A study of the suitability of autoencoders for preprocessing data in breast cancer experimentation

Breast cancer is the most common cause of cancer death in women. Today, post-transcriptional protein products of the genes involved in breast cancer can be identified by immunohistochemistry. However, this method has problems arising from the intra-observer and inter-observer variability in the assess ment of pathologic variables, which may result in misleading conclusions. Using an optimal selection of preprocessing techniques may help to reduce observer variability. Deep learning has emerged as a powerful technique for any tasks related to machine learning such as classification and regression. The aim of this work is to use autoencoders (neural networks commonly used to feed deep learning architec tures) to improve the quality of the data for developing immunohistochemistry signatures with prognos tic value in breast cancer. Our testing on data from 222 patients with invasive non-special type breast carcinoma shows that an automatic binarization of experimental data after autoencoding could outper form other classical preprocessing techniques (such as human-dependent or automatic binarization only) when applied to the prognosis of breast cancer by immunohistochemical signaturesMinisterio de Economía y Competitividad TIN2014-55894-C2-1-

Autoencoded DNA methylation data to predict breast cancer recurrence: Machine learning models and gene-weight significance

Breast cancer is the most frequent cancer in women and the second most frequent overall after lung cancer. Although the 5-year survival rate of breast cancer is relatively high, recurrence is also common which often involves metastasis with its consequent threat for patients. DNA methylation-derived databases have become an interesting primary source for supervised knowledge extraction regarding breast cancer. Unfortunately, the study of DNA methylation involves the processing of hundreds of thousands of features for every patient. DNA methylation is featured by High Dimension Low Sample Size which has shown well-known issues regarding feature selection and generation. Autoencoders (AEs) appear as a specific technique for conducting nonlinear feature fusion. Our main objective in this work is to design a procedure to summarize DNA methylation by taking advantage of AEs. Our proposal is able to generate new features from the values of CpG sites of patients with and without recurrence. Then, a limited set of relevant genes to characterize breast cancer recurrence is proposed by the application of survival analysis and a pondered ranking of genes according to the distribution of their CpG sites. To test our proposal we have selected a dataset from The Cancer Genome Atlas data portal and an AE with a single-hidden layer. The literature and enrichment analysis (based on genomic context and functional annota tion) conducted regarding the genes obtained with our experiment confirmed that all of these genes were related to breast cancer recurrence.Ministerio de Economía y Competitividad TIN2014-55894-C2-RMinisterio de Economía y Competitividad TIN2017-88209-C2-2-

A survey of neural network-based cancer prediction models from microarray data

Neural networks are powerful tools used widely for building cancer prediction models from microarray data. We review the most recently proposed models to highlight the roles of neural networks in predicting cancer from gene expression data. We identified articles published between 2013–2018 in scientific databases using keywords such as cancer classification, cancer analysis, cancer prediction, cancer clustering and microarray data. Analyzing the studies reveals that neural network methods have been either used for filtering (data engineering) the gene expressions in a prior step to prediction; predicting the existence of cancer, cancer type or the survivability risk; or for clustering unlabeled samples. This paper also discusses some practical issues that can be considered when building a neural network-based cancer prediction model. Results indicate that the functionality of the neural network determines its general architecture. However, the decision on the number of hidden layers, neurons, hypermeters and learning algorithm is made using trail-and-error techniques

Autoencoder-based techniques for improved classification in settings with high dimensional and small sized data

Neural network models have been widely tested and analysed usinglarge sized high dimensional datasets. In real world application prob-lems, the available datasets are often limited in size due to reasonsrelated to the cost or difficulties encountered while collecting the data.This limitation in the number of examples may challenge the clas-sification algorithms and degrade their performance. A motivatingexample for this kind of problem is predicting the health status of atissue given its gene expression, when the number of samples availableto learn from is very small.Gene expression data has distinguishing characteristics attracting themachine learning research community. The high dimensionality ofthe data is one of the integral features that has to be considered whenbuilding predicting models. A single sample of the data is expressedby thousands of gene expressions compared to the benchmark imagesand texts that only have a few hundreds of features and commonlyused for analysing the existing models. Gene expression data samplesare also distributed unequally among the classes; in addition, theyinclude noisy features which degrade the prediction accuracy of themodels. These characteristics give rise to the need for using effec-tive dimensionality reduction methods that are able to discover thecomplex relationships between the features such as the autoencoders. This thesis investigates the problem of predicting from small sizedhigh dimensional datasets by introducing novel autoencoder-basedtechniques to increase the classification accuracy of the data. Twoautoencoder-based methods for generating synthetic data examplesand synthetic representations of the data were respectively introducedin the first stage of the study. Both of these methods are applicableto the testing phase of the autoencoder and showed successful in in-creasing the predictability of the data.Enhancing the autoencoder’s ability in learning from small sized im-balanced data was investigated in the second stage of the projectto come up with techniques that improved the autoencoder’s gener-ated representations. Employing the radial basis activation mecha-nism used in radial-basis function networks, which learn in a super-vised manner, was a solution provided by this thesis to enhance therepresentations learned by unsupervised algorithms. This techniquewas later applied to stochastic variational autoencoders and showedpromising results in learning discriminating representations from thegene expression data.The contributions of this thesis can be described by a number of differ-ent methods applicable to different stages (training and testing) anddifferent autoencoder models (deterministic and stochastic) which, in-dividually, allow for enhancing the predictability of small sized highdimensional datasets compared to well known baseline methods

Advanced Computational Methods for Oncological Image Analysis

[Cancer is the second most common cause of death worldwide and encompasses highly variable clinical and biological scenarios. Some of the current clinical challenges are (i) early diagnosis of the disease and (ii) precision medicine, which allows for treatments targeted to specific clinical cases. The ultimate goal is to optimize the clinical workflow by combining accurate diagnosis with the most suitable therapies. Toward this, large-scale machine learning research can define associations among clinical, imaging, and multi-omics studies, making it possible to provide reliable diagnostic and prognostic biomarkers for precision oncology. Such reliable computer-assisted methods (i.e., artificial intelligence) together with clinicians’ unique knowledge can be used to properly handle typical issues in evaluation/quantification procedures (i.e., operator dependence and time-consuming tasks). These technical advances can significantly improve result repeatability in disease diagnosis and guide toward appropriate cancer care. Indeed, the need to apply machine learning and computational intelligence techniques has steadily increased to effectively perform image processing operations—such as segmentation, co-registration, classification, and dimensionality reduction—and multi-omics data integration.

Predictive analytics framework for electronic health records with machine learning advancements : optimising hospital resources utilisation with predictive and epidemiological models

The primary aim of this thesis was to investigate the feasibility and robustness of predictive machine-learning models in the context of improving hospital resources’ utilisation with data- driven approaches and predicting hospitalisation with hospital quality assessment metrics such as length of stay. The length of stay predictions includes the validity of the proposed methodological predictive framework on each hospital’s electronic health records data source. In this thesis, we relied on electronic health records (EHRs) to drive a data-driven predictive inpatient length of stay (LOS) research framework that suits the most demanding hospital facilities for hospital resources’ utilisation context. The thesis focused on the viability of the methodological predictive length of stay approaches on dynamic and demanding healthcare facilities and hospital settings such as the intensive care units and the emergency departments. While the hospital length of stay predictions are (internal) healthcare inpatients outcomes assessment at the time of admission to discharge, the thesis also considered (external) factors outside hospital control, such as forecasting future hospitalisations from the spread of infectious communicable disease during pandemics. The internal and external splits are the thesis’ main contributions. Therefore, the thesis evaluated the public health measures during events of uncertainty (e.g. pandemics) and measured the effect of non-pharmaceutical intervention during outbreaks on future hospitalised cases. This approach is the first contribution in the literature to examine the epidemiological curves’ effect using simulation models to project the future hospitalisations on their strong potential to impact hospital beds’ availability and stress hospital workflow and workers, to the best of our knowledge. The main research commonalities between chapters are the usefulness of ensembles learning models in the context of LOS for hospital resources utilisation. The ensembles learning models anticipate better predictive performance by combining several base models to produce an optimal predictive model. These predictive models explored the internal LOS for various chronic and acute conditions using data-driven approaches to determine the most accurate and powerful predicted outcomes. This eventually helps to achieve desired outcomes for hospital professionals who are working in hospital settings

Deep Learning in Medical Image Analysis

The accelerating power of deep learning in diagnosing diseases will empower physicians and speed up decision making in clinical environments. Applications of modern medical instruments and digitalization of medical care have generated enormous amounts of medical images in recent years. In this big data arena, new deep learning methods and computational models for efficient data processing, analysis, and modeling of the generated data are crucially important for clinical applications and understanding the underlying biological process. This book presents and highlights novel algorithms, architectures, techniques, and applications of deep learning for medical image analysis

Facilitating and Enhancing the Performance of Model Selection for Energy Time Series Forecasting in Cluster Computing Environments

Applying Machine Learning (ML) manually to a given problem setting is a tedious and time-consuming process which brings many challenges with it, especially in the context of Big Data. In such a context, gaining insightful information, finding patterns, and extracting knowledge from large datasets are quite complex tasks. Additionally, the configurations of the underlying Big Data infrastructure introduce more complexity for configuring and running ML tasks. With the growing interest in ML the last few years, particularly people without extensive ML expertise have a high demand for frameworks assisting people in applying the right ML algorithm to their problem setting. This is especially true in the field of smart energy system applications where more and more ML algorithms are used e.g. for time series forecasting. Generally, two groups of non-expert users are distinguished to perform energy time series forecasting. The first one includes the users who are familiar with statistics and ML but are not able to write the necessary programming code for training and evaluating ML models using the well-known trial-and-error approach. Such an approach is time consuming and wastes resources for constructing multiple models. The second group is even more inexperienced in programming and not knowledgeable in statistics and ML but wants to apply given ML solutions to their problem settings. The goal of this thesis is to scientifically explore, in the context of more concrete use cases in the energy domain, how such non-expert users can be optimally supported in creating and performing ML tasks in practice on cluster computing environments. To support the first group of non-expert users, an easy-to-use modular extendable microservice-based ML solution for instrumenting and evaluating ML algorithms on top of a Big Data technology stack is conceptualized and evaluated. Our proposed solution facilitates applying trial-and-error approach by hiding the low level complexities from the users and introduces the best conditions to efficiently perform ML tasks in cluster computing environments. To support the second group of non-expert users, the first solution is extended to realize meta learning approaches for automated model selection. We evaluate how meta learning technology can be efficiently applied to the problem space of data analytics for smart energy systems to assist energy system experts which are not data analytics experts in applying the right ML algorithms to their data analytics problems. To enhance the predictive performance of meta learning, an efficient characterization of energy time series datasets is required. To this end, Descriptive Statistics Time based Meta Features (DSTMF), a new kind of meta features, is designed to accurately capture the deep characteristics of energy time series datasets. We find that DSTMF outperforms the other state-of-the-art meta feature sets introduced in the literature to characterize energy time series datasets in terms of the accuracy of meta learning models and the time needed to extract them. Further enhancement in the predictive performance of the meta learning classification model is achieved by training the meta learner on new efficient meta examples. To this end, we proposed two new approaches to generate new energy time series datasets to be used as training meta examples by the meta learner depending on the type of time series dataset (i.e. generation or energy consumption time series). We find that extending the original training sets with new meta examples generated by our approaches outperformed the case in which the original is extended by new simulated energy time series datasets

Towards a multipurpose neural network approach to novelty detection

Novelty detection, the identification of data that is unusual or different in some way, is relevant in a wide number of real-world scenarios, ranging from identifying unusual weather conditions to detecting evidence of damage in mechanical systems. However, utilising novelty detection approaches in a particular scenario presents significant challenges to the non-expert user. They must first select an appropriate approach from the novelty detection literature for their scenario. Then, suitable values must be determined for any parameters of the chosen approach. These challenges are at best time consuming and at worst prohibitively difficult for the user. Worse still, if no suitable approach can be found from the literature, then the user is left with the impossible task of designing a novelty detector themselves. In order to make novelty detection more accessible, an approach is required which does not pose the above challenges. This thesis presents such an approach, which aims to automatically construct novelty detectors for specific applications. The approach combines a neural network model, recently proposed to explain a phenomenon observed in the neural pathways of the retina, with an evolutionary algorithm that is capable of simultaneously evolving the structure and weights of a neural network in order to optimise its performance in a particular task. The proposed approach was evaluated over a number of very different novelty detection tasks. It was found that, in each task, the approach successfully evolved novelty detectors which outperformed a number of existing techniques from the literature. A number of drawbacks with the approach were also identified, and suggestions were given on ways in which these may potentially be overcome