Objective Classification of Galaxy Spectra using the Information Bottleneck Method

A new method for classification of galaxy spectra is presented, based on a recently introduced information theoretical principle, the `Information Bottleneck'. For any desired number of classes, galaxies are classified such that the information content about the spectra is maximally preserved. The result is classes of galaxies with similar spectra, where the similarity is determined via a measure of information. We apply our method to approximately 6000 galaxy spectra from the ongoing 2dF redshift survey, and a mock-2dF catalogue produced by a Cold Dark Matter-based semi-analytic model of galaxy formation. We find a good match between the mean spectra of the classes found in the data and in the models. For the mock catalogue, we find that the classes produced by our algorithm form an intuitively sensible sequence in terms of physical properties such as colour, star formation activity, morphology, and internal velocity dispersion. We also show the correlation of the classes with the projections resulting from a Principal Component Analysis.Comment: submitted to MNRAS, 17 pages, Latex, with 14 figures embedde

Validação de heterogeneidade estrutural em dados de Crio-ME por comitês de agrupadores

Orientadores: Fernando José Von Zuben, Rodrigo Villares PortugalDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Elétrica e de ComputaçãoResumo: Análise de Partículas Isoladas é uma técnica que permite o estudo da estrutura tridimensional de proteínas e outros complexos macromoleculares de interesse biológico. Seus dados primários consistem em imagens de microscopia eletrônica de transmissão de múltiplas cópias da molécula em orientações aleatórias. Tais imagens são bastante ruidosas devido à baixa dose de elétrons utilizada. Reconstruções 3D podem ser obtidas combinando-se muitas imagens de partículas em orientações similares e estimando seus ângulos relativos. Entretanto, estados conformacionais heterogêneos frequentemente coexistem na amostra, porque os complexos moleculares podem ser flexíveis e também interagir com outras partículas. Heterogeneidade representa um desafio na reconstrução de modelos 3D confiáveis e degrada a resolução dos mesmos. Entre os algoritmos mais populares usados para classificação estrutural estão o agrupamento por k-médias, agrupamento hierárquico, mapas autoorganizáveis e estimadores de máxima verossimilhança. Tais abordagens estão geralmente entrelaçadas à reconstrução dos modelos 3D. No entanto, trabalhos recentes indicam ser possível inferir informações a respeito da estrutura das moléculas diretamente do conjunto de projeções 2D. Dentre estas descobertas, está a relação entre a variabilidade estrutural e manifolds em um espaço de atributos multidimensional. Esta dissertação investiga se um comitê de algoritmos de não-supervisionados é capaz de separar tais "manifolds conformacionais". Métodos de "consenso" tendem a fornecer classificação mais precisa e podem alcançar performance satisfatória em uma ampla gama de conjuntos de dados, se comparados a algoritmos individuais. Nós investigamos o comportamento de seis algoritmos de agrupamento, tanto individualmente quanto combinados em comitês, para a tarefa de classificação de heterogeneidade conformacional. A abordagem proposta foi testada em conjuntos sintéticos e reais contendo misturas de imagens de projeção da proteína Mm-cpn nos estados "aberto" e "fechado". Demonstra-se que comitês de agrupadores podem fornecer informações úteis na validação de particionamentos estruturais independetemente de algoritmos de reconstrução 3DAbstract: Single Particle Analysis is a technique that allows the study of the three-dimensional structure of proteins and other macromolecular assemblies of biological interest. Its primary data consists of transmission electron microscopy images from multiple copies of the molecule in random orientations. Such images are very noisy due to the low electron dose employed. Reconstruction of the macromolecule can be obtained by averaging many images of particles in similar orientations and estimating their relative angles. However, heterogeneous conformational states often co-exist in the sample, because the molecular complexes can be flexible and may also interact with other particles. Heterogeneity poses a challenge to the reconstruction of reliable 3D models and degrades their resolution. Among the most popular algorithms used for structural classification are k-means clustering, hierarchical clustering, self-organizing maps and maximum-likelihood estimators. Such approaches are usually interlaced with the reconstructions of the 3D models. Nevertheless, recent works indicate that it is possible to infer information about the structure of the molecules directly from the dataset of 2D projections. Among these findings is the relationship between structural variability and manifolds in a multidimensional feature space. This dissertation investigates whether an ensemble of unsupervised classification algorithms is able to separate these "conformational manifolds". Ensemble or "consensus" methods tend to provide more accurate classification and may achieve satisfactory performance across a wide range of datasets, when compared with individual algorithms. We investigate the behavior of six clustering algorithms both individually and combined in ensembles for the task of structural heterogeneity classification. The approach was tested on synthetic and real datasets containing a mixture of images from the Mm-cpn chaperonin in the "open" and "closed" states. It is shown that cluster ensembles can provide useful information in validating the structural partitionings independently of 3D reconstruction methodsMestradoEngenharia de ComputaçãoMestre em Engenharia Elétric

Generative Adversarial Networks (GANs): Challenges, Solutions, and Future Directions

Generative Adversarial Networks (GANs) is a novel class of deep generative models which has recently gained significant attention. GANs learns complex and high-dimensional distributions implicitly over images, audio, and data. However, there exists major challenges in training of GANs, i.e., mode collapse, non-convergence and instability, due to inappropriate design of network architecture, use of objective function and selection of optimization algorithm. Recently, to address these challenges, several solutions for better design and optimization of GANs have been investigated based on techniques of re-engineered network architectures, new objective functions and alternative optimization algorithms. To the best of our knowledge, there is no existing survey that has particularly focused on broad and systematic developments of these solutions. In this study, we perform a comprehensive survey of the advancements in GANs design and optimization solutions proposed to handle GANs challenges. We first identify key research issues within each design and optimization technique and then propose a new taxonomy to structure solutions by key research issues. In accordance with the taxonomy, we provide a detailed discussion on different GANs variants proposed within each solution and their relationships. Finally, based on the insights gained, we present the promising research directions in this rapidly growing field.Comment: 42 pages, Figure 13, Table

To Compress or Not to Compress -- Self-Supervised Learning and Information Theory: A Review

Deep neural networks have demonstrated remarkable performance in supervised learning tasks but require large amounts of labeled data. Self-supervised learning offers an alternative paradigm, enabling the model to learn from data without explicit labels. Information theory has been instrumental in understanding and optimizing deep neural networks. Specifically, the information bottleneck principle has been applied to optimize the trade-off between compression and relevant information preservation in supervised settings. However, the optimal information objective in self-supervised learning remains unclear. In this paper, we review various approaches to self-supervised learning from an information-theoretic standpoint and present a unified framework that formalizes the \textit{self-supervised information-theoretic learning problem}. We integrate existing research into a coherent framework, examine recent self-supervised methods, and identify research opportunities and challenges. Moreover, we discuss empirical measurement of information-theoretic quantities and their estimators. This paper offers a comprehensive review of the intersection between information theory, self-supervised learning, and deep neural networks

Kernel Feature Extraction Methods for Remote Sensing Data Analysis

Technological advances in the last decades have improved our capabilities of collecting and storing high data volumes. However, this makes that in some fields, such as remote sensing several problems are generated in the data processing due to the peculiar characteristics of their data. High data volume, high dimensionality, heterogeneity and their nonlinearity, make that the analysis and extraction of relevant information from these images could be a bottleneck for many real applications. The research applying image processing and machine learning techniques along with feature extraction, allows the reduction of the data dimensionality while keeps the maximum information. Therefore, developments and applications of feature extraction methodologies using these techniques have increased exponentially in remote sensing. This improves the data visualization and the knowledge discovery. Several feature extraction methods have been addressed in the literature depending on the data availability, which can be classified in supervised, semisupervised and unsupervised. In particular, feature extraction can use in combination with kernel methods (nonlinear). The process for obtaining a space that keeps greater information content is facilitated by this combination. One of the most important properties of the combination is that can be directly used for general tasks including classification, regression, clustering, ranking, compression, or data visualization. In this Thesis, we address the problems of different nonlinear feature extraction approaches based on kernel methods for remote sensing data analysis. Several improvements to the current feature extraction methods are proposed to transform the data in order to make high dimensional data tasks easier, such as classification or biophysical parameter estimation. This Thesis focus on three main objectives to reach these improvements in the current feature extraction methods: The first objective is to include invariances into supervised kernel feature extraction methods. Throughout these invariances it is possible to generate virtual samples that help to mitigate the problem of the reduced number of samples in supervised methods. The proposed algorithm is a simple method that essentially generates new (synthetic) training samples from available labeled samples. These samples along with original samples should be used in feature extraction methods obtaining more independent features between them that without virtual samples. The introduction of prior knowledge by means of the virtual samples could obtain classification and biophysical parameter estimation methods more robust than without them. The second objective is to use the generative kernels, i.e. probabilistic kernels, that directly learn by means of clustering techniques from original data by finding local-to-global similarities along the manifold. The proposed kernel is useful for general feature extraction purposes. Furthermore, the kernel attempts to improve the current methods because the kernel not only contains labeled data information but also uses the unlabeled information of the manifold. Moreover, the proposed kernel is parameter free in contrast with the parameterized functions such as, the radial basis function (RBF). Using probabilistic kernels is sought to obtain new unsupervised and semisupervised methods in order to reduce the number and cost of labeled data in remote sensing. Third objective is to develop new kernel feature extraction methods for improving the features obtained by the current methods. Optimizing the functional could obtain improvements in new algorithm. For instance, the Optimized Kernel Entropy Component Analysis (OKECA) method. The method is based on the Independent Component Analysis (ICA) framework resulting more efficient than the standard Kernel Entropy Component Analysis (KECA) method in terms of dimensionality reduction. In this Thesis, the methods are focused on remote sensing data analysis. Nevertheless, feature extraction methods are used to analyze data of several research fields whereas data are multidimensional. For these reasons, the results are illustrated into experimental sequence. First, the projections are analyzed by means of Toy examples. The algorithms are tested through standard databases with supervised information to proceed to the last step, the analysis of remote sensing images by the proposed methods

Information-Theoretic Compressive Measurement Design

An information-theoretic projection design framework is proposed, of interest for feature design and compressive measurements. Both Gaussian and Poisson measurement models are considered. The gradient of a proposed information-theoretic metric (ITM) is derived, and a gradient-descent algorithm is applied in design; connections are made to the information bottleneck. The fundamental solution structure of such design is revealed in the case of a Gaussian measurement model and arbitrary input statistics. This new theoretical result reveals how ITM parameter settings impact the number of needed projection measurements, with this verified experimentally. The ITM achieves promising results on real data, for both signal recovery and classification