Design and assessment of a computer-assisted artificial intelligence system for predicting preterm labor in women attending regular check-ups. Emphasis in imbalance data learning technique

Tesis por compendio[ES] El parto prematuro, definido como el nacimiento antes de las 37 semanas de gestación, es una importante preocupación mundial con implicaciones para la salud de los recién nacidos y los costes económicos. Afecta aproximadamente al 11% de todos los nacimientos, lo que supone más de 15 millones de individuos en todo el mundo. Los métodos actuales para predecir el parto prematuro carecen de precisión, lo que conduce a un sobrediagnóstico y a una viabilidad limitada en entornos clínicos. La electrohisterografía (EHG) ha surgido como una alternativa prometedora al proporcionar información relevante sobre la electrofisiología uterina. Sin embargo, los sistemas de predicción anteriores basados en EHG no se han trasladado de forma efectiva a la práctica clínica, debido principalmente a los sesgos en el manejo de datos desbalanceados y a la necesidad de modelos de predicción robustos y generalizables. Esta tesis doctoral pretende desarrollar un sistema de predicción del parto prematuro basado en inteligencia artificial utilizando EHG y datos obstétricos de mujeres sometidas a controles prenatales regulares. Este sistema implica la extracción de características relevantes, la optimización del subespacio de características y la evaluación de estrategias para abordar el reto de los datos desbalanceados para una predicción robusta. El estudio valida la eficacia de las características temporales, espectrales y no lineales para distinguir entre casos de parto prematuro y a término. Las nuevas medidas de entropía, en concreto la dispersión y la entropía de burbuja, superan a las métricas de entropía tradicionales en la identificación del parto prematuro. Además, el estudio trata de maximizar la información complementaria al tiempo que minimiza la redundancia y las características de ruido para optimizar el subespacio de características para una predicción precisa del parto prematuro mediante un algoritmo genético. Además, se ha confirmado la fuga de información entre el conjunto de datos de entrenamiento y el de prueba al generar muestras sintéticas antes de la partición de datos, lo que da lugar a una capacidad de generalización sobreestimada del sistema predictor. Estos resultados subrayan la importancia de particionar y después remuestrear para garantizar la independencia de los datos entre las muestras de entrenamiento y de prueba. Se propone combinar el algoritmo genético y el remuestreo en la misma iteración para hacer frente al desequilibrio en el aprendizaje de los datos mediante el enfoque de particio'n-remuestreo, logrando un área bajo la curva ROC del 94% y una precisión media del 84%. Además, el modelo demuestra un F1-score y una sensibilidad de aproximadamente el 80%, superando a los estudios existentes que consideran el enfoque de remuestreo después de particionar. Esto revela el potencial de un sistema de predicción de parto prematuro basado en EHG, permitiendo estrategias orientadas al paciente para mejorar la prevención del parto prematuro, el bienestar materno-fetal y la gestión óptima de los recursos hospitalarios. En general, esta tesis doctoral proporciona a los clínicos herramientas valiosas para la toma de decisiones en escenarios de riesgo materno-fetal de parto prematuro. Permite a los clínicos diseñar estrategias orientadas al paciente para mejorar la prevención y el manejo del parto prematuro. La metodología propuesta es prometedora para el desarrollo de un sistema integrado de predicción del parto prematuro que pueda mejorar la planificación del embarazo, optimizar la asignación de recursos y reducir el riesgo de parto prematuro.[CA] El part prematur, definit com el naixement abans de les 37 setmanes de gestacio', e's una important preocupacio' mundial amb implicacions per a la salut dels nounats i els costos econo¿mics. Afecta aproximadament a l'11% de tots els naixements, la qual cosa suposa me's de 15 milions d'individus a tot el mo'n. Els me¿todes actuals per a predir el part prematur manquen de precisio', la qual cosa condueix a un sobrediagno¿stic i a una viabilitat limitada en entorns cl¿'nics. La electrohisterografia (EHG) ha sorgit com una alternativa prometedora en proporcionar informacio' rellevant sobre l'electrofisiologia uterina. No obstant aixo¿, els sistemes de prediccio' anteriors basats en EHG no s'han traslladat de manera efectiva a la pra¿ctica cl¿'nica, degut principalment als biaixos en el maneig de dades desequilibrades i a la necessitat de models de prediccio' robustos i generalitzables. Aquesta tesi doctoral prete'n desenvolupar un sistema de prediccio' del part prematur basat en intel·lige¿ncia artificial utilitzant EHG i dades obste¿triques de dones sotmeses a controls prenatals regulars. Aquest sistema implica l'extraccio' de caracter¿'stiques rellevants, l'optimitzacio' del subespai de caracter¿'stiques i l'avaluacio' d'estrate¿gies per a abordar el repte de les dades desequilibrades per a una prediccio' robusta. L'estudi valguda l'efica¿cia de les caracter¿'stiques temporals, espectrals i no lineals per a distingir entre casos de part prematur i a terme. Les noves mesures d'entropia, en concret la dispersio' i l'entropia de bambolla, superen a les me¿triques d'entropia tradicionals en la identificacio' del part prematur. A me's, l'estudi tracta de maximitzar la informacio' complementa¿ria al mateix temps que minimitza la redunda¿ncia i les caracter¿'stiques de soroll per a optimitzar el subespai de caracter¿'stiques per a una prediccio' precisa del part prematur mitjan¿cant un algorisme gene¿tic. A me's, hem confirmat la fugida d'informacio' entre el conjunt de dades d'entrenament i el de prova en generar mostres sinte¿tiques abans de la particio' de dades, la qual cosa dona lloc a una capacitat de generalitzacio' sobreestimada del sistema predictor. Aquests resultats subratllen la importa¿ncia de particionar i despre's remostrejar per a garantir la independe¿ncia de les dades entre les mostres d'entrenament i de prova. Proposem combinar l'algorisme gene¿tic i el remostreig en la mateixa iteracio' per a fer front al desequilibri en l'aprenentatge de les dades mitjan¿cant l'enfocament de particio'-remostrege, aconseguint una a¿rea sota la corba ROC del 94% i una precisio' mitjana del 84%. A me's, el model demostra una puntuacio' F1 i una sensibilitat d'aproximadament el 80%, superant als estudis existents que consideren l'enfocament de remostreig despre's de particionar. Aixo¿ revela el potencial d'un sistema de prediccio' de part prematur basat en EHG, permetent estrate¿gies orientades al pacient per a millorar la prevencio' del part prematur, el benestar matern-fetal i la gestio' o¿ptima dels recursos hospitalaris. En general, aquesta tesi doctoral proporciona als cl¿'nics eines valuoses per a la presa de decisions en escenaris de risc matern-fetal de part prematur. Permet als cl¿'nics dissenyar estrate¿gies orientades al pacient per a millorar la prevencio' i el maneig del part prematur. La metodologia proposada e's prometedora per al desenvolupament d'un sistema integrat de prediccio' del part prematur que puga millorar la planificacio' de l'embara¿s, optimitzar l'assignacio' de recursos i millorar la qualitat de l'atencio'.[EN] Preterm delivery, defined as birth before 37 weeks of gestation, is a significant global concern with implications for the health of newborns and economic costs. It affects approximately 11% of all births, amounting to more than 15 million individuals worldwide. Current methods for predicting preterm labor lack precision, leading to overdiagnosis and limited practicality in clinical settings. Electrohysterography (EHG) has emerged as a promising alternative by providing relevant information about uterine electrophysiology. However, previous prediction systems based on EHG have not effectively translated into clinical practice, primarily due to biases in handling imbalanced data and the need for robust and generalizable prediction models. This doctoral thesis aims to develop an artificial intelligence based preterm labor prediction system using EHG and obstetric data from women undergoing regular prenatal check-ups. This system entails extracting relevant features, optimizing the feature subspace, and evaluating strategies to address the imbalanced data challenge for robust prediction. The study validates the effectiveness of temporal, spectral, and non-linear features in distinguishing between preterm and term labor cases. Novel entropy measures, namely dispersion and bubble entropy, outperform traditional entropy metrics in identifying preterm labor. Additionally, the study seeks to maximize complementary information while minimizing redundancy and noise features to optimize the feature subspace for accurate preterm delivery prediction by a genetic algorithm. Furthermore, we have confirmed leakage information between train and test data set when generating synthetic samples before data partitioning giving rise to an overestimated generalization capability of the predictor system. These results emphasize the importance of using partitioning-resampling techniques for ensuring data independence between train and test samples. We propose to combine genetic algorithm and resampling method at the same iteration to deal with imbalanced data learning using partition-resampling pipeline, achieving an Area Under the ROC Curve of 94% and Average Precision of 84%. Moreover, the model demonstrates an F1-score and recall of approximately 80%, outperforming existing studies on partition-resampling pipeline. This finding reveals the potential of an EHG-based preterm birth prediction system, enabling patient-oriented strategies for enhanced preterm labor prevention, maternal-fetal well-being, and optimal hospital resource management. Overall, this doctoral thesis provides clinicians with valuable tools for decision-making in preterm labor maternal-fetal risk scenarios. It enables clinicians to design a patient-oriented strategies for enhanced preterm birth prevention and management. The proposed methodology holds promise for the development of an integrated preterm birth prediction system that can enhance pregnancy planning, optimize resource allocation, and ultimately improve the outcomes for both mother and baby.Nieto Del Amor, F. (2023). Design and assessment of a computer-assisted artificial intelligence system for predicting preterm labor in women attending regular check-ups. Emphasis in imbalance data learning technique [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/200900Compendi

Methods to Improve the Prediction Accuracy and Performance of Ensemble Models

The application of ensemble predictive models has been an important research area in predicting medical diagnostics, engineering diagnostics, and other related smart devices and related technologies. Most of the current predictive models are complex and not reliable despite numerous efforts in the past by the research community. The performance accuracy of the predictive models have not always been realised due to many factors such as complexity and class imbalance. Therefore there is a need to improve the predictive accuracy of current ensemble models and to enhance their applications and reliability and non-visual predictive tools. The research work presented in this thesis has adopted a pragmatic phased approach to propose and develop new ensemble models using multiple methods and validated the methods through rigorous testing and implementation in different phases. The first phase comprises of empirical investigations on standalone and ensemble algorithms that were carried out to ascertain their performance effects on complexity and simplicity of the classifiers. The second phase comprises of an improved ensemble model based on the integration of Extended Kalman Filter (EKF), Radial Basis Function Network (RBFN) and AdaBoost algorithms. The third phase comprises of an extended model based on early stop concepts, AdaBoost algorithm, and statistical performance of the training samples to minimize overfitting performance of the proposed model. The fourth phase comprises of an enhanced analytical multivariate logistic regression predictive model developed to minimize the complexity and improve prediction accuracy of logistic regression model. To facilitate the practical application of the proposed models; an ensemble non-invasive analytical tool is proposed and developed. The tool links the gap between theoretical concepts and practical application of theories to predict breast cancer survivability. The empirical findings suggested that: (1) increasing the complexity and topology of algorithms does not necessarily lead to a better algorithmic performance, (2) boosting by resampling performs slightly better than boosting by reweighting, (3) the prediction accuracy of the proposed ensemble EKF-RBFN-AdaBoost model performed better than several established ensemble models, (4) the proposed early stopped model converges faster and minimizes overfitting better compare with other models, (5) the proposed multivariate logistic regression concept minimizes the complexity models (6) the performance of the proposed analytical non-invasive tool performed comparatively better than many of the benchmark analytical tools used in predicting breast cancers and diabetics ailments. The research contributions to ensemble practice are: (1) the integration and development of EKF, RBFN and AdaBoost algorithms as an ensemble model, (2) the development and validation of ensemble model based on early stop concepts, AdaBoost, and statistical concepts of the training samples, (3) the development and validation of predictive logistic regression model based on breast cancer, and (4) the development and validation of a non-invasive breast cancer analytic tools based on the proposed and developed predictive models in this thesis. To validate prediction accuracy of ensemble models, in this thesis the proposed models were applied in modelling breast cancer survivability and diabetics’ diagnostic tasks. In comparison with other established models the simulation results of the models showed improved predictive accuracy. The research outlines the benefits of the proposed models, whilst proposes new directions for future work that could further extend and improve the proposed models discussed in this thesis

Identification of gene pathways implicated in Alzheimer's disease using longitudinal imaging phenotypes with sparse regression

We present a new method for the detection of gene pathways associated with a multivariate quantitative trait, and use it to identify causal pathways associated with an imaging endophenotype characteristic of longitudinal structural change in the brains of patients with Alzheimer's disease (AD). Our method, known as pathways sparse reduced-rank regression (PsRRR), uses group lasso penalised regression to jointly model the effects of genome-wide single nucleotide polymorphisms (SNPs), grouped into functional pathways using prior knowledge of gene-gene interactions. Pathways are ranked in order of importance using a resampling strategy that exploits finite sample variability. Our application study uses whole genome scans and MR images from 464 subjects in the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. 66,182 SNPs are mapped to 185 gene pathways from the KEGG pathways database. Voxel-wise imaging signatures characteristic of AD are obtained by analysing 3D patterns of structural change at 6, 12 and 24 months relative to baseline. High-ranking, AD endophenotype-associated pathways in our study include those describing chemokine, Jak-stat and insulin signalling pathways, and tight junction interactions. All of these have been previously implicated in AD biology. In a secondary analysis, we investigate SNPs and genes that may be driving pathway selection, and identify a number of previously validated AD genes including CR1, APOE and TOMM40

Linear and Order Statistics Combiners for Pattern Classification

Several researchers have experimentally shown that substantial improvements can be obtained in difficult pattern recognition problems by combining or integrating the outputs of multiple classifiers. This chapter provides an analytical framework to quantify the improvements in classification results due to combining. The results apply to both linear combiners and order statistics combiners. We first show that to a first order approximation, the error rate obtained over and above the Bayes error rate, is directly proportional to the variance of the actual decision boundaries around the Bayes optimum boundary. Combining classifiers in output space reduces this variance, and hence reduces the "added" error. If N unbiased classifiers are combined by simple averaging, the added error rate can be reduced by a factor of N if the individual errors in approximating the decision boundaries are uncorrelated. Expressions are then derived for linear combiners which are biased or correlated, and the effect of output correlations on ensemble performance is quantified. For order statistics based non-linear combiners, we derive expressions that indicate how much the median, the maximum and in general the ith order statistic can improve classifier performance. The analysis presented here facilitates the understanding of the relationships among error rates, classifier boundary distributions, and combining in output space. Experimental results on several public domain data sets are provided to illustrate the benefits of combining and to support the analytical results.Comment: 31 page

Big Data Analytics for Complex Systems

The evolution of technology in all fields led to the generation of vast amounts of data by modern systems. Using data to extract information, make predictions, and make decisions is the current trend in artificial intelligence. The advancement of big data analytics tools made accessing and storing data easier and faster than ever, and machine learning algorithms help to identify patterns in and extract information from data. The current tools and machines in health, computer technologies, and manufacturing can generate massive raw data about their products or samples. The author of this work proposes a modern integrative system that can utilize big data analytics, machine learning, super-computer resources, and industrial health machines’ measurements to build a smart system that can mimic the human intelligence skills of observations, detection, prediction, and decision-making. The applications of the proposed smart systems are included as case studies to highlight the contributions of each system. The first contribution is the ability to utilize big data revolutionary and deep learning technologies on production lines to diagnose incidents and take proper action. In the current digital transformational industrial era, Industry 4.0 has been receiving researcher attention because it can be used to automate production-line decisions. Reconfigurable manufacturing systems (RMS) have been widely used to reduce the setup cost of restructuring production lines. However, the current RMS modules are not linked to the cloud for online decision-making to take the proper decision; these modules must connect to an online server (super-computer) that has big data analytics and machine learning capabilities. The online means that data is centralized on cloud (supercomputer) and accessible in real-time. In this study, deep neural networks are utilized to detect the decisive features of a product and build a prediction model in which the iFactory will make the necessary decision for the defective products. The Spark ecosystem is used to manage the access, processing, and storing of the big data streaming. This contribution is implemented as a closed cycle, which for the best of our knowledge, no one in the literature has introduced big data analysis using deep learning on real-time applications in the manufacturing system. The code shows a high accuracy of 97% for classifying the normal versus defective items. The second contribution, which is in Bioinformatics, is the ability to build supervised machine learning approaches based on the gene expression of patients to predict proper treatment for breast cancer. In the trial, to personalize treatment, the machine learns the genes that are active in the patient cohort with a five-year survival period. The initial condition here is that each group must only undergo one specific treatment. After learning about each group (or class), the machine can personalize the treatment of a new patient by diagnosing the patients’ gene expression. The proposed model will help in the diagnosis and treatment of the patient. The future work in this area involves building a protein-protein interaction network with the selected genes for each treatment to first analyze the motives of the genes and target them with the proper drug molecules. In the learning phase, a couple of feature-selection techniques and supervised standard classifiers are used to build the prediction model. Most of the nodes show a high-performance measurement where accuracy, sensitivity, specificity, and F-measure ranges around 100%. The third contribution is the ability to build semi-supervised learning for the breast cancer survival treatment that advances the second contribution. By understanding the relations between the classes, we can design the machine learning phase based on the similarities between classes. In the proposed research, the researcher used the Euclidean matrix distance among each survival treatment class to build the hierarchical learning model. The distance information that is learned through a non-supervised approach can help the prediction model to select the classes that are away from each other to maximize the distance between classes and gain wider class groups. The performance measurement of this approach shows a slight improvement from the second model. However, this model reduced the number of discriminative genes from 47 to 37. The model in the second contribution studies each class individually while this model focuses on the relationships between the classes and uses this information in the learning phase. Hierarchical clustering is completed to draw the borders between groups of classes before building the classification models. Several distance measurements are tested to identify the best linkages between classes. Most of the nodes show a high-performance measurement where accuracy, sensitivity, specificity, and F-measure ranges from 90% to 100%. All the case study models showed high-performance measurements in the prediction phase. These modern models can be replicated for different problems within different domains. The comprehensive models of the newer technologies are reconfigurable and modular; any newer learning phase can be plugged-in at both ends of the learning phase. Therefore, the output of the system can be an input for another learning system, and a newer feature can be added to the input to be considered for the learning phase

Automatic Selection of Molecular Descriptors using Random Forest: Application to Drug Discovery

The optimal selection of chemical features (molecular descriptors) is an essential pre-processing step for the efficient application of computational intelligence techniques in virtual screening for identification of bioactive molecules in drug discovery. The selection of molecular descriptors has key influence in the accuracy of affinity prediction. In order to improve this prediction, we examined a Random Forest (RF)-based approach to automatically select molecular descriptors of training data for ligands of kinases, nuclear hormone receptors, and other enzymes. The reduction of features to use during prediction dramatically reduces the computing time over existing approaches and consequently permits the exploration of much larger sets of experimental data. To test the validity of the method, we compared the results of our approach with the ones obtained using manual feature selection in our previous study (Perez-Sanchez et al., 2014). The main novelty of this work in the field of drug discovery is the use of RF in two different ways: feature ranking and dimensionality reduction, and classification using the automatically selected feature subset. Our RF-based method out-performs classification results provided by Support Vector Machine (SVM) and Neural Networks (NN) approaches

Machine Learning Approaches for Improving Prediction Performance of Structure-Activity Relationship Models

In silico bioactivity prediction studies are designed to complement in vivo and in vitro efforts to assess the activity and properties of small molecules. In silico methods such as Quantitative Structure-Activity/Property Relationship (QSAR) are used to correlate the structure of a molecule to its biological property in drug design and toxicological studies. In this body of work, I started with two in-depth reviews into the application of machine learning based approaches and feature reduction methods to QSAR, and then investigated solutions to three common challenges faced in machine learning based QSAR studies. First, to improve the prediction accuracy of learning from imbalanced data, Synthetic Minority Over-sampling Technique (SMOTE) and Edited Nearest Neighbor (ENN) algorithms combined with bagging as an ensemble strategy was evaluated. The Friedman’s aligned ranks test and the subsequent Bergmann-Hommel post hoc test showed that this method significantly outperformed other conventional methods. SMOTEENN with bagging became less effective when IR exceeded a certain threshold (e.g., \u3e40). The ability to separate the few active compounds from the vast amounts of inactive ones is of great importance in computational toxicology. Deep neural networks (DNN) and random forest (RF), representing deep and shallow learning algorithms, respectively, were chosen to carry out structure-activity relationship-based chemical toxicity prediction. Results suggest that DNN significantly outperformed RF (p \u3c 0.001, ANOVA) by 22-27% for four metrics (precision, recall, F-measure, and AUPRC) and by 11% for another (AUROC). Lastly, current features used for QSAR based machine learning are often very sparse and limited by the logic and mathematical processes used to compute them. Transformer embedding features (TEF) were developed as new continuous vector descriptors/features using the latent space embedding from a multi-head self-attention. The significance of TEF as new descriptors was evaluated by applying them to tasks such as predictive modeling, clustering, and similarity search. An accuracy of 84% on the Ames mutagenicity test indicates that these new features has a correlation to biological activity. Overall, the findings in this study can be applied to improve the performance of machine learning based Quantitative Structure-Activity/Property Relationship (QSAR) efforts for enhanced drug discovery and toxicology assessments

Feature selection and classification for Metagenomics diagnosis of Inflammatory Bowel Diseases

Durante questo progetto ho potuto implementare degli algoritmi di feature selection basati su Recursive Feature Elimination e Randomised Logistic Regression allo scopo di classificare, attraverso marcatori genetici, malattie infiammatorie intestinali