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14th brazilian symposium on Bioinformatics, BSB 2021

14th Brazilian Symposium on Bioinformatics, BSB 2021

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14th brazilian symposium on Bioinformatics, BSB 2021

ISBN: (纸本)9783030918132

the proceedings contain 15 papers. the special focus in this conference is on Bioinformatics. the topics include: Feature Importance Analysis of Non-coding DNA/RNA Sequences Based on Machine Learning Approaches;heuristics for Cycle Packing of Adjacency Graphs for Genomes with Repeated Genes;preface;comparative Transcriptome Profiling of Maytenus ilicifolia Root and Leaf;PIMBA: A PIpeline for MetaBarcoding Analysis;CEvADA: Co-Evolution Analysis Data Archive;FluxPRT: An Adaptable and Extensible Proteomics LIMS;MathPIP: Classification of Proinflammatory Peptides Using Mathematical Descriptors;metagenomic Insights of the Microbial Community from a Polluted River in Brazil 2020;Mesoscopic Evaluation of DNA Mismatches in PCR Primer-Target Hybridisation to Detect SARS-CoV-2 Variants of Concern;Hypusine Plays a Role in the Translation of Short mRNAs and Mediates the Polyamine and Autophagy Pathways in Saccharomyces Cerevisiae;topological Characterization of Cancer Driver Genes Using Reactome Super Pathways Networks;CellHeap: A Workflow for Optimizing COVID-19 Single-Cell RNA-Seq Data processing in the Santos Dumont Supercomputer.

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Viscosity solutions of a level-set method for anisotropic geometric diffusion in image processing

Viscosity solutions of a level-set method for anisotropic ge...

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19th brazilian symposium on computer graphics and image processing (SIBGRAPI 2006)

作者： Preusser, Tobias Univ Bremen Ctr Comp Syst & Visualizat CeVis D-28359 Bremen Germany

We discuss the existence of viscosity solutions for a class of anisotropic level-set methods which can be seen as an extension of the mean-curvature motion with a nonlinear anisotropic diffusion tensor. In an earlier work (Mikula et al. in Comput. Vis. Sci. 6(4):197-209, [2004];Preusser and Rumpf in SIAM J. Appl. Math. 62(5):1772-1793, [2002]) we have applied such methods for the denoising and enhancement of static images and image sequences. the models are characterized by the fact that-unlike the mean-curvature motion-they are capable of retaining important geometric structures like edges and corners of the level-sets. the article reviews the definition of the model and discusses its geometric behavior. the proof of the existence of viscosity solutions for these models is based on a fixed point argument which utilizes a compactness property of the diffusion tensor. For the application to image processing suitable regularizations of the diffusion tensor are presented for which the compactness assumptions of the existence proof hold. Finally, we consider the half relaxed limits of the solutions of auxiliary problems to show the compactness of the solution operator and thus the existence of a solution to the original problem.

关键词： image processing anisotropic diffusion level set method viscosity solution half relaxed limits

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From bag-of-visual-words to bag-of-visual-phrases using n-grams

From bag-of-visual-words to bag-of-visual-phrases using n-gr...

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2013 26th Conference on graphics, Patterns and images, SIBGRAPI 2013

作者： Pedrosa, Glauco V. Traina, Agma J.M. Instituto de Ciencias Matematicas e de Computacao - ICMC Universidade de Sao Paulo - USP Brazil

ISBN: (纸本)9780769550992

the Bag-of-Visual-Words has emerged as an effective modeling approach to represent local image features. It describes local image features by assigning them a visual word according to a visual dictionary. the image representation is given by the frequency of each visual word in the image, as a similar representation used in textual documents. In this paper, we present a novel approach building a high-level description using a group of words (phrases) for representing an image. We introduce the use of n-grams for image representation, based on the idea of 'Bag-of-Visual-Phrases'. In the field of computational linguistics, an n-gram is a phrase formed by a sequence of n-consecutive words. As analogy, we represent an image by a combination of n-consecutive visual words. We made representative experiments using three public benchmark databases of textures and nature scenes and two medical databases to demonstrate an area that can benefit from the proposed technique. Our proposed Bag-of-Visual-Phrases approach improved up to 44% the retrieval precision and up to 33% the classification rate compared to the traditional Bag-of-Visual-Words, being a valuable asset for content-based image retrieval and image classification. © 2013 IEEE.

关键词： image representation

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image segmentation by image foresting transform with non-smooth connectivity functions

Image segmentation by image foresting transform with non-smo...

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2013 26th Conference on graphics, Patterns and images, SIBGRAPI 2013

作者： Mansilla, Lucy A.C. Miranda, Paulo A.V. Vechiatto Cappabianco, Fabio A.M. 05508-090 Sao Paulo SP Brazil Instituto de Ciencia e Tecnologia Universidade Federal de Sao Paulo Sao Jose dos Campos SP Brazil

ISBN: (纸本)9780769550992

In the framework of the image Foresting Transform (IFT), there is a class of connectivity functions that were vaguely explored, which corresponds to the non-smooth connectivity functions (NSCF). these functions are more adaptive to cope with the problems of field in homogeneity, which are common in MR images of 3 Tesla. In this work, we investigate the NSCF from the standpoint of theoretical and experimental aspects. We formally classify several non-smooth functions according to a proposed diagram representation. then, we investigate some theoretical properties for some specific regions of the diagram. Our analysis reveals that many NSCFs are, in fact, the result of a sequence of optimizations, each of them involving a maximal set of elements, in a well-structured way. Our experimental results indicate that substantial improvements can be obtained by NSCFs in the 3D segmentation of MR images of 3 Tesla, when compared to smooth connectivity functions. © 2013 IEEE.

关键词： image segmentation

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An automatic system for spermiogram analysis based on image processing techniques and Support Vector Machines 14

An automatic system for spermiogram analysis based on image ...

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14th International symposium on Medical Information processing and Analysis

作者： Revollo, Natalia V. Delrieux, Claudio A. Gonzalez-Jose, Rolando Izetta R, Javier UNS CONICET Inst Invest Ingn Elect Avda Alem 1253 Bahia Blanca Buenos Aires Argentina Consejo Nacl Invest Cient & Tecn Ctr Nacl Patagon Inst Patagon Ciencias Sociales & Humanas Bvd Brown 2915U9120ACD Puerto Madryn Chubut Argentina UNS CONICET Dept Ingn Elect & Comp Av Alem 1253 Bahia Blanca Buenos Aires Argentina UNJu Fac Ingn Italo Palanca 10 San Salvador De Jujuy Argentina

ISBN: (数字)9781510626065

ISBN: (纸本)9781510626065

image-based diagnosis becoming one of the most important areas in medicine, as the diversity and sophistication of imaging techniques are being increasingly used in hospitals and medical centers. this, however, raises the issue of having image analysis capabilities that go with this trend, to be able to use medical imagery to provide fast and accurate diagnosis. In andrology in particular, the spermiogram analysis is considered the most significant study to evaluate the male reproductive capacity. Spermiograms can be produced with relatively little effort and cost, since they require only standard procedures for sample treatment. However, an adequate assessment of sperm quality requires the careful inspection by higly trained specialists, requiring time, and being prone to high inter- and intra-specialist variances. In this paper we present a system for automatic spermiogram analysis using image processing and machine learning techniques. the system was trained using a repository of spermiograms and the opinion of several experts in andrology and in human reproduction, using different information sources and classification criteria. the results are aimed to develop a SaaS CASA (computer Assisted Sperm Analysis) system that can provide results over the Internet.

关键词： sperm analysis image processing techniques machine learning segmentation classification

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image Re-Ranking Acceleration on GPUs

Image Re-Ranking Acceleration on GPUs

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25th International symposium on computer Architecture and High Performance Computing (SBAC-PAD)

作者： Guimaraes Pedronette, Daniel Carlos Torres, Ricardo da S. Borin, Edson Breternitz, Mauricio Univ Estadual Sao Paulo UNESP Dept Stat Appl Math & Comp Rio Claro Brazil Univ Campinas UNICAMP Inst Comp Campinas SP Brazil Adv Micro Devices AMD Austin MN USA

ISBN: (纸本)9781479929276

Huge image collections are becoming available lately. In this scenario, the use of Content-Based image Retrieval (CBIR) systems has emerged as a promising approach to support image searches. the objective of CBIR systems is to retrieve the most similar images in a collection, given a query image, by taking into account image visual properties such as texture, color, and shape. In these systems, the effectiveness of the retrieval process depends heavily on the accuracy of ranking approaches. Recently, re-ranking approaches have been proposed to improve the effectiveness of CBIR systems by taking into account the relationships among images. the re-ranking approaches consider the relationships among all images in a given dataset. these approaches typically demands a huge amount of computational power, which hampers its use in practical situations. On the other hand, these methods can be massively parallelized. In this paper, we propose to speedup the computation of the RL-Sim algorithm, a recently proposed image re-ranking approach, by using the computational power of graphics processing Units (GPU). GPUs are emerging as relatively inexpensive parallel processors that are becoming available on a wide range of computer systems. We address the image re-ranking performance challenges by proposing a parallel solution designed to fit the computational model of GPUs. We conducted an experimental evaluation considering different implementations and devices. Experimental results demonstrate that significant performance gains can be obtained. Our approach achieves speedups of 7x from serial implementation considering the overall algorithm and up to 36x on its core steps.

关键词： content-based image retrieval image re-ranking parallel computing OpenCL GPU

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Topologically-Guided Color image Enhancement 14th

Topologically-Guided Color Image Enhancement

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14th International symposium on Visual Computing (ISVC)

作者： Tu, Junyi Rosen, Paul Univ S Florida Tampa FL 33620 USA

ISBN: (纸本)9783030337230;9783030337223

Enhancement is an important step in post-processing digital images for personal use, in medical imaging, and for object recognition. Most existing manual techniques rely on region selection, similarity, and/or thresholding for editing, never really considering the topological structure of the image. In this paper, we leverage the contour tree to extract a hierarchical representation of the topology of an image. We propose 4 topology-aware transfer functions for editing features of the image using local topological properties, instead of global image properties. Finally, we evaluate our approach with grayscale and color images.

关键词： image editing Topological Data Analysis Contour tree

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Structural analysis of histological images to aid diagnosis of cervical cancer

Structural analysis of histological images to aid diagnosis ...

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25th Conference on graphics, Patterns and images, SIBGRAPI 2012

作者： Miranda, Gisele Helena Barboni Barrera, Junior Soares, Edson Garcia Felipe, Joaquim Cezar Department of Computing and Mathematics Faculty of Philosophy Sciences and Languages of Ribeirão Preto USP Brazil Department of Computer Science Institute of Mathematics and Statistics USP Brazil Department of Pathology Faculty of Medicine of Ribeirão Preto USP Brazil

ISBN: (纸本)9780769548296

the use of computational techniques in the processing of histopathological images allows the study of the structural organization of tissues and their pathological changes. the overall objective of this work includes the proposal, the implementation and the evaluation of a methodology for the analysis of cervical intraepithelial neoplasia (CIN) from histopathological images. For this pourpose, a pipeline of morphological operators were implemented for the segmentation of cell nuclei and the Delaunay Triangulation were used in order to represent the tissue architecture. Also, clustering algorithms and graph morphology were used to automatically obtain the boundary between the histological layers of the epithelial tissue. Similarity criteria and adjacency relations between the triangles of the network were explored. the proposed method was evaluated concerning the detection of the presence of lesions in the tissue as well as the their malignancy grading. © 2012 IEEE.

关键词： Tissue

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MRI iterative super resolution with wiener filter regularization

MRI iterative super resolution with wiener filter regulariza...

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2013 26th Conference on graphics, Patterns and images, SIBGRAPI 2013

作者： Aguena, Marcia L.S. Mascarenha, Nelson D.A. Anacleto, Junia C. Fels, Sidney S. Departamento de Computacao UFSCar - Universidade Federal de Sao Carlos Sao Carlos SP Brazil Dept. of Electrical and Computer Engineering University of British Columbia Vancouver BC Canada

ISBN: (纸本)9780769550992

the swallowing process affects several aspects of one's welfare, as nutrition, hydration, respiration and hearing. Magnetic resonance imaging (MRI) has been a valuable tool to study swallowing, since it is a non-invasive procedure that can dynamically capture the shapes of the tongue and other elements involved in the process. the resolution enhancement of the MRI frames support directly diseases diagnoses, helping the visual analysis, or can be a pre-processing tool to segmentation, classification, recognition or modelling. MRI frames with better resolution, with less blurring or noise can be obtained changing the acquisition process, or using more powerful devices, but the cost of this solution is higher than applying computational Super-Resolution (SR) techniques. this paper studies a Bayesian approach to provide a Wiener filter to regularize the conjugate gradient solution, and promote an adaptation of an iterative SR method for non-rigid registration that can be generalized to other iterative SR methods. © 2013 IEEE.

关键词： Magnetic resonance imaging

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image Enhancement using Chaotic Maps and Bio-inspired Multi-objective Optimization

Image Enhancement using Chaotic Maps and Bio-inspired Multi-...

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14th International symposium on Signals, Circuits and Systems (ISSCS)

作者： Bejinariu, Silviu-Ioan Costin, Hariton Rotaru, Florin Luca, Ramona Romanian Acad Iasi Branch Inst Comp Sci Iasi Romania Gr T Popa Univ Med & Pharm Fac Med Bioengn Iasi Romania

ISBN: (纸本)9781728138961

image enhancement is a preprocessing step required in most image processing and computer vision applications because a high quality image leads to better and accurate processing results. Usually the image quality is subjectively associated to its contrast, but, by increasing the contrast, other distortions can be created. In this paper is proposed a context-free image enhancement method based on the multi-objective Particle Swarm Optimization algorithm combined with chaotic sequences. As objective functions, the expected contrast gain and tone distortion are used. the experiments revealed that for the particle swarm algorithm the results are better when the chaotic maps are used instead of the standard random evolution. the results are also superior to those obtained by the traditional histogram equalization method.

关键词： Optimization image enhancement Histograms Distortion Linear programming Particle swarm optimization Transfer functions

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