Forecasting using non-linear techniques in time series analysis : an overview of techniques and main issues

The development of techniques in non linear time series analysis has emerged from its time series background and developed over the last few decades into a range of techniques which aim to fill a gap in the ability to model and forecast certain types of data sets such a chaotic determinate systems. These systems are found in many diverse areas of natural and human spheres. This study outlines the background within which these techniques developed, the fundamental elements on which they are based and details some of the predictive techniques. This study aims to provide some insight into their mechanisms and their potential.peer-reviewe

A method to detect and represent temporal patterns from time series data and its application for analysis of physiological data streams

In critical care, complex systems and sensors continuously monitor patients??? physiological features such as heart rate, respiratory rate thus generating significant amounts of data every second. This results to more than 2 million records generated per patient in an hour. It???s an immense challenge for anyone trying to utilize this data when making critical decisions about patient care. Temporal abstraction and data mining are two research fields that have tried to synthesize time oriented data to detect hidden relationships that may exist in the data. Various researchers have looked at techniques for generating abstractions from clinical data. However, the variety and speed of data streams generated often overwhelms current systems which are not designed to handle such data. Other attempts have been to understand the complexity in time series data utilizing mining techniques, however, existing models are not designed to detect temporal relationships that might exist in time series data (Inibhunu & McGregor, 2016). To address this challenge, this thesis has proposed a method that extends the existing knowledge discovery frameworks to include components for detecting and representing temporal relationships in time series data. The developed method is instantiated within the knowledge discovery component of Artemis, a cloud based platform for processing physiological data streams. This is a unique approach that utilizes pattern recognition principles to facilitate functions for; (a) temporal representation of time series data with abstractions, (b) temporal pattern generation and quantification (c) frequent patterns identification and (d) building a classification system. This method is applied to a neonatal intensive care case study with a motivating problem that discovery of specific patterns from patient data could be crucial for making improved decisions within patient care. Another application is in chronic care to detect temporal relationships in ambulatory patient data before occurrence of an adverse event. The research premise is that discovery of hidden relationships and patterns in data would be valuable in building a classification system that automatically characterize physiological data streams. Such characterization could aid in detection of new normal and abnormal behaviors in patients who may have life threatening conditions

Using conceptual graphs for clinical guidelines representation and knowledge visualization

The intrinsic complexity of the medical domain requires the building of some tools to assist the clinician and improve the patient’s health care. Clinical practice guidelines and protocols (CGPs) are documents with the aim of guiding decisions and criteria in specific areas of healthcare and they have been represented using several languages, but these are difficult to understand without a formal background. This paper uses conceptual graph formalism to represent CGPs. The originality here is the use of a graph-based approach in which reasoning is based on graph-theory operations to support sound logical reasoning in a visual manner. It allows users to have a maximal understanding and control over each step of the knowledge reasoning process in the CGPs exploitation. The application example concentrates on a protocol for the management of adult patients with hyperosmolar hyperglycemic state in the Intensive Care Unit

Deep Symbolic Learning Architecture for Variant Calling in NGS

[EN]The Variant Detection process (Variant Calling) is fundamental in bioinformatics, demanding maximum precision and reliability. This study examines an innovative integration strategy between a traditional pipeline developed in-house and an advanced Intelligent System (IS). Although the original pipeline already had tools based on traditional algorithms, it had limitations, particularly in the detection of rare or unknown variants. Therefore, SI was introduced with the aim of providing an additional layer of analysis, capitalizing on deep and symbolic learning techniques to improve and enhance previous detections. The main technical challenge lay in interoperability. To overcome this, NextFlow, a scripting language designed to manage complex bioinformatics workflows, was employed. Through NextFlow, communication and efficient data transfer between the original pipeline and the SI were facilitated, thus guaranteeing compatibility and reproducibility. After the Variant Calling process of the original system, the results were transmitted to the SI, where a meticulous sequence of analysis was implemented, from preprocessing to data fusion. As a result, an optimized set of variants was generated that was integrated with previous results. Variants corroborated by both tools were considered to be of high reliability, while discrepancies indicated areas for detailed investigations. The product of this integration advanced to subsequent stages of the pipeline, usually annotation or interpretation, contextualizing the variants from biological and clinical perspectives. This adaptation not only maintained the original functionalities of the pipeline, but was also enhanced with the SI, establishing a new standard in the Variant Calling process. This research offers a robust and efficient model for the detection and analysis of genomic variants, highlighting the promise and applicability of blended learning in bioinformaticsThis study has been funded by the AIR Genomics project (with file number CCTT3/20/SA/0003), through the call 2020 R&D PROJECTS ORIENTED TO THE EXCELLENCE AND COMPETITIVE IMPROVEMENT OF THE CCTT by the Institute of Business Competitiveness of Castilla y León and FEDER fund

Neurocognitive Informatics Manifesto.

Informatics studies all aspects of the structure of natural and artificial information systems. Theoretical and abstract approaches to information have made great advances, but human information processing is still unmatched in many areas, including information management, representation and understanding. Neurocognitive informatics is a new, emerging field that should help to improve the matching of artificial and natural systems, and inspire better computational algorithms to solve problems that are still beyond the reach of machines. In this position paper examples of neurocognitive inspirations and promising directions in this area are given

Conceptual graph-based knowledge representation for supporting reasoning in African traditional medicine

Although African patients use both conventional or modern and traditional healthcare simultaneously, it has been proven that 80% of people rely on African traditional medicine (ATM). ATM includes medical activities stemming from practices, customs and traditions which were integral to the distinctive African cultures. It is based mainly on the oral transfer of knowledge, with the risk of losing critical knowledge. Moreover, practices differ according to the regions and the availability of medicinal plants. Therefore, it is necessary to compile tacit, disseminated and complex knowledge from various Tradi-Practitioners (TP) in order to determine interesting patterns for treating a given disease. Knowledge engineering methods for traditional medicine are useful to model suitably complex information needs, formalize knowledge of domain experts and highlight the effective practices for their integration to conventional medicine. The work described in this paper presents an approach which addresses two issues. First it aims at proposing a formal representation model of ATM knowledge and practices to facilitate their sharing and reusing. Then, it aims at providing a visual reasoning mechanism for selecting best available procedures and medicinal plants to treat diseases. The approach is based on the use of the Delphi method for capturing knowledge from various experts which necessitate reaching a consensus. Conceptual graph formalism is used to model ATM knowledge with visual reasoning capabilities and processes. The nested conceptual graphs are used to visually express the semantic meaning of Computational Tree Logic (CTL) constructs that are useful for formal specification of temporal properties of ATM domain knowledge. Our approach presents the advantage of mitigating knowledge loss with conceptual development assistance to improve the quality of ATM care (medical diagnosis and therapeutics), but also patient safety (drug monitoring)

Dynamic Risk Models for Characterising Chronic Diseases' Behaviour Using Process Mining Techniques

[ES] Los modelos de riesgo en el ámbito de la salud son métodos estadísticos que brindan advertencias tempranas sobre el riesgo de una persona de sufrir un episodio adverso en el futuro. Por lo general, utilizan la información almacenada de forma rutinaria en los sistemas de información hospitalaria para ofrecer una probabilidad individual de desarrollar un resultado negativo futuro en un período determinado. Concretamente, en el campo de las enfermedades crónicas que comparten factores de riesgo comunes, los modelos de riesgo se basan en el análisis de esos factores de riesgo -tensión arterial elevada, glucemia elevada, lípidos sanguíneos anormales, sobrepeso y obesidad- y sus medidas biométricas asociadas. Estas medidas se recopilan durante la práctica clínica de manera periódica y, se incorporan a los modelos de riesgo para apoyar a los médicos en la toma de decisiones. Para crear modelos de riesgo que incluyan la variable temporal, se podrían utilizar técnicas basadas en datos (Data-Driven), de forma que se tuviera en cuenta el historial de los pacientes almacenado en los registros médicos electrónicos, extrayendo conocimiento de los datos en bruto. Sin embargo, en el ámbito de la salud, los resultados de la minería de datos suelen ser percibidos por los expertos en salud como cajas negras y, en consecuencia, no confían en sus decisiones. El paradigma Interactivo permite a los expertos comprender los resultados, para que los profesionales puedan corregir esos modelos de acuerdo con su conocimiento y experiencia, proporcionando modelos perceptivos y cognitivos. En este contexto, la minería de procesos es una técnica de minería de datos que permite la implementación del paradigma Interactivo, ofreciendo una comprensión clara del proceso de atención y proporcionando modelos comprensibles para el ser humano. Las condiciones crónicas generalmente se describen mediante imágenes estáticas de variables, como factores genéticos, fisiológicos, ambientales y de comportamiento. Sin embargo, la perspectiva dinámica, temporal y de comportamiento no se consideran comúnmente en los modelos de riesgo. Eso significa que el último estado de riesgo se convierte en el estado real del paciente. No obstante, la condición de los pacientes podría verse influenciada por sus condiciones dinámicas pasadas. El objetivo de esta tesis es proporcionar una visión novedosa del riesgo asociado a un paciente, basada en tecnologías Data-Driven que ofrezcan una visión dinámica de su evolución con respecto a su condición crónica. Técnicamente, supone abordar los modelos de riesgo incorporando la perspectiva dinámica y comportamental de los pacientes gracias a la información incluida en la Historia Clínica Electrónica. Los resultados obtenidos a lo largo de esta tesis muestran cómo las tecnologías de minería de procesos pueden aportar una visión dinámica e interactiva de los modelos de riesgo de enfermedades crónicas. Estos resultados pueden ayudar a los profesionales de la salud en la práctica diaria para una mejor comprensión del estado de salud de los pacientes y una mejor clasificación de su estado de riesgo.[CA] Els models de risc en l'àmbit de la salut són mètodes estadístics que brinden advertències primerenques sobre el risc d'una persona de patir un episodi advers en el futur. Generalment, utilitzen la informació emmagatzemada de forma rutinària en els sistemes d'informació hospitalària per a oferir una probabilitat individual de desenrotllar un resultat negatiu futur en un període determinat. Concretament, en el camp de les malalties cròniques que compartixen factors de risc comú, els models de risc es basen en l'anàlisi d'eixos factors de risc -tensió arterial elevada, glucèmia elevada, lípids sanguinis anormals, sobrecàrrega i obesitat- i les seues mesures biomètriques associades. Estes mesures es recopilen durant la pràctica clínica ben sovint de manera periòdica i, en conseqüència, s'incorporen als models de risc i recolzen la presa de decisions dels metges. Per a crear estos models de risc que incloguen la variable temporal es podrien utilitzar tècniques basades en dades (Data-Driven) , de manera que es tinguera en compte l'historial dels pacients disponible en els registres mèdics electrònics, extraient coneixement de les dades en brut. No obstant això, en l'àmbit de la salut, els resultats de la mineria de dades solen ser percebuts pels experts en salut com a caixes negres i, en conseqüència, no confien en les decisions dels algoritmes. El paradigma Interactiu permet als experts comprendre els resultats, perquè els professionals puguen corregir eixos models d'acord amb el seu coneixement i experiència, proporcionant models perceptius i cognitius. En este context, la mineria de processos és una tècnica de mineria de dades que permet la implementació del paradigma Interactiu, oferint una comprensió clara del procés d'atenció i proporcionant models comprensibles per al ser humà. Les condicions cròniques generalment es descriuen per mitjà d'imatges estàtiques de variables, com a factors genètics, fisiològics, ambientals i de comportament. No obstant això, la perspectiva dinàmica, temporal i de comportament no es consideren comunament en els models de risc. Això significa que l'últim estat de risc es convertix en l'estat real del pacient. No obstant això, la condició dels pacients podria veure's influenciada per les seues condicions dinàmiques passades. L'objectiu d'esta tesi és proporcionar una visió nova del risc, associat a un pacient, basada en tecnologies Data-Driven que oferisquen una visió dinàmica de l'evo\-lució dels pacients respecte a la seua condició crònica. Tècnicament, suposa abordar els models de risc incorporant la perspectiva dinàmica i el comportament dels pacients als models de risc gràcies a la informació inclosa en la Història Clínica Electrònica. Els resultats obtinguts al llarg d'esta tesi mostren com les tecnologies de mineria de processos poden aportar una visió dinàmica i interactiva dels models de risc de malalties cròniques. Estos resultats poden ajudar els professionals de la salut en la pràctica diària per a una millor comprensió de l'estat de salut dels pacients i una millor classificació del seu estat de risc.[EN] Risk models in the healthcare domain are statistical methods that provide early warnings about a person's risk for an adverse episode in the future. They usually use the information routinely stored in Hospital Information Systems to offer an individual probability for developing a future negative outcome in a given period. Concretely, in the field of chronic diseases that share common risk factors, risk models are based on the analysis of those risk factors -raised blood pressure, raised glucose levels, abnormal blood lipids, and overweight and obesity- and their associated biometric measures. These measures are collected during clinical practice frequently in a periodic manner, and accordingly, they are incorporated into the risk models to support clinicians' decision-making. Data-Driven techniques could be used to create these temporal-aware risk models, considering the patients' history included in Electronic Health Records, and extracting knowledge from raw data. However, in the healthcare domain, Data Mining results are usually perceived by the health experts as black-boxes, and in consequence, they do not trust in the algorithms' decisions. The Interactive paradigm allows experts to understand the results, in that sense, professionals can correct those models according to their knowledge and experience, providing perceptual and cognitive models. In this context, Process Mining is a Data Mining technique that enables the implementation of the Interactive paradigm, offering a clear care process understanding and providing human-understandable models. Chronic conditions are usually described by static pictures of variables, such as genetic, physiological, environmental, and behavioural factors. Nevertheless, the dynamic, temporal, and behavioural perspectives are not commonly considered in the risk models. That means the last status of the risk becomes the actual status of the patient. However, the patients' condition could be influenced by their past dynamic circumstances. The objective of this thesis is to provide a novel risk vision based on Data-Driven technologies offering a dynamic view of the patients' evolution regarding their chro\-nic condition. Technically, it supposes to approach risk models incorporating the dynamic and behavioural perspective of patients to the risk models thanks to the information included in the Electronic Health Records. The results obtained throughout this thesis show how Process Mining technologies can bring a dynamic and interactive view of chronic disease risk models. These results can support health professionals in daily practice for a better understanding of the patients' health condition and a better classification of their risk status.Valero Ramón, Z. (2022). Dynamic Risk Models for Characterising Chronic Diseases' Behaviour Using Process Mining Techniques [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/181652TESI

An Uncertainty Visual Analytics Framework for Functional Magnetic Resonance Imaging

Improving understanding of the human brain is one of the leading pursuits of modern scientific research. Functional magnetic resonance imaging (fMRI) is a foundational technique for advanced analysis and exploration of the human brain. The modality scans the brain in a series of temporal frames which provide an indication of the brain activity either at rest or during a task. The images can be used to study the workings of the brain, leading to the development of an understanding of healthy brain function, as well as characterising diseases such as schizophrenia and bipolar disorder. Extracting meaning from fMRI relies on an analysis pipeline which can be broadly categorised into three phases: (i) data acquisition and image processing; (ii) image analysis; and (iii) visualisation and human interpretation. The modality and analysis pipeline, however, are hampered by a range of uncertainties which can greatly impact the study of the brain function. Each phase contains a set of required and optional steps, containing inherent limitations and complex parameter selection. These aspects lead to the uncertainty that impacts the outcome of studies. Moreover, the uncertainties that arise early in the pipeline, are compounded by decisions and limitations further along in the process. While a large amount of research has been undertaken to examine the limitations and variable parameter selection, statistical approaches designed to address the uncertainty have not managed to mitigate the issues. Visual analytics, meanwhile, is a research domain which seeks to combine advanced visual interfaces with specialised interaction and automated statistical processing designed to exploit human expertise and understanding. Uncertainty visual analytics (UVA) tools, which aim to minimise and mitigate uncertainties, have been proposed for a variety of data, including astronomical, financial, weather and crime. Importantly, UVA approaches have also seen success in medical imaging and analysis. However, there are many challenges surrounding the application of UVA to each research domain. Principally, these involve understanding what the uncertainties are and the possible effects so they may be connected to visualisation and interaction approaches. With fMRI, the breadth of uncertainty arising in multiple stages along the pipeline and the compound effects, make it challenging to propose UVAs which meaningfully integrate into pipeline. In this thesis, we seek to address this challenge by proposing a unified UVA framework for fMRI. To do so, we first examine the state-of-the-art landscape of fMRI uncertainties, including the compound effects, and explore how they are currently addressed. This forms the basis of a field we term fMRI-UVA. We then present our overall framework, which is designed to meet the requirements of fMRI visual analysis, while also providing an indication and understanding of the effects of uncertainties on the data. Our framework consists of components designed for the spatial, temporal and processed imaging data. Alongside the framework, we propose two visual extensions which can be used as standalone UVA applications or be integrated into the framework. Finally, we describe a conceptual algorithmic approach which incorporates more data into an existing measure used in the fMRI analysis pipeline

Human activity recognition for the use in intelligent spaces

The aim of this Graduation Project is to develop a generic biological inspired activity recognition system for the use in intelligent spaces. Intelligent spaces form the context for this project. The goal is to develop a working prototype that can learn and recognize human activities from a limited training set in all kinds of spaces and situations. For testing purposes, the office environment is chosen as subject for the intelligent space. The purpose of the intelligent space, in this case the office, is left out of the scope of the project. The scope is limited to the perceptive system of the intelligent space. The notion is that the prototype should not be bound to a specific space, but it should be a generic perceptive system able to cope in any given space within the build environment. The fact that no space is the same, developing a prototype without any domain knowledge in which it can learn and recognize activities, is the main challenge of this project. In al layers of the prototype, the data processing is kept as abstract and low level as possible to keep it as generic as possible. This is done by using local features, scale invariant descriptors and by using hidden Markov models for pattern recognition. The novel approach of the prototype is that it combines structure as well as motion features in one system making it able to train and recognize a variety of activities in a variety of situations. From rhythmic expressive actions with a simple cyclic pattern to activities where the movement is subtle and complex like typing and reading, can all be trained and recognized. The prototype has been tested on two very different data sets. The first set in which the videos are shot in a controlled environment in which simple actions were performed. The second set in which videos are shot in a normal office where daily office activities are captured and categorized afterwards. The prototype has given some promising results proving it can cope with very different spaces, actions and activities. The aim of this Graduation Project is to develop a generic biological inspired activity recognition system for the use in intelligent spaces. Intelligent spaces form the context for this project. The goal is to develop a working prototype that can learn and recognize human activities from a limited training set in all kinds of spaces and situations. For testing purposes, the office environment is chosen as subject for the intelligent space. The purpose of the intelligent space, in this case the office, is left out of the scope of the project. The scope is limited to the perceptive system of the intelligent space. The notion is that the prototype should not be bound to a specific space, but it should be a generic perceptive system able to cope in any given space within the build environment. The fact that no space is the same, developing a prototype without any domain knowledge in which it can learn and recognize activities, is the main challenge of this project. In al layers of the prototype, the data processing is kept as abstract and low level as possible to keep it as generic as possible. This is done by using local features, scale invariant descriptors and by using hidden Markov models for pattern recognition. The novel approach of the prototype is that it combines structure as well as motion features in one system making it able to train and recognize a variety of activities in a variety of situations. From rhythmic expressive actions with a simple cyclic pattern to activities where the movement is subtle and complex like typing and reading, can all be trained and recognized. The prototype has been tested on two very different data sets. The first set in which the videos are shot in a controlled environment in which simple actions were performed. The second set in which videos are shot in a normal office where daily office activities are captured and categorized afterwards. The prototype has given some promising results proving it can cope with very different spaces, actions and activities