Biologically Inspired Computer Vision/ Applications of Computational Models of Primate Visual Systems in Computer Vision and Image Processing

Biologically Inspired Computer VisionApplications of Computational Models of Primate Visual Systems in Computer Vision and Image Processing Reza Hojjaty Saeedy Abstract Biological vision systems are remarkable at extracting and analyzing the information that is essential for vital functional needs. They perform all these tasks with both high sensitivity and strong reliability. They can efficiently and quickly solve most of the difficult computa- tional problems that are still challenging for artificial systems, such as scene segmentation, 3D/depth perception, motion recognition, etc. So it is no surprise that biological vision systems have been a source of inspiration for computer vision problems. In this research, we aim to provide a computer vision task centric framework out of models primarily originating in biological vision studies. We try to address two specific tasks here: saliency detection and object classification. In both of these tasks we use features extracted from computational models of biological vision systems as a starting point for further processing. Saliency maps are 2D topographic maps that catch the most conspicuous regions of a scene, i.e. the pixels in an image that stand out against their neighboring pixels. So these maps can be thought of as representations of the human attention process and thus have a lot of applications in computer vision. We propose a cascade that combines two well- known computational models for perception of color and orientation in order to simulate the responses of the primary areas of the primate visual cortex. We use these responses as inputs to a spiking neural network(SNN) and finally the output of this SNN will serve as the input to our post-processing algorithm for saliency detection. Object classification/detection is the most studied task in computer vision and machine learning and it is interesting that while it looks trivial for humans it is a difficult problem for artificial systems. For this part of the thesis we also design a pipeline including feature extraction using biologically inspired systems, manifold learning for dimensionality reduction and self-organizing(vector quantization) neural network as a supervised method for prototype learning

Biologically Inspired Computer Vision/ Applications of Computational Models of Primate Visual Systems in Computer Vision and Image Processing

Biologically Inspired Computer VisionApplications of Computational Models of Primate Visual Systems in Computer Vision and Image Processing Reza Hojjaty Saeedy Abstract Biological vision systems are remarkable at extracting and analyzing the information that is essential for vital functional needs. They perform all these tasks with both high sensitivity and strong reliability. They can efficiently and quickly solve most of the difficult computa- tional problems that are still challenging for artificial systems, such as scene segmentation, 3D/depth perception, motion recognition, etc. So it is no surprise that biological vision systems have been a source of inspiration for computer vision problems. In this research, we aim to provide a computer vision task centric framework out of models primarily originating in biological vision studies. We try to address two specific tasks here: saliency detection and object classification. In both of these tasks we use features extracted from computational models of biological vision systems as a starting point for further processing. Saliency maps are 2D topographic maps that catch the most conspicuous regions of a scene, i.e. the pixels in an image that stand out against their neighboring pixels. So these maps can be thought of as representations of the human attention process and thus have a lot of applications in computer vision. We propose a cascade that combines two well- known computational models for perception of color and orientation in order to simulate the responses of the primary areas of the primate visual cortex. We use these responses as inputs to a spiking neural network(SNN) and finally the output of this SNN will serve as the input to our post-processing algorithm for saliency detection. Object classification/detection is the most studied task in computer vision and machine learning and it is interesting that while it looks trivial for humans it is a difficult problem for artificial systems. For this part of the thesis we also design a pipeline including feature extraction using biologically inspired systems, manifold learning for dimensionality reduction and self-organizing(vector quantization) neural network as a supervised method for prototype learning

ePointDA: An End-to-End Simulation-to-Real Domain Adaptation Framework for LiDAR Point Cloud Segmentation

Due to its robust and precise distance measurements, LiDAR plays an important role in scene understanding for autonomous driving. Training deep neural networks (DNNs) on LiDAR data requires large-scale point-wise annotations, which are time-consuming and expensive to obtain. Instead, simulation-to-real domain adaptation (SRDA) trains a DNN using unlimited synthetic data with automatically generated labels and transfers the learned model to real scenarios. Existing SRDA methods for LiDAR point cloud segmentation mainly employ a multi-stage pipeline and focus on feature-level alignment. They require prior knowledge of real-world statistics and ignore the pixel-level dropout noise gap and the spatial feature gap between different domains. In this paper, we propose a novel end-to-end framework, named ePointDA, to address the above issues. Specifically, ePointDA consists of three modules: self-supervised dropout noise rendering, statistics-invariant and spatially-adaptive feature alignment, and transferable segmentation learning. The joint optimization enables ePointDA to bridge the domain shift at the pixel-level by explicitly rendering dropout noise for synthetic LiDAR and at the feature-level by spatially aligning the features between different domains, without requiring the real-world statistics. Extensive experiments adapting from synthetic GTA-LiDAR to real KITTI and SemanticKITTI demonstrate the superiority of ePointDA for LiDAR point cloud segmentation.Comment: Accepted by AAAI 202

Comparing Features of Three-Dimensional Object Models Using Registration Based on Surface Curvature Signatures

This dissertation presents a technique for comparing local shape properties for similar three-dimensional objects represented by meshes. Our novel shape representation, the curvature map, describes shape as a function of surface curvature in the region around a point. A multi-pass approach is applied to the curvature map to detect features at different scales. The feature detection step does not require user input or parameter tuning. We use features ordered by strength, the similarity of pairs of features, and pruning based on geometric consistency to efficiently determine key corresponding locations on the objects. For genus zero objects, the corresponding locations are used to generate a consistent spherical parameterization that defines the point-to-point correspondence used for the final shape comparison

Computational Spectroscopy in Solution by Integration of Variational and Perturbative Approaches on Top of Clusterized Molecular Dynamics

Multiscale QM/MM approaches have become the most suitable and effective methods for the investigation of spectroscopic properties of medium-or large-size chromophores in condensed phases. On these grounds, we are developing a novel workflow aimed at improving the generality, reliability, and ease of use of the available tools. In the present paper, we report the latest developments of such an approach with specific reference to a general workplan starting with the addition of acetonitrile to the panel of solvents already available in the General Liquid Optimized Boundary (GLOB) model enforcing nonperiodic boundary conditions (NPBC). Next, the solvatochromic shifts induced by acetonitrile on both rigid (uracil and thymine) and flexible (thyrosine) chromophores have been studied introducing in our software a number of new features ranging from rigid-geometry NPBC molecular dynamics based on the quaternion formalism to a full integration of variational (ONIOM) and perturbative (perturbed matrix method (PMM)) approaches for describing different solute-solvent topologies and local fluctuations, respectively. Finally, thymine and uracil have been studied also in methanol to point out the generality of the computational strategy. While further developments are surely needed, the strengths of our integrated approach even in its present version are demonstrated by the accuracy of the results obtained by an unsupervised approach and coupled to a computational cost strongly reduced with respect to that of conventional QM/MM models without any appreciable accuracy deterioration

Topographic mappings and feed-forward neural networks

This thesis is a study of the generation of topographic mappings - dimension reducing transformations of data that preserve some element of geometric structure - with feed-forward neural networks. As an alternative to established methods, a transformational variant of Sammon's method is proposed, where the projection is effected by a radial basis function neural network. This approach is related to the statistical field of multidimensional scaling, and from that the concept of a 'subjective metric' is defined, which permits the exploitation of additional prior knowledge concerning the data in the mapping process. This then enables the generation of more appropriate feature spaces for the purposes of enhanced visualisation or subsequent classification. A comparison with established methods for feature extraction is given for data taken from the 1992 Research Assessment Exercise for higher educational institutions in the United Kingdom. This is a difficult high-dimensional dataset, and illustrates well the benefit of the new topographic technique. A generalisation of the proposed model is considered for implementation of the classical multidimensional scaling (¸mds}) routine. This is related to Oja's principal subspace neural network, whose learning rule is shown to descend the error surface of the proposed ¸mds model. Some of the technical issues concerning the design and training of topographic neural networks are investigated. It is shown that neural network models can be less sensitive to entrapment in the sub-optimal global minima that badly affect the standard Sammon algorithm, and tend to exhibit good generalisation as a result of implicit weight decay in the training process. It is further argued that for ideal structure retention, the network transformation should be perfectly smooth for all inter-data directions in input space. Finally, there is a critique of optimisation techniques for topographic mappings, and a new training algorithm is proposed. A convergence proof is given, and the method is shown to produce lower-error mappings more rapidly than previous algorithms

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