/Objectives: Over the past few decades, ML and other AI tools have been explored extensively in sepsis, with models developed for the early detection, diagnosis, prognosis, and even real-time management of treatment strategies. Methods: This review was conducted according to the SPIDER (Sample, Phenomenon of Interest, Design, Evaluation, Research Type) framework to define the study methodology. A critical overview of each paper was conducted by three different reviewers, selecting those that provided original and comprehensive data relevant to the specific topic of the review and contributed significantly to the conceptual or practical framework discussed, without dwelling on technical aspects of the models used. Results: A total of 194 articles were found; 28 were selected. Articles were categorized and analyzed based on their focus-early prediction, diagnosis, mortality or improvement in the treatment of sepsis. The scientific literature presents mixed outcomes; while some studies demonstrate improvements in mortality rates and clinical management, others highlight challenges, such as a high incidence of false positives and the lack of external validation. This review is designed for clinicians and healthcare professionals, and aims to provide an overview of the application of AI in sepsis management, reviewing the main studies and methodologies used to assess its effectiveness, limitations, and future potential.

Early detection of sepsis using machine learning algorithms: a systematic review and network meta-analysis

Background

With machine learning (ML) carving a niche in diverse medical disciplines, its role in sepsis prediction, a condition where the 'golden hour' is critical, is of paramount interest. This study assesses the factors influencing the efficacy of ML models in sepsis prediction, aiming to optimize their use in clinical practice.

Methods

We searched Medline, PubMed, Google Scholar, and CENTRAL for studies published from inception to October 2023. We focused on studies predicting sepsis in real-time settings in adult patients in any hospital settings without language limits. The primary outcome was area under the curve (AUC) of the receiver operating characteristic. This meta-analysis was conducted according to PRISMA-NMA guidelines and Cochrane Handbook recommendations. A Network Meta-Analysis using the CINeMA approach compared ML models against traditional scoring systems, with meta-regression identifying factors affecting model quality.

Results

From 3,953 studies, 73 articles encompassing 457,932 septic patients and 256 models were analyzed. The pooled AUC for ML models was 0.825 and it significantly outperformed traditional scoring systems. Neural Network and Decision Tree models demonstrated the highest AUC metrics. Significant factors influencing AUC included ML model type, dataset type, and prediction window.

Conclusion

This study establishes the superiority of ML models, especially Neural Network and Decision Tree types, in sepsis prediction. It highlights the importance of model type and dataset characteristics for prediction accuracy, emphasizing the necessity for standardized reporting and validation in ML healthcare applications. These findings call for broader clinical implementation to evaluate the effectiveness of these models in diverse patient groups.

Systematic review registration

https://inplasy.com/inplasy-2023-12-0062/, identifier, INPLASY2023120062.

Artificial intelligence and prescription of antibiotic therapy: present and future

INTRODUCTION

In the past few years, the use of artificial intelligence in healthcare has grown exponentially. Prescription of antibiotics is not exempt from its rapid diffusion, and various machine learning (ML) techniques, from logistic regression to deep neural networks and large language models, have been explored in the literature to support decisions regarding antibiotic prescription.

AREAS COVERED

In this narrative review, we discuss promises and challenges of the application of ML-based clinical decision support systems (ML-CDSSs) for antibiotic prescription. A search was conducted in PubMed up to April 2024.

EXPERT OPINION

Prescribing antibiotics is a complex process involving various dynamic phases. In each of these phases, the support of ML-CDSSs has shown the potential, and also the actual ability in some studies, to favorably impacting relevant clinical outcomes. Nonetheless, before widely exploiting this massive potential, there are still crucial challenges ahead that are being intensively investigated, pertaining to the transparency of training data, the definition of the sufficient degree of prediction explanations when predictions are obtained through black box models, and the legal and ethical framework for decision responsibility whenever an antibiotic prescription is supported by ML-CDSSs.

Early Warning Systems for Critical Illness Outside the Intensive Care Unit

Early warning systems (EWSs) are designed and deployed to create a rapid assessment and response for patients with clinical deterioration outside the intensive care unit (ICU). These models incorporate patient-level data such as vital signs and laboratory values to detect or prevent adverse clinical events, such as vital signs and laboratories to allow detection and prevention of adverse clinical events such as cardiac arrest, intensive care transfer, or sepsis. The applicability, development, clinical utility, and general perception of EWS in clinical practice vary widely. Here, we review the field as it has grown from early vital sign-based scoring systems to contemporary multidimensional algorithms and predictive technologies for clinical decompensation outside the ICU.

[Data-driven intensive care: a lack of comprehensive datasets]

Intensive care units provide a data-rich environment with the potential to generate datasets in the realm of big data, which could be utilized to train powerful machine learning (ML) models. However, the currently available datasets are too small and exhibit too little diversity due to their limitation to individual hospitals. This lack of extensive and varied datasets is a primary reason for the limited generalizability and resulting low clinical utility of current ML models. Often, these models are based on data from single centers and suffer from poor external validity. There is an urgent need for the development of large-scale, multicentric, and multinational datasets. Ensuring data protection and minimizing re-identification risks pose central challenges in this process. The "Amsterdam University Medical Center database (AmsterdamUMCdb)" and the "Salzburg Intensive Care database (SICdb)" demonstrate that open access datasets are possible in Europe while complying with the data protection regulations of the General Data Protection Regulation (GDPR). Another challenge in building intensive care datasets is the absence of semantic definitions in the source data and the heterogeneity of data formats. Establishing binding industry standards for the semantic definition is crucial to ensure seamless semantic interoperability between datasets.

Predicting sepsis in-hospital mortality with machine learning: a multi-center study using clinical and inflammatory biomarkers

BACKGROUND

This study aimed to develop and validate an interpretable machine-learning model that utilizes clinical features and inflammatory biomarkers to predict the risk of in-hospital mortality in critically ill patients suffering from sepsis.

METHODS

We enrolled all patients diagnosed with sepsis in the Medical Information Mart for Intensive Care IV (MIMIC-IV, v.2.0), eICU Collaborative Research Care (eICU-CRD 2.0), and the Amsterdam University Medical Centers databases (AmsterdamUMCdb 1.0.2). LASSO regression was employed for feature selection. Seven machine-learning methods were applied to develop prognostic models. The optimal model was chosen based on its accuracy, F1 score and area under curve (AUC) in the validation cohort. Moreover, we utilized the SHapley Additive exPlanations (SHAP) method to elucidate the effects of the features attributed to the model and analyze how individual features affect the model's output. Finally, Spearman correlation analysis examined the associations among continuous predictor variables. Restricted cubic splines (RCS) explored potential non-linear relationships between continuous risk factors and in-hospital mortality.

RESULTS

3535 patients with sepsis were eligible for participation in this study. The median age of the participants was 66 years (IQR, 55-77 years), and 56% were male. After selection, 12 of the 45 clinical parameters collected on the first day after ICU admission remained associated with prognosis and were used to develop machine-learning models. Among seven constructed models, the eXtreme Gradient Boosting (XGBoost) model achieved the best performance, with an AUC of 0.94 and an F1 score of 0.937 in the validation cohort. Feature importance analysis revealed that Age, AST, invasive ventilation treatment, and serum urea nitrogen (BUN) were the top four features of the XGBoost model with the most significant impact. Inflammatory biomarkers may have prognostic value. Furthermore, SHAP force analysis illustrated how the constructed model visualized the prediction of the model.

CONCLUSIONS

This study demonstrated the potential of machine-learning approaches for early prediction of outcomes in patients with sepsis. The SHAP method could improve the interoperability of machine-learning models and help clinicians better understand the reasoning behind the outcome.

Analysis of prognostic factors in patients with emergency sepsis

BACKGROUND

Emergency sepsis is a common and serious infectious disease, and its prognosis is influenced by a number of factors.

AIM

To analyse the factors influencing the prognosis of patients with emergency sepsis in order to provide a basis for individualised patient treatment and care. By retrospectively analysing the clinical data collected, we conducted a comprehensive analysis of factors such as age, gender, underlying disease, etiology and site of infection, inflammatory indicators, multi-organ failure, cardiovascular function, therapeutic measures, immune status and severity of infection.

METHODS

Data collection: Clinical data were collected from patients diagnosed with acute sepsis, including basic information, laboratory findings, medical history and treatment options. Variable selection: Variables associated with prognosis were selected, including age, gender, underlying disease, etiology and site of infection, inflammatory indicators, multi-organ failure, cardiovascular function, treatment measures, immune status and severity of infection. Data analysis: The data collected are analysed using appropriate statistical methods such as multiple regression analysis and survival analysis. The impact of each factor on prognosis was assessed according to prognostic indicators, such as survival, length of stay and complication rates.

RESULTS

Descriptive statistics: Descriptive statistics were performed on the data collected from the patients, including their basic characteristics and clinical presentation.

CONCLUSION

Type 2 diabetes mellitus were independent factors affecting the prognosis of patients with sepsis.