Papers by Sergio Silva Dias
Resumo: O estudo de processos do mundo real pode se tornar uma tarefa ar- dua. Objetos reais, esp... more Resumo: O estudo de processos do mundo real pode se tornar uma tarefa ar- dua. Objetos reais, especialmente aqueles relacionados a processos industriais, sao dificieis de modelar e compreender. Este trabalho busca reduzir a distância entre modelar um processo industrial e compreende-lo, baseando-se em Analise Formal de Conceitos para obter regras a partir de redes neurais previamente treinadas. Neste artigo uma ferramenta, Sophiann, e apresentada. A ideia prin- cipal e auxiliar usuarios na aprendizagem de processos industriais complexos. Abstract: Learning about real world process is not an easy task. Real objects, specially those related to industrial process, are difficult to model and under- stand. This work aims to reduce the gap between modelling an industrial pro- cess and understanding it. It is based on Formal Concept Analysis to obtain rules from neural networks previously trained. In this paper a tool, named Sophiann, is presented. The main idea is to help users learn abou...
Revista de Informática Teórica e Aplicada, 2011
Este trabalho apresenta um arcabouço para o desenvolvimento de algoritmos da análise formal de co... more Este trabalho apresenta um arcabouço para o desenvolvimento de algoritmos da análise formal de conceitos (AFC). Seu principal componente é um gerador de contextos formais sintéticos cujos parâmetros podem ser ajustados de forma a permitir testar os algoritmos em situações de interesse. Presentes também no arcabouço estão alguns algoritmos básicos da AFC e alguns contextos formais obtidos a partir de bases de dados reais, desde um relativamente pequeno a um muito grande, este último normalmente impraticável em sua forma original. Para exemplificar a avaliação do desempenho de algoritmos via o arcabouço, seus algoritmos básicos são avaliados por meio de dados sintéticos e reais. Originalmente desenvolvido para servir como instrumento de auxílio ao aprendizado dos principais algoritmos da AFC, nada impede que o mesmo possa ser usado para avaliação de novos algoritmos. Para isto é de especial importância o fato de que os parâmetros na geração de dados são ajustáveis de forma a cobrir situações de interesse.
Concept lattices reduction: Definition, analysis and classification
Expert Systems with Applications, 2015
Survey of the main existing techniques for concept lattices reduction.Classification of technique... more Survey of the main existing techniques for concept lattices reduction.Classification of techniques in three classes based on seven dimensions.Analyzing reduction techniques with formal concept analysis.Considerations are carried out about computational complexity and feasibility. Formal concept analysis (FCA) is currently considered an important formalism for knowledge representation, extraction and analysis with applications in different areas. A problem identified in several applications is the computational cost due to the large number of formal concepts generated. Even when that number is not very large, the essential aspects, those effectively needed, can be immersed in a maze of irrelevant details. In fact, the problem of obtaining a concept lattice of appropriate complexity and size is one of the most important problems of FCA. In literature, several different approaches to control the complexity and size of a concept lattice have been described, but so far they have not been properly analyzed, compared and classified. We propose the classification of techniques for concept lattice reduction in three groups: redundant information removal, simplification, and selection. The main techniques to reduce concept lattice are analyzed and classified based on seven dimensions, each one composed of a set of characteristics. Considerations are made about the applicability and computational complexity of approaches of different classes.
Mathematics and Computers in Simulation, 2015
Formal Concept Analysis (FCA) is a mathematical framework that offers conceptual data analysis an... more Formal Concept Analysis (FCA) is a mathematical framework that offers conceptual data analysis and knowledge discovery. One of the main issues of knowledge discovery is knowledge reduction. The objective of this paper is to investigate the knowledge reduction in FCA and propose a method based on Non-Negative Matrix Factorization (NMF) for addressing the issue. Experiments on real world and benchmark datasets offer the evidence for the performance of the proposed method. c
Hematology Reports, 2009
Hematopoietic stem cell (HSC) chemotaxis, adhesion, proliferation, quiescence and differentiation... more Hematopoietic stem cell (HSC) chemotaxis, adhesion, proliferation, quiescence and differentiation are regulated by interactions with bone marrow (BM) niches. Two niches have been identified in the adult BM: the endosteal (close to the bone) and the perivascular niche (close to blood vessels). A vast body of literature has revealed the molecular basis for the interaction of HSCs with the two niches. However, the signals that regulate the communication between the two niches have not been well defined. Taking in consideration several clinical and experimental arguments this review highlights the molecular cues, involved in the communication between the BM niches, which regulate the basic properties of HSCs in physiological and malignant conditions. As such, it aims at clarifying the most important advances in basic and clinical research focusing on the role of different factors in the regulation of the BM microenvironment.
2012 IEEE 12th International Conference on Advanced Learning Technologies, 2012
We designed and implemented a prototype software system based on proactive computing, as an add-o... more We designed and implemented a prototype software system based on proactive computing, as an add-on to existing technology enhanced learning platforms. In this paper, we show how our proactive engine augmented with the adequate proactive scenarios enhances the assignments subsystem of the Moodle™ learning management system by providing personalized, adaptive and intelligent support to both online learners and teachers.
2012 IEEE 12th International Conference on Advanced Learning Technologies, 2012
In this paper, we show how to implement a system that adds proactivity to Moodle TM to reach a pe... more In this paper, we show how to implement a system that adds proactivity to Moodle TM to reach a personalized and adaptive support for both students and teachers, by providing an engine to run proactive rules, based on events and non-events, to enhance the users' e-learning process.
Triangulating Gaussian-Like Surfaces of Molecules with Millions of Atoms
Computational Electrostatics for Biological Applications, 2014
Triangulating molecular surfaces is an important requirement in computational biology and bioinfo... more Triangulating molecular surfaces is an important requirement in computational biology and bioinformatics not only to visualize molecules and molecular complexes on computer screen, but also to measure their areas and volumes, as well as to infer useful information about interactions between molecules of a molecular complex. Triangulation algorithms for molecular surfaces are very expensive in terms of memory space and time performance, in particular when the number of atoms goes up to the millions. Even so, this paper aims to show that it is possible to triangulate and render molecules with a number of atoms of the order of magnitude of millions of atoms using a single desktop computer.
Triangulating molecular surfaces on multiple GPUs
Proceedings of the 20th European MPI Users' Group Meeting on - EuroMPI '13, 2013
ABSTRACT Current GPU-based workstations are inadequate to triangulate and rendering large molecul... more ABSTRACT Current GPU-based workstations are inadequate to triangulate and rendering large molecular datasets with thousands and hundreds of thousands, not to say millions, of atoms. The problem is not so the lack of processing power, but the memory limitations of current GPU graphics cards. For example, the NVidia GeForce GTX 590 graphics card comes with two 1.5GB GPUs. We tackle here this problem using a OpenMP-CUDA solution that runs on a loosely-coupled GPU cluster. Basically, we propose a fast, scalable, parallel triangulation algorithm for molecular surfaces that takes advantage of multicore processors of CPUs and GPUs of modern hardware architectures, where each CPU core works as the master of a single GPU, being the processing burden distributed over the CPU cores available in a single computer or a cluster. As much as we know, this is the first marching cubes algorithm that triangulates molecular surfaces on multiple GPUs using CUDA and OpenMP.
Parallel Computing, 2015
Standalone GPU-enabled computers are adequate to triangulate and rendering molecular datasets wit... more Standalone GPU-enabled computers are adequate to triangulate and rendering molecular datasets with some tens of thousands of atoms at most. But, a standalone GPU-enabled computer has a limited capacity to host programable graphics cards, which in turn have also their constraints in terms of memory space. Thus, in spite of the huge memory space made available and the tremendous processing power of the current GPU-based graphics cards, there remains a scalability problem when it is necessary to triangulate and render big molecules with hundreds of thousands to millions of atoms. In order to overcome this scalability problem we use an OpenMPI-OpenMP-CUDA solution that runs on a looselycoupled GPU cluster over a LAN (Local Area Network). More specifically, we propose a fast, scalable, parallel triangulation algorithm for molecular surfaces that takes advantage of multicore processors of CPUs and GPUs available over a local network, with each CPU core working as the master of a single GPU. The main contribution of this paper is that likely introduces the first marching cubes algorithm that triangulates molecular surfaces on CUDA devices over a network of GPU-enabled computers.
GPU-based triangulation of the van der Waals surface
2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2010
AbstractThe problem addressed in this paper consists in triangulating the van der Waals surface ... more AbstractThe problem addressed in this paper consists in triangulating the van der Waals surface without computing the geometric intersections of its atoms. Recall that the van der Waals surface is useful in computational molecular biology and biochemistry to, for example, determine ...
Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing - HPDC '10, 2010
Computing molecular surfaces is important to measure areas and volumes of molecules, as well as t... more Computing molecular surfaces is important to measure areas and volumes of molecules, as well as to infer useful information about interactions with other molecules. Over the years many algorithms have been developed to triangulate and to render molecular surfaces. However, triangulation algorithms usually are very expensive in terms of memory storage and time performance, and thus far from real-time performance. Fortunately, the massive computational power of the new generation of low-cost GPUs opens up an opportunity window to solve these problems: real-time performance and cheap computing commodities. This paper just presents a GPU-based algorithm to speed up the triangulation and rendering of molecular surfaces using CUDA. Our triangulation algorithm for molecular surfaces is based on a multi-threaded, parallel version of the Marching Cubes (MC) algorithm. However, the input of our algorithm is not the volume dataset of a given molecule as usual for Marching Cubes, but the atom centers provided by the PDB file of such a molecule. We also carry out a study that compares a serial version (CPU) and a parallel version (GPU) of the MC algorithm in triangulating molecular surfaces as a way to understand how real-time rendering of molecular surfaces can be achieved in the future.
Polygonization of non-homogeneous non-manifold implicit surfaces with tentative topological guarantees
IEEE Congress on Evolutionary Computation, 2010
I. INTRODUCTION Implicit surfaces are widely used in computer graphics and visualization. A 3D im... more I. INTRODUCTION Implicit surfaces are widely used in computer graphics and visualization. A 3D implicit surface S is a zero set of a real function f : Ω ⊆ R3 → R, ie S = {(x, y, z) ∈ R3 : f(x, y, z) = 0}, where Ω is an axis-aligned bounding box enclosing S partially or totally. The ...
Journal of Hematological Malignancies, 2012
In adult bone marrow (BM), hematopoietic stem/progenitor cells (HSPCs) reside in micro-environmen... more In adult bone marrow (BM), hematopoietic stem/progenitor cells (HSPCs) reside in micro-environments which provide instructions for self-renewal, survival, proliferation, differentiation and migration. Adequate response to such complex signals implies communication between HSCs, BM stroma and extracellular matrix molecules (ECM). This is achieved mainly through adhesion molecules. Malignant hematopoietic cells also interact with the BM microenvironment, which provides them with proliferative and survival advantages. Most of the studies on haematological diseases describe cell-ECM interactions as key mechanisms in tumor progression, while genetic alterations of HSC are considered major initiators of the malignant process. However, accumulating evidence suggests that an altered BM microenvironment provides anomalous cell adhesion signals, facilitating tumor initiation. Myeloproliferative and myelodysplastic syndromes are good examples of haematological disorders where alterations in BM microenvironment may play an important role in disease initiation. This review discusses the role for adhesion signals in regulating the BM microenvironment in normalcy and disease.
PLoS ONE, 2011
Neo-blood vessel growth (angiogenesis), which may involve the activation of pre-existing endothel... more Neo-blood vessel growth (angiogenesis), which may involve the activation of pre-existing endothelial cells (EC) and/or the recruitment of bone marrow-derived vascular precursor cells (BM-VPC), is essential for tumor growth. Molecularly, besides the well established roles for Vascular endothelial growth factor (VEGF), recent findings show the Notch signalling pathway, in particular the ligand Delta-like 4 (Dll4), is also essential for adequate tumor angiogenesis; Dll4 inhibition results in impaired, non-functional, angiogenesis and reduced tumor growth. However, the role of BM-VPC in the setting of Notch pathway modulation was not addressed and is the subject of the present report. Here we show that SDF-1 and VEGF, which are produced by tumors, increase Dll4 expression on recruited BM-VPC. Mechanistically, BM-VPC activated, in a Dll4dependent manner, a transcriptional program on mature EC suggestive of EC activation and stabilization. BM-VPC induced ICAM-2 and Fibronectin expression on EC, an effect that was blocked by a Dll4-specific neutralizing antibody. In vivo, transplantation of BM-VPC with decreased Dll4 into tumor-bearing mice resulted in the formation of microvessels with decreased pericyte coverage and reduced fibronectin expression. Consequently, transplantation of BM-VPC with decreased Dll4 resulted in impaired tumor angiogenesis, increased tumor hypoxia and apoptosis, and decreased tumor growth. Taken together, our data suggests that Dll4 expression by BM-VPC affects their communication with tumor vessel endothelial cells, thereby modulating tumor angiogenesis by affecting vascular stability.
PLoS ONE, 2010
Background: Secondary bone marrow (BM) myelodysplastic syndromes (MDS) are increasingly common, a... more Background: Secondary bone marrow (BM) myelodysplastic syndromes (MDS) are increasingly common, as a result of radio or chemotherapy administered to a majority of cancer patients. Patients with secondary MDS have increased BM cell apoptosis, which results in BM dysfunction (cytopenias), and an increased risk of developing fatal acute leukemias. In the present study we asked whether TNF-a, known to regulate cell apoptosis, could modulate the onset of secondary MDS.
PLoS ONE, 2008
Bone marrow (BM) derived vascular precursor cells (BM-PC, endothelial progenitors) are involved i... more Bone marrow (BM) derived vascular precursor cells (BM-PC, endothelial progenitors) are involved in normal and malignant angiogenesis, in ischemia and in wound healing. However, the mechanisms by which BM-PC stimulate the pre-existing endothelial cells at sites of vascular remodelling/recovery, and their contribution towards the formation of new blood vessels are still undisclosed. In the present report, we exploited the possibility that members of the Notch signalling pathway, expressed by BM-PC during endothelial differentiation, might regulate their pro-angiogenic or pro-wound healing properties. We demonstrate that Notch pathway modulates the adhesion of BM-PC to extracellular matrix (ECM) in vitro via regulation of integrin alpha3beta1; and that Notch pathway inhibition on BM-PC impairs their capacity to stimulate endothelial cell tube formation on matrigel and to promote endothelial monolayer recovery following wounding in vitro. Moreover, we show that activation of Notch pathway on BM-PC improved wound healing in vivo through angiogenesis induction. Conversely, inoculation of BM-PC pre-treated with a gamma secretase inhibitor (GSI) into wounded mice failed to induce angiogenesis at the wound site and did not promote wound healing, presumably due to a lower frequency of BM-PC at the wound area. Our data suggests that Notch pathway regulates BM-PC adhesion to ECM at sites of vascular repair and that it also regulates the capacity of BM-PC to stimulate angiogenesis and to promote wound healing. Drug targeting of the Notch pathway on BM-PC may thus represent a novel strategy to modulate neo-angiogenesis and vessel repair.
Molecular Cancer Research, 2011
VEGF receptors 1 (FLT-1) and 2 (KDR) are expressed on subsets of acute myeloid leukemia (AML) and... more VEGF receptors 1 (FLT-1) and 2 (KDR) are expressed on subsets of acute myeloid leukemia (AML) and acute lymphoid leukemia cells, in which they induce cell survival, proliferation, and migration. However, little is known about possible cofactors that regulate VEGF receptor expression and activation on leukemia cells. Here we show that cholesterol accumulates in leukemia-rich sites within bone marrow of xenotransplanted severe combined immunodeficient (SCID) mice. Therefore, we hypothesized that cholesterol-rich domains might regulate FLT-1 signaling and chemotaxis of acute leukemias. We then showed that FLT-1 accumulates in discrete cholesterol-rich membrane domains where it associates with caveolin-1 and that placenta growth factor (PlGF)/VEGF stimulation promotes FLT-1 localization in such cholesterol-rich domains. Accordingly, FLT-1 localization and its phosphorylation are abrogated by methyl-β-cyclodextrin (MβCD), which removes cellular cholesterol, and by nystatin, an inhibitor ...
Leukemia, 2007
Mutations in ras proto-oncogenes are associated with lower mdr1 gene expression in adult acute my... more Mutations in ras proto-oncogenes are associated with lower mdr1 gene expression in adult acute myeloid leukaemia.
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Papers by Sergio Silva Dias