Overcoming the Barriers That Obscure the Interlinking and Analysis of Clinical Data Through Harmonization and Incremental Learning

A "smart" Imputation Approach for Effective Quality Control Across Complex Clinical Data Structures

The overwhelming need to improve the quality of complex data structures in healthcare is more important than ever. Although data quality has been the point of interest in many studies, none of them has focused on the development of quantitative and explainable methods for data imputation. In this work, we propose a "smart" imputation workflow to address missing data across complex data structures in the context of in silico clinical trials. AI algorithms were utilized to produce high-quality virtual patient profiles. A search algorithm was then developed to extract the best virtual patient profiles through the definition of a profile matching score (PMS). A case study was conducted, where the real dataset was randomly contaminated with multiple missing values (e.g., 10 to 50%). In total, 10000 virtual patient profiles with less than 0.02 Kullback-Leibler (KL) divergence were produced to estimate the PMS distribution. The best generator achieved the lowest average squared absolute difference (0.4) and average correlation difference (0.02) with the real dataset highlighting its increased effectiveness for data imputation across complex clinical data structures.

Federated Learning for Healthcare: Systematic Review and Architecture Proposal

The use of machine learning (ML) with electronic health records (EHR) is growing in popularity as a means to extract knowledge that can improve the decision-making process in healthcare. Such methods require training of high-quality learning models based on diverse and comprehensive datasets, which are hard to obtain due to the sensitive nature of medical data from patients. In this context, federated learning (FL) is a methodology that enables the distributed training of machine learning models with remotely hosted datasets without the need to accumulate data and, therefore, compromise it. FL is a promising solution to improve ML-based systems, better aligning them to regulatory requirements, improving trustworthiness and data sovereignty. However, many open questions must be addressed before the use of FL becomes widespread. This article aims at presenting a systematic literature review on current research about FL in the context of EHR data for healthcare applications. Our analysis highlights the main research topics, proposed solutions, case studies, and respective ML methods. Furthermore, the article discusses a general architecture for FL applied to healthcare data based on the main insights obtained from the literature review. The collected literature corpus indicates that there is extensive research on the privacy and confidentiality aspects of training data and model sharing, which is expected given the sensitive nature of medical data. Studies also explore improvements to the aggregation mechanisms required to generate the learning model from distributed contributions and case studies with different types of medical data.

ICU admission and mortality classifiers for COVID-19 patients based on subgroups of dynamically associated profiles across multiple timepoints

The coronavirus disease 2019 (COVID-19) which is caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is consistently causing profound wounds in the global healthcare system due to its increased transmissibility. Currently, there is an urgent unmet need to identify the underlying dynamic associations among COVID-19 patients and distinguish patient subgroups with common clinical profiles towards the development of robust classifiers for ICU admission and mortality. To address this need, we propose a four step pipeline which: (i) enhances the quality of multiple timeseries clinical data through an automated data curation workflow, (ii) deploys Dynamic Bayesian Networks (DBNs) for the detection of features with increased connectivity based on dynamic association analysis across multiple points, (iii) utilizes Self Organizing Maps (SOMs) and trajectory analysis for the early identification of COVID-19 patients with common clinical profiles, and (iv) trains robust multiple additive regression trees (MART) for ICU admission and mortality classification based on the extracted homogeneous clusters, to identify risk factors and biomarkers for disease progression. The contribution of the extracted clusters and the dynamically associated clinical data improved the classification performance for ICU admission to sensitivity 0.83 and specificity 0.83, and for mortality to sensitivity 0.74 and specificity 0.76. Additional information was included to enhance the performance of the classifiers yielding an increase by 4% in sensitivity and specificity for mortality. According to the risk factor analysis, the number of lymphocytes, SatO2, PO2/FiO2, and O2 supply type were highlighted as risk factors for ICU admission and the percentage of neutrophils and lymphocytes, PO2/FiO2, LDH, and ALP for mortality, among others. To our knowledge, this is the first study that combines dynamic modeling with clustering analysis to identify homogeneous groups of COVID-19 patients towards the development of robust classifiers for ICU admission and mortality.

A federated AI strategy for the classification of patients with Mucosa Associated Lymphoma Tissue (MALT) lymphoma across multiple harmonized cohorts

Mucosa Associated Lymphoma Tissue (MALT) type is an extremely rare type of lymphoma which occurs in less than 3% of patients with primary Sjögren's Syndrome (pSS). No reported studies so far have been able to investigate risk factors for MALT development across multiple cohort databases with sufficient statistical power. Here, we present a generalized, federated AI (artificial intelligence) strategy which enables the training of AI algorithms across multiple harmonized databases. A case study is conducted towards the development of MALT classification models across 17 databases on pSS. Advanced AI algorithms were developed, including federated Multinomial Naïve Bayes (FMNB), federated gradient boosting trees (FGBT), FGBT with dropouts (FDART), and the federated Multilayer Perceptron (FMLP). The FDART with dropout rate 0.3 achieved the best performance with sensitivity 0.812, and specificity 0.829, yielding 8 biomarkers as prominent for MALT development.

A computational pipeline for data augmentation towards the improvement of disease classification and risk stratification models: A case study in two clinical domains

Virtual population generation is an emerging field in data science with numerous applications in healthcare towards the augmentation of clinical research databases with significant lack of population size. However, the impact of data augmentation on the development of AI (artificial intelligence) models to address clinical unmet needs has not yet been investigated. In this work, we assess whether the aggregation of real with virtual patient data can improve the performance of the existing risk stratification and disease classification models in two rare clinical domains, namely the primary Sjögren's Syndrome (pSS) and the hypertrophic cardiomyopathy (HCM), for the first time in the literature. To do so, multivariate approaches, such as, the multivariate normal distribution (MVND), and straightforward ones, such as, the Bayesian networks, the artificial neural networks (ANNs), and the tree ensembles are compared against their performance towards the generation of high-quality virtual data. Both boosting and bagging algorithms, such as, the Gradient boosting trees (XGBoost), the AdaBoost and the Random Forests (RFs) were trained on the augmented data to evaluate the performance improvement for lymphoma classification and HCM risk stratification. Our results revealed the favorable performance of the tree ensemble generators, in both domains, yielding virtual data with goodness-of-fit 0.021 and KL-divergence 0.029 in pSS and 0.029, 0.027 in HCM, respectively. The application of the XGBoost on the augmented data revealed an increase by 10.9% in accuracy, 10.7% in sensitivity, 11.5% in specificity for lymphoma classification and 16.1% in accuracy, 16.9% in sensitivity, 13.7% in specificity in HCM risk stratification.