Metabolic profiling on 2D NMR TOCSY spectra using machine learning

Due to the dynamicity of biological cells, the role of metabolic profiling in discovering biological fingerprints of diseases, and their evolution, as well as the cellular pathway of different biological or chemical stimuli is most significant. Two-dimensional nuclear magnetic resonance (2D NMR) is one of the fundamental and strong analytical instruments for metabolic profiling. Though, total correlation spectroscopy (2D NMR 1H -1H TOCSY) can be used to improve spectral overlap of 1D NMR, strong peak shift, signal overlap, spectral crowding and matrix effects in complex biological mixtures are extremely challenging in 2D NMR analysis. In this work, we introduce an automated metabolic deconvolution and assignment based on the deconvolution of 2D TOCSY of real breast cancer tissue, in addition to different differentiation pathways of adipose tissue-derived human Mesenchymal Stem cells. A major alternative to the common approaches in NMR based machine learning where images of the spectra are used as an input, our metabolic assignment is based only on the vertical and horizontal frequencies of metabolites in the 1H-1H TOCSY. One- and multi-class Kernel null foley–Sammon transform, support vector machines, polynomial classifier kernel density estimation, and support vector data description classifiers were tested in semi-supervised learning and novelty detection settings. The classifiers’ performance was evaluated by comparing the conventional human-based methodology and automatic assignments under different initial training sizes settings. The results of our novel metabolic profiling methods demonstrate its suitability, robustness, and speed in automated nontargeted NMR metabolic analysis

Fully Integrated Biochip Platforms for Advanced Healthcare

Recent advances in microelectronics and biosensors are enabling developments of innovative biochips for advanced healthcare by providing fully integrated platforms for continuous monitoring of a large set of human disease biomarkers. Continuous monitoring of several human metabolites can be addressed by using fully integrated and minimally invasive devices located in the sub-cutis, typically in the peritoneal region. This extends the techniques of continuous monitoring of glucose currently being pursued with diabetic patients. However, several issues have to be considered in order to succeed in developing fully integrated and minimally invasive implantable devices. These innovative devices require a high-degree of integration, minimal invasive surgery, long-term biocompatibility, security and privacy in data transmission, high reliability, high reproducibility, high specificity, low detection limit and high sensitivity. Recent advances in the field have already proposed possible solutions for several of these issues. The aim of the present paper is to present a broad spectrum of recent results and to propose future directions of development in order to obtain fully implantable systems for the continuous monitoring of the human metabolism in advanced healthcare applications

EDMON - Electronic Disease Surveillance and Monitoring Network: A Personalized Health Model-based Digital Infectious Disease Detection Mechanism using Self-Recorded Data from People with Type 1 Diabetes

Through time, we as a society have been tested with infectious disease outbreaks of different magnitude, which often pose major public health challenges. To mitigate the challenges, research endeavors have been focused on early detection mechanisms through identifying potential data sources, mode of data collection and transmission, case and outbreak detection methods. Driven by the ubiquitous nature of smartphones and wearables, the current endeavor is targeted towards individualizing the surveillance effort through a personalized health model, where the case detection is realized by exploiting self-collected physiological data from wearables and smartphones. This dissertation aims to demonstrate the concept of a personalized health model as a case detector for outbreak detection by utilizing self-recorded data from people with type 1 diabetes. The results have shown that infection onset triggers substantial deviations, i.e. prolonged hyperglycemia regardless of higher insulin injections and fewer carbohydrate consumptions. Per the findings, key parameters such as blood glucose level, insulin, carbohydrate, and insulin-to-carbohydrate ratio are found to carry high discriminative power. A personalized health model devised based on a one-class classifier and unsupervised method using selected parameters achieved promising detection performance. Experimental results show the superior performance of the one-class classifier and, models such as one-class support vector machine, k-nearest neighbor and, k-means achieved better performance. Further, the result also revealed the effect of input parameters, data granularity, and sample sizes on model performances. The presented results have practical significance for understanding the effect of infection episodes amongst people with type 1 diabetes, and the potential of a personalized health model in outbreak detection settings. The added benefit of the personalized health model concept introduced in this dissertation lies in its usefulness beyond the surveillance purpose, i.e. to devise decision support tools and learning platforms for the patient to manage infection-induced crises

Temporal models for mining, ranking and recommendation in the Web

Due to their first-hand, diverse and evolution-aware reflection of nearly all areas of life, heterogeneous temporal datasets i.e., the Web, collaborative knowledge bases and social networks have been emerged as gold-mines for content analytics of many sorts. In those collections, time plays an essential role in many crucial information retrieval and data mining tasks, such as from user intent understanding, document ranking to advanced recommendations. There are two semantically closed and important constituents when modeling along the time dimension, i.e., entity and event. Time is crucially served as the context for changes driven by happenings and phenomena (events) that related to people, organizations or places (so-called entities) in our social lives. Thus, determining what users expect, or in other words, resolving the uncertainty confounded by temporal changes is a compelling task to support consistent user satisfaction. In this thesis, we address the aforementioned issues and propose temporal models that capture the temporal dynamics of such entities and events to serve for the end tasks. Specifically, we make the following contributions in this thesis: (1) Query recommendation and document ranking in the Web - we address the issues for suggesting entity-centric queries and ranking effectiveness surrounding the happening time period of an associated event. In particular, we propose a multi-criteria optimization framework that facilitates the combination of multiple temporal models to smooth out the abrupt changes when transitioning between event phases for the former and a probabilistic approach for search result diversification of temporally ambiguous queries for the latter. (2) Entity relatedness in Wikipedia - we study the long-term dynamics of Wikipedia as a global memory place for high-impact events, specifically the reviving memories of past events. Additionally, we propose a neural network-based approach to measure the temporal relatedness of entities and events. The model engages different latent representations of an entity (i.e., from time, link-based graph and content) and use the collective attention from user navigation as the supervision. (3) Graph-based ranking and temporal anchor-text mining inWeb Archives - we tackle the problem of discovering important documents along the time-span ofWeb Archives, leveraging the link graph. Specifically, we combine the problems of relevance, temporal authority, diversity and time in a unified framework. The model accounts for the incomplete link structure and natural time lagging in Web Archives in mining the temporal authority. (4) Methods for enhancing predictive models at early-stage in social media and clinical domain - we investigate several methods to control model instability and enrich contexts of predictive models at the “cold-start” period. We demonstrate their effectiveness for the rumor detection and blood glucose prediction cases respectively. Overall, the findings presented in this thesis demonstrate the importance of tracking these temporal dynamics surround salient events and entities for IR applications. We show that determining such changes in time-based patterns and trends in prevalent temporal collections can better satisfy user expectations, and boost ranking and recommendation effectiveness over time

Framework to predict the metabolic syndrome without doing a blood test: based on machine learning for a clinical decision support system

Metabolic Syndrome (MetS) is a cluster of risk factors that increase the likelihood of heart disease and diabetes mellitus, and researchers have recently linked it to worse outcomes for the novel Covid-19 disease. It is crucial to get diagnosed with time to take preventive measures, especially for patients in locations without proper laboratories and medical consultations. This work presents a new model to diagnose metabolic syndrome using machine learning and non-biochemical variables that healthcare professionals can obtain from initial consultations. For evaluating and comparing the model, this work also proposes a new methodology for performing research on data mining called RAMAD. The methodology standardizes the novel model’s comparison with similar classification models, using their reported variables and previously obtained data from a study in Colombia, using the holdout and random subsampling validation methods to get performance evaluation indicators between the models. The resulting ANN model used three hidden layers and only Hip Circumference, dichotomous Waist Circumference, and dichotomous blood pressure variables. It gave an Area under Receiver Operating Characteristic curves (AROC) of 87.75% by the International Diabetes Federation (IDF) and 85.12% by Harmonized Diagnosis or Joint Interim Statement (HMS) diagnosis criteria, higher than previous models. Thanks to the new methodology, diagnosis models can be thoroughly documented for appropriate future comparisons, thus benefiting the studied diseases’ diagnosis. Medical personnel needs to know the factors involved in the syndrome to start a treatment. So, this work also presents the segmentation of metabolic syndrome in types related to each biochemical variable. It uses the RAMAD methodology together with several machine learning techniques to design a framework to predict MetS and their several types, without using a blood test and only anthropometric and clinical information. The results showed an excellent system for predicting six MetS types that combine several factors mentioned above that have an AROC with a range of 71% to 96%, and an AROC 82.86%. This thesis finishes with the proposal of using a SCRUM Thinking framework for creating mobile health applications to implement the new models and serve as decision tools for healthcare professionals. The standard and fundamental characteristics were analyzed, finding the quality attributes verified in the framework’s early stages. Keywords — Metabolic Syndrome, Segmentation, Quine–McCluskey, Random Subsampling validation, RAMAD, Machine learning, Framework, International Diabetes Federation (IDF), Harmonized Diagnosis or Joint Interim Statement (HMS).DoctoradoDoctor en Ingeniería de Sistemas y Computació

A Proposed Method to Identify the Occurrence of Diabetes in Human Body using Machine Learning Technique

Advanced machine-learning techniques are often used for reasoning-based diagnosis and advanced prediction system within the healthcare industry. The methods and algorithms are based on the historical clinical data and factbased Medicare evaluation. Diabetes is a global problem. Each year people are developing diabetes and due to diabetes, a lot of people are going for organ amputation. According to the World Health Organization (WHO), there is a sharp rise in number of people developing diabetes. In 1980, it was estimated that 180 million people with diabetes worldwide. This number has risen from 108 million to 422 million in 2014. WHO also reported that 1.6 million deaths in 2016 due to diabetes. Diabetes occurs due to insufficient production of insulin from pancreas. Several research show that unhealthy diet, smoking, less exercise, Body Mass Index (BMI) are the primary cause of diabetes. This paper shows the use of machine learning that can identify a patient of being diabetic or non-diabetic based on previous clinical data. In this article, a method is shown to analyze and compare the relationship between different clinical parameters such as age, BMI, Diet-chart, systolic Blood Pressure etc. After evaluating all the factors this research work successfully combined all the related factors in a single mathematical equation which is very effective to analyze the risk percentage and risk evaluation based on given input parameters by the participants or users

Disease diagnosis in smart healthcare: Innovation, technologies and applications

To promote sustainable development, the smart city implies a global vision that merges artificial intelligence, big data, decision making, information and communication technology (ICT), and the internet-of-things (IoT). The ageing issue is an aspect that researchers, companies and government should devote efforts in developing smart healthcare innovative technology and applications. In this paper, the topic of disease diagnosis in smart healthcare is reviewed. Typical emerging optimization algorithms and machine learning algorithms are summarized. Evolutionary optimization, stochastic optimization and combinatorial optimization are covered. Owning to the fact that there are plenty of applications in healthcare, four applications in the field of diseases diagnosis (which also list in the top 10 causes of global death in 2015), namely cardiovascular diseases, diabetes mellitus, Alzheimer’s disease and other forms of dementia, and tuberculosis, are considered. In addition, challenges in the deployment of disease diagnosis in healthcare have been discussed