Recovering Sparse Signals Using Sparse Measurement Matrices in Compressed DNA Microarrays

Microarrays (DNA, protein, etc.) are massively parallel affinity-based biosensors capable of detecting and quantifying a large number of different genomic particles simultaneously. Among them, DNA microarrays comprising tens of thousands of probe spots are currently being employed to test multitude of targets in a single experiment. In conventional microarrays, each spot contains a large number of copies of a single probe designed to capture a single target, and, hence, collects only a single data point. This is a wasteful use of the sensing resources in comparative DNA microarray experiments, where a test sample is measured relative to a reference sample. Typically, only a fraction of the total number of genes represented by the two samples is differentially expressed, and, thus, a vast number of probe spots may not provide any useful information. To this end, we propose an alternative design, the so-called compressed microarrays, wherein each spot contains copies of several different probes and the total number of spots is potentially much smaller than the number of targets being tested. Fewer spots directly translates to significantly lower costs due to cheaper array manufacturing, simpler image acquisition and processing, and smaller amount of genomic material needed for experiments. To recover signals from compressed microarray measurements, we leverage ideas from compressive sampling. For sparse measurement matrices, we propose an algorithm that has significantly lower computational complexity than the widely used linear-programming-based methods, and can also recover signals with less sparsity

On Recovery of Sparse Signals in Compressed DNA Microarrays

Currently, DNA micro arrays comprising tens of thousands of probe spots are employed to test entire genomes in a single experiment. Typically, each microarray spot contains a large number of copies of a single probe, and hence collects only a single data point. This is a wasteful use of the sensing resources in comparative DNA microarray experiments, where a test sample is measured relative to a reference sample. Since only a small fraction of the total number of genes represented by the two samples is differentially expressed, a large fraction of a microarray does not provide any useful information. To this end, in this paper we consider an alternative microarray design wherein each spot is a composite of several different probes, and the total number of spots is potentially much smaller than the number of genes being tested. Fewer spots directly translates to significantly lower costs due to cheaper array manufacturing, simpler image acquisition and processing, and smaller amount of genomic material needed for experiments. To recover signals from compressed microarray measurements, we leverage ideas from compressive sampling. Experimental verification of the proposed methodology is presented

An optimization framework for unsupervised identification of rare copy number variation from SNP array data

A highly sensitive and configurable method for calling copy number variants from SNP array data is presented that can identify even rare CNV

Mutational signatures and mutable motifs in cancer genomes

Cancer is a genetic disorder, meaning that a plethora of different mutations, whether somatic or germ line, underlie the etiology of the ‘Emperor of Maladies’. Point mutations, chromosomal rearrangements and copy number changes, whether they have occurred spontaneously in predisposed individuals or have been induced by intrinsic or extrinsic (environmental) mutagens, lead to the activation of oncogenes and inactivation of tumor suppressor genes, thereby promoting malignancy. This scenario has now been recognized and experimentally confirmed in a wide range of different contexts. Over the past decade, a surge in available sequencing technologies has allowed the sequencing of whole genomes from liquid malignancies and solid tumors belonging to different types and stages of cancer, giving birth to the new field of cancer genomics. One of the most striking discoveries has been that cancer genomes are highly enriched with mutations of specific kinds. It has been suggested that these mutations can be classified into ‘families’ based on their mutational signatures. A mutational signature may be regarded as a type of base substitution (e.g. C:G to T:A) within a particular context of neighboring nucleotide sequence (the bases upstream and/or downstream of the mutation). These mutational signatures, supplemented by mutable motifs (a wider mutational context), promise to help us to understand the nature of the mutational processes that operate during tumor evolution because they represent the footprints of interactions between DNA, mutagens and the enzymes of the repair/replication/modification pathway

Methods for change-point detection with additional interpretability

The main purpose of this dissertation is to introduce and critically assess some novel statistical methods for change-point detection that help better understand the nature of processes underlying observable time series. First, we advocate the use of change-point detection for local trend estimation in financial return data and propose a new approach developed to capture the oscillatory behaviour of financial returns around piecewise-constant trend functions. Core of the method is a data-adaptive hierarchically-ordered basis of Unbalanced Haar vectors which decomposes the piecewise-constant trend underlying observed daily returns into a binary-tree structure of one-step constant functions. We illustrate how this framework can provide a new perspective for the interpretation of change points in financial returns. Moreover, the approach yields a family of forecasting operators for financial return series which can be adjusted flexibly depending on the forecast horizon or the loss function. Second, we discuss change-point detection under model misspecification, focusing in particular on normally distributed data with changing mean and variance. We argue that ignoring the presence of changes in mean or variance when testing for changes in, respectively, variance or mean, can affect the application of statistical methods negatively. After illustrating the difficulties arising from this kind of model misspecification we propose a new method to address these using sequential testing on intervals with varying length and show in a simulation study how this approach compares to competitors in mixed-change situations. The third contribution of this thesis is a data-adaptive procedure to evaluate EEG data, which can improve the understanding of an epileptic seizure recording. This change-point detection method characterizes the evolution of frequencyspecific energy as measured on the human scalp. It provides new insights to this high dimensional high frequency data and has attractive computational and scalability features. In addition to contrasting our method with existing approaches, we analyse and interpret the method’s output in the application to a seizure data set

Natural Disaster Detection Using Wavelet and Artificial Neural Network

Indonesia, by the location of its geographic and geologic, it have more potential encounters for natural disasters. This nation is traversed by three tectonic plates, namely: IndoAustralian, the Eurasian and the Pacific plates. One of the tools employed to detect danger and send an early disaster warning is sensor device for ocean waves, but it has drawbacks related to the very limited time gap between information/warnings obtained and the real disaster event, which is only less than 30 minutes. Natural disaster early detection information system is essential to prevent potential danger. The system can make use of the pattern recognition of satellite imagery sequences that take place before and during the natural disaster. This study is conducted to determine the right wavelet to compress the satellite image sequences and to perform the pattern recognition process of a natural disaster employing an artificial neural network. This study makes use of satellite imagery sequences of tornadoes and hurricanes

Untangling hotel industry’s inefficiency: An SFA approach applied to a renowned Portuguese hotel chain

The present paper explores the technical efficiency of four hotels from Teixeira Duarte Group - a renowned Portuguese hotel chain. An efficiency ranking is established from these four hotel units located in Portugal using Stochastic Frontier Analysis. This methodology allows to discriminate between measurement error and systematic inefficiencies in the estimation process enabling to investigate the main inefficiency causes. Several suggestions concerning efficiency improvement are undertaken for each hotel studied.info:eu-repo/semantics/publishedVersio

Classifiers and machine learning techniques for image processing and computer vision

Orientador: Siome Klein GoldensteinTese (doutorado) - Universidade Estadual de Campinas, Instituto da ComputaçãoResumo: Neste trabalho de doutorado, propomos a utilizaçãoo de classificadores e técnicas de aprendizado de maquina para extrair informações relevantes de um conjunto de dados (e.g., imagens) para solução de alguns problemas em Processamento de Imagens e Visão Computacional. Os problemas de nosso interesse são: categorização de imagens em duas ou mais classes, detecçãao de mensagens escondidas, distinção entre imagens digitalmente adulteradas e imagens naturais, autenticação, multi-classificação, entre outros. Inicialmente, apresentamos uma revisão comparativa e crítica do estado da arte em análise forense de imagens e detecção de mensagens escondidas em imagens. Nosso objetivo é mostrar as potencialidades das técnicas existentes e, mais importante, apontar suas limitações. Com esse estudo, mostramos que boa parte dos problemas nessa área apontam para dois pontos em comum: a seleção de características e as técnicas de aprendizado a serem utilizadas. Nesse estudo, também discutimos questões legais associadas a análise forense de imagens como, por exemplo, o uso de fotografias digitais por criminosos. Em seguida, introduzimos uma técnica para análise forense de imagens testada no contexto de detecção de mensagens escondidas e de classificação geral de imagens em categorias como indoors, outdoors, geradas em computador e obras de arte. Ao estudarmos esse problema de multi-classificação, surgem algumas questões: como resolver um problema multi-classe de modo a poder combinar, por exemplo, caracteríisticas de classificação de imagens baseadas em cor, textura, forma e silhueta, sem nos preocuparmos demasiadamente em como normalizar o vetor-comum de caracteristicas gerado? Como utilizar diversos classificadores diferentes, cada um, especializado e melhor configurado para um conjunto de caracteristicas ou classes em confusão? Nesse sentido, apresentamos, uma tecnica para fusão de classificadores e caracteristicas no cenário multi-classe através da combinação de classificadores binários. Nós validamos nossa abordagem numa aplicação real para classificação automática de frutas e legumes. Finalmente, nos deparamos com mais um problema interessante: como tornar a utilização de poderosos classificadores binarios no contexto multi-classe mais eficiente e eficaz? Assim, introduzimos uma tecnica para combinação de classificadores binarios (chamados classificadores base) para a resolução de problemas no contexto geral de multi-classificação.Abstract: In this work, we propose the use of classifiers and machine learning techniques to extract useful information from data sets (e.g., images) to solve important problems in Image Processing and Computer Vision. We are particularly interested in: two and multi-class image categorization, hidden messages detection, discrimination among natural and forged images, authentication, and multiclassification. To start with, we present a comparative survey of the state-of-the-art in digital image forensics as well as hidden messages detection. Our objective is to show the importance of the existing solutions and discuss their limitations. In this study, we show that most of these techniques strive to solve two common problems in Machine Learning: the feature selection and the classification techniques to be used. Furthermore, we discuss the legal and ethical aspects of image forensics analysis, such as, the use of digital images by criminals. We introduce a technique for image forensics analysis in the context of hidden messages detection and image classification in categories such as indoors, outdoors, computer generated, and art works. From this multi-class classification, we found some important questions: how to solve a multi-class problem in order to combine, for instance, several different features such as color, texture, shape, and silhouette without worrying about the pre-processing and normalization of the combined feature vector? How to take advantage of different classifiers, each one custom tailored to a specific set of classes in confusion? To cope with most of these problems, we present a feature and classifier fusion technique based on combinations of binary classifiers. We validate our solution with a real application for automatic produce classification. Finally, we address another interesting problem: how to combine powerful binary classifiers in the multi-class scenario more effectively? How to boost their efficiency? In this context, we present a solution that boosts the efficiency and effectiveness of multi-class from binary techniques.DoutoradoEngenharia de ComputaçãoDoutor em Ciência da Computaçã

Analyzing Granger causality in climate data with time series classification methods

Attribution studies in climate science aim for scientifically ascertaining the influence of climatic variations on natural or anthropogenic factors. Many of those studies adopt the concept of Granger causality to infer statistical cause-effect relationships, while utilizing traditional autoregressive models. In this article, we investigate the potential of state-of-the-art time series classification techniques to enhance causal inference in climate science. We conduct a comparative experimental study of different types of algorithms on a large test suite that comprises a unique collection of datasets from the area of climate-vegetation dynamics. The results indicate that specialized time series classification methods are able to improve existing inference procedures. Substantial differences are observed among the methods that were tested