Exploring neuroevolution fitness landscapes for optimization and generalization

Tese de mestrado, Engenharia Informática (Interação e Conhecimento) Universidade de Lisboa, Faculdade de Ciências, 2020Paisagens de aptidão (fitness landscapes) são um conceito útil e largamente investigado para estudar as dinâmicas de meta-heurísticas. Nas últimas duas décadas têm sido utilizadas com sucesso para estimar as capacidades de otimização de diversos tipos de algoritmos evolutivos, tal como algoritmos genéticos e programação genética. No entanto, até à data nunca foram utilizadas para estudar o desempenho de algoritmos de aprendizagem automática em dados nunca vistos durante o treino, e nunca foram aplicadas para estudar as paisagens geradas por neuroevolução. Coincidentemente, apesar de já existir há quase três décadas e ainda ser uma área de investigação com um crescimento rápido e dinâmico, a neuroevolução ainda tem falta de fundações teóricas e metodológicas, fundações essas que podem ser dadas através da aplicação de paisagens de aptidão. Esta dissertação tem como objetivo preencher estas lacunas ao aplicar paisagens de aptidão à neuroevolução, usando este conceito para inferir informação útil sobre a capacidade de aprendizagem e generalização deste método de aprendizagem automática. De forma a realizar esta tarefa, desenvolvemos e usámos um algoritmo de neuroevolução baseado em gramáticas que gera redes neuronais convolucionais, e estudámos a dinâmica de três operadores de mutação distintos usados para evoluir múltiplos aspetos das redes neuronais. De forma a caracterizar as paisagens de aptidão, estudámos a autocorrelação (autocorrelation), medida entrópica de rugosidade (entropic measure of ruggedness), nuvens de aptidão (fitness clouds), medidas de gradiente (gradient measures) e o coeficiente de declive negativo (negative slope coefficient), e ao mesmo tempo discutimos porque é que apesar de não usarmos outras medidas, tais como redes de ótimos locais (local óptima networks) e correlação aptidão distância (fitness distance correlation), estas podem providenciar resultados interessantes. Também propomos o uso de duas novas medidas de avaliação: nuvens de densidade, uma nova medida desenvolvida nesta tese com capacidade de dar informação visual sobre a distribuição de amostras, e a medida de sobreajustamento (overfitting), que é derivada de uma medida já existente e usada em programação genética. Os resultados demonstram que as medidas usadas são apropriadas e produzem resultados precisos no que toca a estimar tanto a capacidade de aprendizagem como a habilidade de generalização das configuração de neuroevolução consideradas.Fitness landscapes are a useful and widely investigated concept for studying the dynamics of meta-heuristics. In the last two decades, they have been successfully used for estimating the optimization capabilities of different flavors of evolutionary algorithms, including genetic algorithms and genetic programming. However, so far they have not been used for studying the performance of Machine Learning (ML) algorithms on unseen data, and they have not been applied to study neuroevolution landscapes. Coincidentally, despite having existed for almost three decades and still being a dynamic and rapidly growing research field, neuroevolution still lacks theoretical and methodological foundations, which could be provided by the application of fitness landscapes. This thesis aims to fill these gaps by applying fitness landscapes to neuroevolution, using this concept to infer useful information about the learning and generalization ability of the ML method. For this task, we developed and used a grammar-based neuroevolution approach to generate convolutional neural networks, and studied the dynamics of three different mutation operators used to evolve multiple aspects of the networks. To characterize fitness landscapes, we studied autocorrelation, entropic measure of ruggedness, fitness clouds, gradient measures and negative slope coefficient, while also discussing why other measures such as local optima networks and fitness distance correlation, despite not being used, could provide interesting results. Also, we propose the use of two additional evaluation measures: density clouds, a new measure developed in this thesis that can provide visual information regarding the distribution of samples, and overfitting measure, which is derived from a measure used in genetic programming. The results show that the used measures are appropriate and produce accurate results when estimating both the learning capability and the generalization ability of the considered neuroevolution configurations

Global burden of 369 diseases and injuries in 204 countries and territories, 1990–2019: a systematic analysis for the Global Burden of Disease Study 2019

Background: In an era of shifting global agendas and expanded emphasis on non-communicable diseases and injuries along with communicable diseases, sound evidence on trends by cause at the national level is essential. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) provides a systematic scientific assessment of published, publicly available, and contributed data on incidence, prevalence, and mortality for a mutually exclusive and collectively exhaustive list of diseases and injuries. Methods: GBD estimates incidence, prevalence, mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life-years (DALYs) due to 369 diseases and injuries, for two sexes, and for 204 countries and territories. Input data were extracted from censuses, household surveys, civil registration and vital statistics, disease registries, health service use, air pollution monitors, satellite imaging, disease notifications, and other sources. Cause-specific death rates and cause fractions were calculated using the Cause of Death Ensemble model and spatiotemporal Gaussian process regression. Cause-specific deaths were adjusted to match the total all-cause deaths calculated as part of the GBD population, fertility, and mortality estimates. Deaths were multiplied by standard life expectancy at each age to calculate YLLs. A Bayesian meta-regression modelling tool, DisMod-MR 2.1, was used to ensure consistency between incidence, prevalence, remission, excess mortality, and cause-specific mortality for most causes. Prevalence estimates were multiplied by disability weights for mutually exclusive sequelae of diseases and injuries to calculate YLDs. We considered results in the context of the Socio-demographic Index (SDI), a composite indicator of income per capita, years of schooling, and fertility rate in females younger than 25 years. Uncertainty intervals (UIs) were generated for every metric using the 25th and 975th ordered 1000 draw values of the posterior distribution. Findings: Global health has steadily improved over the past 30 years as measured by age-standardised DALY rates. After taking into account population growth and ageing, the absolute number of DALYs has remained stable. Since 2010, the pace of decline in global age-standardised DALY rates has accelerated in age groups younger than 50 years compared with the 1990–2010 time period, with the greatest annualised rate of decline occurring in the 0–9-year age group. Six infectious diseases were among the top ten causes of DALYs in children younger than 10 years in 2019: lower respiratory infections (ranked second), diarrhoeal diseases (third), malaria (fifth), meningitis (sixth), whooping cough (ninth), and sexually transmitted infections (which, in this age group, is fully accounted for by congenital syphilis; ranked tenth). In adolescents aged 10–24 years, three injury causes were among the top causes of DALYs: road injuries (ranked first), self-harm (third), and interpersonal violence (fifth). Five of the causes that were in the top ten for ages 10–24 years were also in the top ten in the 25–49-year age group: road injuries (ranked first), HIV/AIDS (second), low back pain (fourth), headache disorders (fifth), and depressive disorders (sixth). In 2019, ischaemic heart disease and stroke were the top-ranked causes of DALYs in both the 50–74-year and 75-years-and-older age groups. Since 1990, there has been a marked shift towards a greater proportion of burden due to YLDs from non-communicable diseases and injuries. In 2019, there were 11 countries where non-communicable disease and injury YLDs constituted more than half of all disease burden. Decreases in age-standardised DALY rates have accelerated over the past decade in countries at the lower end of the SDI range, while improvements have started to stagnate or even reverse in countries with higher SDI. Interpretation: As disability becomes an increasingly large component of disease burden and a larger component of health expenditure, greater research and developm nt investment is needed to identify new, more effective intervention strategies. With a rapidly ageing global population, the demands on health services to deal with disabling outcomes, which increase with age, will require policy makers to anticipate these changes. The mix of universal and more geographically specific influences on health reinforces the need for regular reporting on population health in detail and by underlying cause to help decision makers to identify success stories of disease control to emulate, as well as opportunities to improve. Funding: Bill & Melinda Gates Foundation. © 2020 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 licens

Characterisation of microbial attack on archaeological bone

As part of an EU funded project to investigate the factors influencing bone preservation in the archaeological record, more than 250 bones from 41 archaeological sites in five countries spanning four climatic regions were studied for diagenetic alteration. Sites were selected to cover a range of environmental conditions and archaeological contexts. Microscopic and physical (mercury intrusion porosimetry) analyses of these bones revealed that the majority (68%) had suffered microbial attack. Furthermore, significant differences were found between animal and human bone in both the state of preservation and the type of microbial attack present. These differences in preservation might result from differences in early taphonomy of the bones. © 2003 Elsevier Science Ltd. All rights reserved

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field