On the intelligent management of sepsis in the intensive care unit

The management of the Intensive Care Unit (ICU) in a hospital has its own, very specific requirements that involve, amongst others, issues of risk-adjusted mortality and average length of stay; nurse turnover and communication with physicians; technical quality of care; the ability to meet patient's family needs; and avoid medical error due rapidly changing circumstances and work overload. In the end, good ICU management should lead to an improvement in patient outcomes. Decision making at the ICU environment is a real-time challenge that works according to very tight guidelines, which relate to often complex and sensitive research ethics issues. Clinicians in this context must act upon as much available information as possible, and could therefore, in general, benefit from at least partially automated computer-based decision support based on qualitative and quantitative information. Those taking executive decisions at ICUs will require methods that are not only reliable, but also, and this is a key issue, readily interpretable. Otherwise, any decision tool, regardless its sophistication and accuracy, risks being rendered useless. This thesis addresses this through the design and development of computer based decision making tools to assist clinicians at the ICU. It focuses on one of the main problems that they must face: the management of the Sepsis pathology. Sepsis is one of the main causes of death for non-coronary ICU patients. Its mortality rate can reach almost up to one out of two patients for septic shock, its most acute manifestation. It is a transversal condition affecting people of all ages. Surprisingly, its definition has only been standardized two decades ago as a systemic inflammatory response syndrome with confirmed infection. The research reported in this document deals with the problem of Sepsis data analysis in general and, more specifically, with the problem of survival prediction for patients affected with Severe Sepsis. The tools at the core of the investigated data analysis procedures stem from the fields of multivariate and algebraic statistics, algebraic geometry, machine learning and computational intelligence. Beyond data analysis itself, the current thesis makes contributions from a clinical point of view, as it provides substantial evidence to the debate about the impact of the preadmission use of statin drugs in the ICU outcome. It also sheds light into the dependence between Septic Shock and Multi Organic Dysfunction Syndrome. Moreover, it defines a latent set of Sepsis descriptors to be used as prognostic factors for the prediction of mortality and achieves an improvement on predictive capability over indicators currently in use.La gestió d'una Unitat de Cures Intensives (UCI) hospitalària presenta uns requisits força específics incloent, entre altres, la disminució de la taxa de mortalitat, la durada de l'ingrès, la rotació d'infermeres i la comunicació entre metges amb al finalitad de donar una atenció de qualitat atenent als requisits tant dels malalts com dels familiars. També és força important controlar i minimitzar els error mèdics deguts a canvis sobtats i a la presa ràpida de deicisions assistencials. Al cap i a la fi, la bona gestió de la UCI hauria de resultar en una reducció de la mortalitat i durada d'estada. La presa de decisions en un entorn de crítics suposa un repte de presa de decisions en temps real d'acord a unes guies clíniques molt restrictives i que, pel que fa a la recerca, poden resultar en problemes ètics força sensibles i complexos. Per tant, el personal sanitari que ha de prendre decisions sobre la gestió de malalts crítics no només requereix eines de suport a la decisió que siguin fiables sinó que, a més a més, han de ser interpretables. Altrament qualsevol eina de decisió que no presenti aquests trets no és considerarà d'utilitat clínica. Aquesta tesi doctoral adreça aquests requisits mitjançant el desenvolupament d'eines de suport a la decisió per als intensivistes i es focalitza en un dels principals problemes als que s'han denfrontar: el maneig del malalt sèptic. La Sèpsia és una de les principals causes de mortalitats a les UCIS no-coronàries i la seva taxa de mortalitat pot arribar fins a la meitat dels malalts amb xoc sèptic, la seva manifestació més severa. La Sèpsia és un síndrome transversal, que afecta a persones de totes les edats. Sorprenentment, la seva definició ha estat estandaritzada, fa només vint anys, com a la resposta inflamatòria sistèmica a una infecció corfimada. La recerca presentada en aquest document fa referència a l'anàlisi de dades de la Sèpsia en general i, de forma més específica, al problema de la predicció de la supervivència de malalts afectats amb Sèpsia Greu. Les eines i mètodes que formen la clau de bòveda d'aquest treball provenen de diversos camps com l'estadística multivariant i algebràica, geometria algebraica, aprenentatge automàtic i inteligència computacional. Més enllà de l'anàlisi per-se, aquesta tesi també presenta una contribució des de el punt de vista clínic atès que presenta evidència substancial en el debat sobre l'impacte de l'administració d'estatines previ a l'ingrès a la UCI en els malalts sèptics. També s'aclareix la forta dependència entre el xoc sèptic i el Síndrome de Disfunció Multiorgànica. Finalment, també es defineix un conjunt de descriptors latents de la Sèpsia com a factors de pronòstic per a la predicció de la mortalitat, que millora sobre els mètodes actualment més utilitzats en la UCI

Blood pressure assessment with differential pulse transit time and deep learning: a proof of concept

Modern clinical environments are laden with technology devices continuously gathering physiological data from patients. This is especially true in critical care environments, where life-saving decisions may have to be made on the basis of signals from monitoring devices. Hemodynamic monitoring is essential in dialysis, surgery, and in critically ill patients. For the most severe patients, blood pressure is normally assessed through a catheter, which is an invasive procedure that may result in adverse effects. Blood pressure can also be monitored noninvasively through different methods and these data can be used for the continuous assessment of pressure using machine learning methods. Previous studies have found pulse transit time to be related to blood pressure. In this short paper, we propose to study the feasibility of implementing a data-driven model based on restricted Boltzmann machine artificial neural networks, delivering a first proof of concept for the validity and viability of a method for blood pressure prediction based on these models.Peer ReviewedPostprint (author's final draft

Enabling interpretation of the outcome of a human obesity prediction machine learning analysis from genomic data

In this brief paper, we address the medical problem of human obesity prediction from genomic data. Genomic datasets may contain a huge number of features and they often have to be analyzed within the realm of Big Data technologies. As a medical problem, obesity prediction would welcome interpretables outcomes. Therefore, the analyst would benefit from appraches in which the problem of very high data dimensionality could be eased as much as possible. Feature selection can be an essential part of such approaches. In this context, though, traditional machine learning methods may struggle. Here, we propose a pipeline to address this problem using partitioning strategies: both vertical, by dividing the data based on gender, and horizontal, by splitting each of the analyzed chromosomes into 5,000-instances subsets. For each, Minimum Redundancy and Maximum Relevance feature selection is used to find rankings of the single nucleotide polymorphisms most relevant for classification in the medical dataset.Preprin

Assessment of electrocardiograms with pretraining and shallow networks

Objective: Clinical Decision Support Systems normally resort to annotated signals for the automatic assessment of ECG signals. In this paper we put forward a new method for the assessment of normal/abnormal heart function from raw ECG signals (i.e. signals without annotation) based on shallow neural networks with pretraining. Methodology: this paper resorts to a prospective clinical study that took place at Hospital Cll´inic in Barcelona, Spain. This study took place in 2010-2012 and recruited 1390 patients. For each patient we recorded a 12-lead ECG and diagnosis was conducted by the Cardiology service at the same hospital. Two datasets were produced, the first contained the automatically annotated version of all input signals and the second contained the raw signals obtained from the ECG. Results: The new method was tested through crossvalidation with a cohort of 200 test patients. Performance was compared for both annotated and raw datasets. For the annotated dataset and a shallow network with pretraining we obtained an accuracy of 0.8639, a sensitivity of 0.9560 and specificity of 0.7143. The raw dataset yielded an accuracy of 0.8426, a sensitivity of 0.8977 and a specificity of 0.7785. Conclusion: Shallow networks with pretraining automatically obtain a representation of the input data without resorting to any annotation and thus simplify the process of assessing normality of ECG signals. Despite the fact that sensitivity has decreased, accuracy is not much lower than that obtained with standard methods. Specificity is improved with the new method. These results open up a promising line of research for the automatic assessment of ECG signals.Peer ReviewedPostprint (published version

A Quotient Basis Kernel for the prediction of mortality in severe sepsis patients

In this paper, we describe a novel kernel for multinomial distributions, namely the Quotient Basis Kernel (QBK), which is based on a suitable reparametrization of the input space through algebraic geometry and statistics. The QBK is used here for data transformation prior to classification in a medical problem concerning the prediction of mortality in patients suffering severe sepsis. This is a common clinical syndrome, often treated at the Intensive Care Unit (ICU) in a time-critical context. Mortality prediction results with Support Vector Machines using QBK compare favorably with those obtained using alternative kernels and standard clinical procedures.Postprint (published version

Machine learning in critical care: state-of-the-art and a sepsis case study

Background: Like other scientific fields, such as cosmology, high-energy physics, or even the life sciences, medicine and healthcare face the challenge of an extremely quick transformation into data-driven sciences. This challenge entails the daunting task of extracting usable knowledge from these data using algorithmic methods. In the medical context this may for instance realized through the design of medical decision support systems for diagnosis, prognosis and patient management. The intensive care unit (ICU), and by extension the whole area of critical care, is becoming one of the most data-driven clinical environments. Results: The increasing availability of complex and heterogeneous data at the point of patient attention in critical care environments makes the development of fresh approaches to data analysis almost compulsory. Computational Intelligence (CI) and Machine Learning (ML) methods can provide such approaches and have already shown their usefulness in addressing problems in this context. The current study has a dual goal: it is first a review of the state-of-the-art on the use and application of such methods in the field of critical care. Such review is presented from the viewpoint of the different subfields of critical care, but also from the viewpoint of the different available ML and CI techniques. The second goal is presenting a collection of results that illustrate the breath of possibilities opened by ML and CI methods using a single problem, the investigation of septic shock at the ICU. Conclusion: We have presented a structured state-of-the-art that illustrates the broad-ranging ways in which ML and CI methods can make a difference in problems affecting the manifold areas of critical care. The potential of ML and CI has been illustrated in detail through an example concerning the sepsis pathology. The new definitions of sepsis and the relevance of using the systemic inflammatory response syndrome (SIRS) in its diagnosis have been considered. Conditional independence models have been used to address this problem, showing that SIRS depends on both organ dysfunction measured through the Sequential Organ Failure (SOFA) score and the ICU outcome, thus concluding that SIRS should still be considered in the study of the pathophysiology of Sepsis. Current assessment of the risk of dead at the ICU lacks specificity. ML and CI techniques are shown to improve the assessment using both indicators already in place and other clinical variables that are routinely measured. Kernel methods in particular are shown to provide the best performance balance while being amenable to representation through graphical models, which increases their interpretability and, with it, their likelihood to be accepted in medical practice.Peer ReviewedPostprint (published version

Pipeline design to identify key features and classify the chemotherapy response on lung cancer patients using large-scale genetic data

Background: During the last decade, the interest to apply machine learning algorithms to genomic data has increased in many bioinformatics applications. Analyzing this type of data entails difficulties for managing high-dimensional data, class imbalance for knowledge extraction, identifying important features and classifying individuals. In this study, we propose a general framework to tackle these challenges with different machine learning algorithms and techniques. We apply the configuration of this framework on lung cancer patients, identifying genetic signatures for classifying response to drug treatment response. We intersect these relevant SNPs with the GWAS Catalog of the National Human Genome Research Institute and explore the Regulomedb, GTEx databases for functional analysis purposes. Results: The machine learning based solution proposed in this study is a scalable and flexible alternative to the classical uni-variate regression approach to analyze large-scale data. From 36 experiments executed using the machine learning framework design, we obtain good classification performance from the top 5 models with the highest cross-validation score and the smallest standard deviation. One thousand two hundred twenty four SNPs corresponding to the key features from the top 20 models (cross validation F1 mean >= 0.65) were compared with the GWAS Catalog finding no intersection with genome-wide significant reported hits. From these, new genetic signatures in MAE, CEP104, PRKCZ and ADRB2 show relevant biological regulatory functionality related to lung physiology. Conclusions: We have defined a machine learning framework using data with an unbalanced large data-set of SNP-arrays and imputed genotyping data from a pharmacogenomics study in lung cancer patients subjected to first-line platinum-based treatment. This approach found genome signals with no genome-wide significance in the uni-variate regression approach (GWAS Catalog) that are valuable for classifying patients, only few of them with related biological function. The effect results of these variants can be explained by the recently proposed omnigenic model hypothesis, which states that complex traits can be influenced mostly by genes outside not only by the “core genes”, mainly found by the genome-wide significant SNPs, but also by the rest of genes outside of the “core pathways” with apparent unrelated biological functionality.Peer ReviewedPostprint (published version

Modelling the cardiovascular system for assessing the blood pressure curve

A four compartment model of the cardiovascular system is developed. To allow for easy interpretation and to minimise the number of parameters, an effort was made to keep the model as simple as possible. Using a standard method (Matlab function fminsearch) to calculate the parameter values led to unacceptable run times or non-convergence. Consequently we developed an algorithm which first finds the most important model parameters and uses these as a basis for a four stage process which accurately determines all parameter values. This process is then applied to data from three ICU patients. Good agreement between the model and measured arterial pressure is demonstrated in all cases

A Pilot Study for Metabolic Profiling of Obesity-Associated Microbial Gut Dysbiosis in Male Wistar Rats

Obesity is one of the most incident and concerning disease worldwide. Definite strategies to prevent obesity and related complications remain elusive. Among the risk factors of the onset of obesity, gut microbiota might play an important role in the pathogenesis of the disease, and it has received extensive attention because it affects the host metabolism. In this study, we aimed to define a metabolic profile of the segregated obesity-associated gut dysbiosis risk factor. The study of the metabolome, in an obesity-associated gut dysbiosis model, provides a relevant way for the discrimination on the different biomarkers in the obesity onset. Thus, we developed a model of this obesity risk factors through the transference of gut microbiota from obese to non-obese male Wistar rats and performed a subsequent metabolic analysis in the receptor rats. Our results showed alterations in the lipid metabolism in plasma and in the phenylalanine metabolism in urine. In consequence, we have identified metabolic changes characterized by: (1) an increase in DG:34:2 in plasma, a decrease in hippurate, (2) an increase in 3-HPPA, and (3) an increase in o-coumaric acid. Hereby, we propose these metabolites as a metabolic profile associated to a segregated dysbiosis state related to obesity disease

Big data analytics for obesity prediction

Feature selection (FS) is essential for the analysis of genomic datasets with millions of features. In such context, Big Data tools are paramount, but the use of standard machine learning models is limited for data with such low instances to features ratios. Apache Spark is a distributed in-memory big data system with the potential to overcome this bottleneck. This study analyzes genomic data related to prediction of human obesity. Since Apache Spark is unable to cope with our dataset containing ˜ 0.74 million features, we propose here a pipeline to solve this problem using partitioning strategies, both vertical, by dividing the data based on gender, and horizontal, by splitting each chromosome into 5,000-instances subsets. For each subset, Minimum Redundancy and Maximum Relevance FS was used to find rankings of the most relevant features. The challenge, thus, is making accurate obesity predictions with parsimonious subsets of features selected from millions of them. We tackle it by defining a 2-phase pipeline: first learning with individual chromosomes and then learning with joined 22 chromosomes from selected features.Peer Reviewe