Multi-objective evolution of artificial neural networks in multi-class medical diagnosis problems with class imbalance

This paper proposes a novel multi-objective optimisation approach to solving both the problem of finding good structural and parametric choices in an ANN and the problem of training a classifier with a heavily skewed data set. The state-of-the-art CMA-PAES-HAGA multi-objective evolutionary algorithm [41] is used to simultaneously optimise the structure, weights, and biases of a population of ANNs with respect to not only the overall classification accuracy, but the classification accuracies of each individual target class. The effectiveness of this approach is then demonstrated on a real-world multi-class problem in medical diagnosis (classification of fetal cardiotocograms) where more than 75% of the data belongs to the majority class and the rest to two other minority classes. The optimised ANN is shown to significantly outperform a standard feed-forward ANN with respect to minority class recognition at the cost of slightly worse performance in terms of overall classification accuracy

Computational intelligence contributions to readmisision risk prediction in Healthcare systems

136 p.The Thesis tackles the problem of readmission risk prediction in healthcare systems from a machine learning and computational intelligence point of view. Readmission has been recognized as an indicator of healthcare quality with primary economic importance. We examine two specific instances of the problem, the emergency department (ED) admission and heart failure (HF) patient care using anonymized datasets from three institutions to carry real-life computational experiments validating the proposed approaches. The main difficulties posed by this kind of datasets is their high class imbalance ratio, and the lack of informative value of the recorded variables. This thesis reports the results of innovative class balancing approaches and new classification architectures

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

The Role of Synthetic Data in Improving Supervised Learning Methods: The Case of Land Use/Land Cover Classification

A thesis submitted in partial fulfillment of the requirements for the degree of Doctor in Information ManagementIn remote sensing, Land Use/Land Cover (LULC) maps constitute important assets for various applications, promoting environmental sustainability and good resource management. Although, their production continues to be a challenging task. There are various factors that contribute towards the difficulty of generating accurate, timely updated LULC maps, both via automatic or photo-interpreted LULC mapping. Data preprocessing, being a crucial step for any Machine Learning task, is particularly important in the remote sensing domain due to the overwhelming amount of raw, unlabeled data continuously gathered from multiple remote sensing missions. However a significant part of the state-of-the-art focuses on scenarios with full access to labeled training data with relatively balanced class distributions. This thesis focuses on the challenges found in automatic LULC classification tasks, specifically in data preprocessing tasks. We focus on the development of novel Active Learning (AL) and imbalanced learning techniques, to improve ML performance in situations with limited training data and/or the existence of rare classes. We also show that much of the contributions presented are not only successful in remote sensing problems, but also in various other multidisciplinary classification problems. The work presented in this thesis used open access datasets to test the contributions made in imbalanced learning and AL. All the data pulling, preprocessing and experiments are made available at https://github.com/joaopfonseca/publications. The algorithmic implementations are made available in the Python package ml-research at https://github.com/joaopfonseca/ml-research

Neural network for ordinal classification of imbalanced data by minimizing a Bayesian cost

Ordinal classification of imbalanced data is a challenging problem that appears in many real world applications. The challenge is to simultaneously consider the order of the classes and the class imbalance, which can notably improve the performance metrics. The Bayesian formulation allows to deal with these two characteristics jointly: It takes into account the prior probability of each class and the decision costs, which can be used to include the imbalance and the ordinal information, respectively. We propose to use the Bayesian formulation to train neural networks, which have shown excellent results in many classification tasks. A loss function is proposed to train networks with a single neuron in the output layer and a threshold based decision rule. The loss is an estimate of the Bayesian classification cost, based on the Parzen windows estimator, which is fitted for a thresholded decision. Experiments with several real datasets show that the proposed method provides competitive results in different scenarios, due to its high flexibility to specify the relative importance of the errors in the classification of patterns of different classes, considering the order and independently of the probability of each class.This work was partially supported by Spanish Ministry of Science and Innovation through Thematic Network "MAPAS"(TIN2017-90567-REDT) and by BBVA Foundation through "2-BARBAS" research grant. Funding for APC: Universidad Carlos III de Madrid (Read & Publish Agreement CRUE-CSIC 2023)