George Teodoro

George Teodoro
Federal University of Minas Gerais | UFMG · Departamento de Ciência da Computação

PhD

About

129
Publications
20,969
Reads
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1,471
Citations
Additional affiliations
August 2011 - August 2013
Georgia Institute of Technology
Position
  • PostDoc Position
July 2011 - August 2013
Emory University
Position
  • Researcher
October 2010 - May 2011
University of Maryland, College Park
Position
  • Researcher

Publications

Publications (129)
Article
The analysis of high resolution whole slide tissue images is a computationally expensive task, which adversely impacts effective use of pathology imaging data in research. We propose runtime solutions to enable efficient execution of pathology image analysis applications on modern distributed memory hybrid platforms equipped with both CPUs and GPUs...
Chapter
Full-text available
In triple negative breast cancer (TNBC) treatment, early prediction of pathological complete response (PCR) from chemotherapy before surgical operations is crucial for optimal treatment planning. We propose a novel deep learning-based system to predict PCR to neoadjuvant chemotherapy for TNBC patients with multi-stained histopathology images of ser...
Article
Background and objective: Computerized pathology image analysis is an important tool in research and clinical settings, which enables quantitative tissue characterization and can assist a pathologist's evaluation. The aim of our study is to systematically quantify and minimize uncertainty in output of computer based pathology image analysis. Meth...
Article
Motivation: In most tissue-based biomedical research, the lack of sufficient pathology training images with well-annotated ground truth inevitably limits the performance of deep learning systems. In this study, we propose a convolutional neural network with foveal blur enriching datasets with multiple local nuclei regions of interest derived from...
Article
Full-text available
This work presents a hardware/software co-design implementation of the morphological reconstruction targeting a System-on-Chip (SoC) FPGA-based embedded system. Our approach processes large images with fast algorithms. This was achieved by the proposal and use of an execution scheme that partitions the input image into sub-images that are independe...
Article
The parallelization of Smith-Waterman sequence comparison tools for long DNA sequences has been a big challenge over the years, requesting the use of several devices and sophisticated optimizations. Pruning is one of these optimizations, which can reduce considerably the amount of computation. This paper proposes MultiBP, a sequence comparison solu...
Conference Paper
In this paper, we propose a method that optimizes a regularization parameter for the regularized Free Form Deformation (FFD) non-rigid image registration. The developed process utilizes autoencoder generated image representations to assess image data generalization quality by the regularization parameter. Both pixel intensity and learned features a...
Conference Paper
Three-dimensional (3D) digital pathology has been emerging for next-generation tissue based cancer research. To enable such histopathology image volume analysis, serial histopathology slides need to be well aligned. In this paper, we propose a histopathology image registration fine tuning method with integrated landmark evaluations by texture and s...
Article
Purpose: Retinal pigment epithelial (RPE) cells serve as a supporter for the metabolism and visual function of photoreceptors and a barrier for photoreceptor protection. Morphology dynamics, spatial organization, distribution density, and growth patterns of RPE cells are important for further research on these RPE main functions. To enable such in...
Article
Nearest neighbors search is a core operation found in several online multimedia services. These services have to handle very large databases, while, at the same time, they must minimize the query response times observed by users. This is specially complex because those services deal with fluctuating query workloads (rates). Consequently, they must...
Article
Full-text available
Nesse artigo é apresentada uma paralelização eficiente do algoritmo de busca por similaridade Product Quantization Approximate Nearest Neighbor Search (PQANNS). Esse método pode responder consultas com uma demanda reduzida de memória e, juntamente com a paralelização proposta, pode lidar de forma eficiente com grandes bases de dados. A execução utili...
Article
Hepatic steatosis droplet quantification with histology biopsies has high clinical significance for risk stratification and management of patients with fatty liver diseases and in the decision to use donor livers for transplantation. However, pathology reviewing processes, when conducted manually, are subject to a high inter- and intra-reader varia...
Preprint
Liver steatosis is known as the abnormal accumulation of lipids within cells. An accurate quantification of steatosis area within the liver histopathological microscopy images plays an important role in liver disease diagnosis and trans-plantation assessment. Such a quantification analysis often requires a precise steatosis segmentation that is cha...
Conference Paper
Full-text available
Nesse artigo é apresentada uma paralelização eficiente do algoritmo de busca por similaridade Product Quantization Approximate Nearest Neighbor Search (PQANNS). Esse método pode responder consultas com uma demanda reduzida de memória e, juntamente com a paralelização proposta, pode lidar de forma eficiente com grandes bases de dados. A execução uti...
Article
This work presents a Field Programmable Gate Array (FPGA) implementation of the fast hybrid (FH) morphological reconstruction algorithm used in image analysis. The FH was implemented in the Cyclone V SoCKit-FPGA using a hardware/software co-design approach. The architecture was described in VHDL and evaluated with brain tissue images. The FH implem...
Preprint
Efficient execution of parameter sensitivity analysis (SA) is critical to allow for its routinely use. The pathology image processing application investigated in this work processes high-resolution whole-slide cancer tissue images from large datasets to characterize and classify the disease. However, the application is parameterized and changes in...
Article
Structural alignments of Ribonucleic acid (RNA) sequences solved by the Sankoff algorithm are computationally expensive and often require constraints to be used in practice. Modern Graphics Processing Units (GPUs) contain more than 1000 cores, which compute in parallel to speed up applications. Here, we present a GPU‐based solution to the RNA struc...
Article
Parameter sensitivity analysis (SA) is an effective tool to gain knowledge about complex analysis applications and assess the variability in their analysis results. However, it is an expensive process as it requires the execution of the target application multiple times with a large number of different input parameter values. In this work, we propo...
Article
Full-text available
Recent advancements in systematic analysis of high resolution whole slide images have increase efficiency of diagnosis, prognosis and prediction of cancer and important diseases. Due to the enormous sizes and dimensions of whole slide images, the analysis requires extensive computing resources which are not commonly available. Images have to be til...
Article
Full-text available
Most of the exact algorithms for biological sequence comparison obtain the optimal result by calculating dynamic programming (DP) matrices with quadratic time and space complexity. Fickett prunes the DP matrices by only computing values inside a band of size k, thus reducing time and space complexity to [Formula: see text]. Myers and Miller (MM) pr...
Conference Paper
Liver steatosis is known as the abnormal accumulation of lipids within cells. An accurate quantification of steatosis area within the liver histopathological microscopy images plays an important role in liver disease diagnosis and transplantation assessment. Such a quantification analysis often requires a precise steatosis segmentation that is chal...
Article
Full-text available
We propose a segmentation method for nuclei in glioblastoma histopathologic images based on a sparse shape prior guided variational level set framework. By spectral clustering and sparse coding, a set of shape priors is exploited to accommodate complicated shape variations. We automate the object contour initialization by a seed detection algorithm...
Article
Full-text available
Digital pathology imaging enables valuable quantitative characterizations of tissue state at the sub-cellular level. While there is a growing set of methods for analysis of whole slide tissue images, many of them are sensitive to changes in input parameters. Evaluating how analysis results are affected by variations in input parameters is important...
Article
Given the increasing number of proposals and definitions of operators in the scope of fractional calculus, it is important to introduce a systematic classification. Nonetheless, many of the definitions that emerged in the literature can not be considered as fractional derivatives. We analyze a list of expressions to have a general overview of the c...
Book
This book constitutes the refereed post-conference proceedings of International Workshops: Polystores and other Systems for Heterogeneous Data, Poly 2018, and Data Management and Analytics for Medicine and Healthcare, DMAH 2018, in Rio de Janeiro, Brazil, in August 2018, held in conjunction with the 44th International Conference on Very Large Data...
Article
Full-text available
IP lookup is a core operation in packet forwarding, which is implemented using a Longest Prefix Matching (LPM) algorithm to find the next hop for an input address. This work proposes and evaluates the use of parallel processors to deploy an optimized IP lookup algorithm based on Bloom filters. We target the implementation on the Intel Xeon Phi (Int...
Preprint
Full-text available
With the increasingly availability of digital microscopy imagery equipments there is a demand for efficient execution of whole slide tissue image applications. Through the process of sensitivity analysis it is possible to improve the output quality of such applications, and thus, improve the desired analysis quality. Due to the high computational c...
Article
We propose a software platform that integrates methods and tools for multi-objective parameter auto-tuning in tissue image segmentation workflows. The goal of our work is to provide an approach for improving the accuracy of nucleus/cell segmentation pipelines by tuning their input parameters. The shape, size, and texture features of nuclei in tissu...
Article
The similarity search in high-dimensional spaces is a core operation found in several online multimedia retrieval applications. With the popularity of these applications, they are required to handle very large and increasing datasets, while keeping the response time low. This problem is worsened in the context of online applications, mostly due to...
Article
Biological sequence comparison is often used as an auxiliary task in the analysis of genetic material. Pairwise comparison algorithms like Smith‐Waterman evaluate two strings representing sequences of proteins, DNA or RNA to obtain optimal alignment between them. Many applications have been proposed to address the sequence comparison problem, prior...
Preprint
We propose a software platform that integrates methods and tools for multi-objective parameter auto- tuning in tissue image segmentation workflows. The goal of our work is to provide an approach for improving the accuracy of nucleus/cell segmentation pipelines by tuning their input parameters. The shape, size and texture features of nuclei in tissu...
Preprint
Highly clumped nuclei clusters captured in fluorescence in situ hybridization microscopy images are common histology entities under investigations in a wide spectrum of tissue-related biomedical investigations. Due to their large scale in presence, computer based image analysis is used to facilitate such analysis with improved analysis efficiency a...
Conference Paper
An accurate steatosis quantification with pathology tissue samples is of high clinical importance. However, such pathology measurement is manually made in most clinical practices, subject to severe reader variability due to large sampling bias and poor reproducibility. Although some computerized automated methods are developed to quantity the steat...
Conference Paper
Full-text available
Highly clumped nuclei captured in fluorescence microscopy images are commonly observed in a wide spectrum of tissue-related biomedical investigations. To ensure the quality of downstream biomedical analyses, it is essential to accurately segment clustered nuclei. However, this presents a technical challenge as fluorescence intensity alone is often...
Conference Paper
Cellular phenotypic features derived from histopathology images are the basis of pathologic diagnosis and are thought to be related to underlying molecular profiles. Due to overwhelming cell numbers and population heterogeneity, it remains challenging to quantitatively compute and compare features of cells with distinct molecular signatures. In thi...
Preprint
Full-text available
An accurate steatosis quantification with pathology tissue samples is of high clinical importance. However, such pathology measurement is manually made in most clinical practices, subject to severe reader variability due to large sampling bias and poor reproducibility. Although some computerized automated methods are developed to quantify the steat...
Preprint
Full-text available
Cellular phenotypic features derived from histopathology images are the basis of pathologic diagnosis and are thought to be related to underlying molecular profiles. Due to overwhelming cell numbers and population heterogeneity, it remains challenging to quantitatively compute and compare features of cells with distinct molecular signatures. In thi...
Article
Full-text available
Biological sequence comparison algorithms that compute the optimal local and global alignments calculate a dynamic programming (DP) matrix with quadratic time complexity. The DP matrix H is calculated with a recurrence relation in which the value of each cell Hi,j is the result of a maximum operation on the cells' values Hi-1, j-1, Hi-1, j and Hi,j...
Article
Full-text available
The Irregular Wavefront Propagation Pattern (IWPP) is a core computing structure in several image analysis operations. Efficient implementation of IWPP on the Intel Xeon Phi is difficult because of the irregular data access and computation characteristics. The traditional IWPP algorithm relies on atomic instructions, which are not available in the...
Article
Full-text available
The Exact Set Similarity Join problem aims to find all similar sets between two collections of sets, with respect to a threshold and a similarity function such as overlap, Jaccard, dice or cosine. The naive approach verifies all pairs of sets and it is often considered impractical due the high number of combinations. So, Exact Set Similarity Join a...
Article
Full-text available
Apresentamos as várias maneiras de definir uma derivada fracionária, na forma de uma introdução histórica ao cálculo fracionário. Partindo do conceito de derivada fracionária, que é uma generalização da integral de Cauchy, abordamos as derivadas fracionárias nos sentidos de Riemann-Liouville e Caputo. Discutimos propostas recentes de novas derivada...
Conference Paper
Full-text available
We investigate efficient sensitivity analysis (SA) of algorithms that segment and classify image features in a large dataset of high-resolution images. Algorithm SA is the process of evaluating variations of methods and parameter values to quantify differences in the output. A SA can be very compute demanding because it requires re-processing the i...
Conference Paper
Full-text available
This work presents a hardware implementation of the morphological reconstruction algorithm for biomedical images analysis. The morphological reconstruction algorithm is based on the Sequential Reconstruction (SR). In this case, a hardware architecture has been developed and implemented by mapping the SR algorithm into an Altera Cyclone IV E FPGA ba...
Article
Full-text available
Multiple Sequence Alignment (MSA) is a basic operation in Bioinformatics, and is used to highlight the similarities among a set of sequences. The MSA problem was proven NP-Hard, thus requiring a high amount of memory and computing power. This problem can be modeled as a search for the path with minimum cost in a graph, and the A-Star algorithm has...
Conference Paper
Full-text available
In this paper, we propose and evaluate Fickett-MM, a parallel strategy that combines the algorithms Fickett and Myers-Miller, splitting a pairwise sequence comparison into multiple comparisons of subsequences and calculating an appropriate Fickett band to each subsequence comparison (block). With this approach, we potentially reduce the number of c...
Conference Paper
Full-text available
Systematic analysis of high resolution whole slide images enables more effective diagnosis, prognosis and prediction of cancer and other important diseases. Due to the enormous sizes and dimensions of whole slide images, the analysis requires extensive computing resources which are not commonly available. Images have to be divided into smaller regi...
Conference Paper
Full-text available
In this paper, we propose a novel segmentation method for cells in histopathologic images based on a sparse shape prior guided variational level set framework. We automate the cell contour initialization by detecting seeds and deform contours by minimizing a new energy functional that incorporates a shape term involving sparse shape priors, an adap...
Conference Paper
High-throughput serial histology imaging provides a new avenue for the routine study of micro-anatomical structures in a 3D space. However, the emergence of serial whole slide imaging poses a new registration challenge, as the gigapixel image size precludes the direct application of conventional registration techniques. In this paper, we develop a...
Article
Full-text available
Motivation: Sensitivity analysis and parameter tuning are important processes in large-scale image analysis. They are very costly because the image analysis workflows are required to be executed several times to systematically correlate output variations with parameter changes or to tune parameters. An integrated solution with minimum user interac...
Article
Full-text available
Background: We describe an informatics framework for researchers and clinical investigators to efficiently perform parameter sensitivity analysis and auto-tuning for algorithms that segment and classify image features in a large dataset of high-resolution images. The computational cost of the sensitivity analysis process can be very high, because t...
Presentation
Sensitivity Analysis is key part of analysis process in whole slide tissue images. Theses analyses are very expensive and to reach a good refinement for the results in the existents workflows it is necessary execute these workflows several times systematically. This paper presents a study of methods for creating Surrogate Models using Region Templa...
Article
Full-text available
This paper proposes and evaluates CUDAlign 4.0, a parallel strategy to obtain the optimal alignment of huge DNA sequences in multi-GPU platforms, using the exact Smith-Waterman (SW) algorithm. In the first phase of CUDAlign 4.0, a huge Dynamic Programming (DP) matrix is computed by multiple GPUs, which asynchronously communicate border elements to...
Article
Full-text available
This paper presents an agent-based simulator for environmental land change that includes efficient and parallel auto-tuning. This simulator extends the Multi-Agent System for Environmental simulation (MASE) by introducing rationality to agents using a mentalistic approach—the Belief-Desire-Intention (BDI) model—and is thus named MASE-BDI. Because t...
Conference Paper
Full-text available
A área de saúde e, em especial, a patologia clinica com análise automatizada de imagens microscópicas é um campo com demanda crescente por poder computacional. Uma barreira para a utilização eficaz de computação nesse cenário é a indisponibilidade de recursos computacionais suficientes, devido aos altos custos relacionados. Dessa forma, nesse artig...