Storage, modeling and analysis of dynamical systems for e-Science applications

• Grant number: 15/01587-0
• Support type: Research Grants - eScience and Data Science Program - Thematic Grants
• Duration: February 01, 2016 - January 31, 2020
• Field of knowledge: Physical Sciences and Mathematics - Computer Science - Computing Methodologies and Techniques
• Principal Investigator: João Eduardo Ferreira
• Grantee: João Eduardo Ferreira
• Home Institution: Instituto de Matemática e Estatística (IME). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Co-Principal Investigators: Marcel Parolin Jackowski ; Paulo Sergio Graziano Magalhães ; Roberto Hirata Junior ; Ronaldo Fumio Hashimoto
• Assoc. researchers: André Fujita ; André Santanchè ; Antonio Maria Francisco Luiz Jose Bonomi ; Ariane Machado Lima ; Carlos Eduardo Driemeier ; Carlos Eduardo Ferreira ; Cléver Ricardo Guareis de Farias ; David Corrêa Martins Junior ; Ester Cerdeira Sabino ; Fábio Vale Scarpare ; Felipe Werndl Trevizan ; Gisela Tunes da Silva ; Henrique Coutinho Junqueira Franco ; Junior Barrera ; Karina Valdivia Delgado ; Leliane Nunes de Barros ; Leonardo Lamas Leandro Ribeiro ; Luciano Vieira de Araújo ; Marcelo da Silva Reis ; Marcio Ferreira da Silva ; Marcio Katsumi Oikawa ; Marco Dimas Gubitoso ; Maria Teresa Borges Pimenta Barbosa ; Michelle Cristina Araujo Picoli ; Otavio Cavalett ; Routo Terada ; Vera Lúcia Reis de Gouveia
• Associated grant(s): 19/10388-2 - 32nd IEEE CBMS International Symposium on Computer-Based Medical Systems, AR.EXT; 16/11515-0 - 25th International Joint Conference on Artificial Intelligence - Advances in Bioinformatics and Artificial Intelligence: Bridging the Gap, AR.EXT
• Associated scholarship(s): 17/01330-5 - 3D image analysis for realistic modeling and simulation of biomass conversion processes, BP.PD; 16/22900-1 - Markov decision processes specified by probabilistic logic programming: representation and solution, BP.DD

Abstract

The astonishing fast rate of technology evolution has given rise to a new era of scientific knowledge discovery. This new age of science, known as e-Science, is described as the new great computational and multidisciplinary team science requiring novel methodologies for data storage, modeling and analysis. In particular, the development of transactional and analytical software systems for e-Science applications when viewed from a dynamic systems perspective, presents a number of new computational challenges. Among them are the scientific knowledge discovery processes, which involve frequent changes of requirements for data storage, modeling and analysis. The need to address scientific dynamic systems in order to cope with complex applications of e-Science has woken up the scientific community for the development of robust and evolutionary software systems to meet these new challenges. Dynamical system is the classical mathematical formalism to represent phenomena that evolute with time, which are of great interest in science. In this project, our main goal is to develop computational models and methodologies to support e-Science applications viewed as dynamic systems. Our fundamental research covers three key research areas, namely storage, modeling, and analysis of dynamic systems. These research areas are significant and relevant to the FAPESP e-Science Program since many of the present e-Science challenges are related to the proper treatment of dynamic systems. Hence, we plan to develop and apply computational methodologies that will ease the development of e-Science applications, thereby contributing to the improvement of worldwide scientific knowledge, while respecting legal and ethical restrictions in data management. (AU)

Scientific publications

(36)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

MORIMITSU, ALEXANDRE; PASSAT, NICOLAS; ALVES, WONDER A. L.; HASHIMOTO, RONALDO F. Efficient component-hypertree construction based on hierarchy of partitions. PATTERN RECOGNITION LETTERS, v. 135, p. 30-37, JUL 2020. Web of Science Citations: 0.

ALVES, WONDER A. L.; GOBBER, CHARLES F.; SILVA, DENNIS J.; MORIMITSU, ALEXANDRE; HASHIMOTO, RONALDO F.; MARCOTEGUI, BEATRIZ. Image segmentation based on ultimate levelings: From attribute filters to machine learning strategies. PATTERN RECOGNITION LETTERS, v. 133, p. 264-271, MAY 2020. Web of Science Citations: 0.

ESTRELA, GUSTAVO; GUBITOSO, MARCO DIMAS; FERREIRA, CARLOS EDUARDO; BARRERA, JUNIOR; REIS, MARCELO S. An Efficient, Parallelized Algorithm for Optimal Conditional Entropy-Based Feature Selection. Entropy, v. 22, n. 4 APR 2020. Web of Science Citations: 0.

FUJITA, ANDRE; LIRA, EDUARDO SILVA; SANTOS, SUZANA DE SIQUEIRA; BANDO, SILVIA YUMI; SOARES, GABRIELA ELEUTERIO; TAKAHASHI, DANIEL YASUMASA. A semi-parametric statistical test to compare complex networks. JOURNAL OF COMPLEX NETWORKS, v. 8, n. 2 APR 2020. Web of Science Citations: 0.

SANCHES, GUILHERME M.; GRAZIANO MAGALHAES, PAULO S.; DOS SANTOS LUCIANO, ANA C.; CAMARGO, LIVIA A.; FRANCO, HENRIQUE C. J. Comprehensive assessment of spatial soil variability related to topographic parameters in sugarcane fields. Geoderma, v. 362, MAR 15 2020. Web of Science Citations: 0.

MACUL FERREIRA DE BARROS, PEDRO; DO ROSARIO, MARIA CONCEICAO; SZEJKO, NATALIA; POLGA, NATALIA; REQUENA, GUARACI DE LIMA; RAVAGNANI, BEATRIZ; FATORI, DANIEL; BATISTUZZO, MARCELO CAMARGO; HOEXTER, MARCELO QUEIROZ; ROHDE, LUIS AUGUSTO; POLANCZYK, GUILHERME VANONI; LECKMAN, JAMES FREDERICK; MIGUEL, EURIPEDES CONSTANTINO; DE ALVARENGA, PEDRO GOMES. Risk factors for obsessive-compulsive symptoms. Follow-up of a community-based youth cohort. EUROPEAN CHILD & ADOLESCENT PSYCHIATRY, FEB 2020. Web of Science Citations: 0.

SILVA, DENNIS J.; ALVES, WONDER A. L.; HASHIMOTO, RONALDO FUMIO. Incremental bit-quads count in component trees: Theory, algorithms, and optimization. PATTERN RECOGNITION LETTERS, v. 129, p. 33-40, JAN 2020. Web of Science Citations: 0.

ANDRES, IGNASI; DE BARROS, LELIANE NUNES; DELGADO, KARINA VALDIVIA. Human-aware Contingent Planning. FUNDAMENTA INFORMATICAE, v. 174, n. 1, p. 63-81, 2020. Web of Science Citations: 0.

FERNANDO ANDRADE; ASUKA NAKATA; NORIKO GOTOH; ANDRÉ FUJITA. Large miRNA survival analysis reveals a prognostic four-biomarker signature for triple negative breast cancer. GENETICS AND MOLECULAR BIOLOGY, v. 43, n. 1, p. -, 2020. Web of Science Citations: 0.

CARASTAN-SANTOS, DANILO; MARTINS-, JR., DAVID C.; SONG, SIANG W.; ROZANTE, LUIZ C. S.; DE CAMARGO, RAPHAEL Y. A hybrid CPU-GPU-MIC algorithm for minimal hitting set enumeration. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, v. 31, n. 18, SI SEP 25 2019. Web of Science Citations: 1.

RIBEIRO, ADELE H.; PAVAN SOLER, JULIA MARIA; HIRATA JR, ROBERTO. Variance-Preserving Estimation of Intensity Values Obtained From Omics Experiments. FRONTIERS IN GENETICS, v. 10, SEP 20 2019. Web of Science Citations: 0.

RODRIGUES, FRANCISCO C. M.; ESPADOTO, MATEUS; HIRATA JR, ROBERTO; TELEA, ALEXANDRU C. Constructing and Visualizing High-Quality Classifier Decision Boundary Maps dagger. INFORMATION, v. 10, n. 9 SEP 2019. Web of Science Citations: 0.

YANCY-CABALLERO, DAISON; LING, LIU Y.; FUJITA, ANDRE; FERREIRA, JOAO E.; DRIEMEIER, CARLOS. Intraparticle Connectivity in Sugarcane Bagasse Unveiled by Pore Network Modeling. BioEnergy Research, v. 12, n. 3, p. 546-557, SEP 2019. Web of Science Citations: 0.

MACIEL CARDOSO, FELIPE; MELONI, SANDRO; SANTANCHE, ANDRE; MORENO, YAMIR. Topical Alignment in Online Social Systems. FRONTIERS IN PHYSICS, v. 7, APR 17 2019. Web of Science Citations: 0.

LISBOA, BIANCA C. G.; OLIVEIRA, KATIA C.; TAHIRA, ANA CAROLINA; BARBOSA, ANDRE ROCHA; FELTRIN, ARTHUR SANT'ANNA; GOUVEIA, GISELE; LIMA, LUZIA; FEIO DOS SANTOS, ANA CECILIA; MARTINS JR, DAVID CORREA; PUGA, RENATO DAVID; MORETTO, ARIANE CRISTINE; DE BRAGANCA PEREIRA, CARLOS ALBERTO; LAFER, BENY; PARAIZO LEITE, RENATA ELAINE; DE LUCENA FERRETTI-REBUSTINI, RENATA ELOAH; FARFEL, JOSE MARCELO; GRINBERG, LEA TENENHOLZ; JACOB-FILHO, WILSON; MIGUEL, EURIPEDES CONSTANTINO; HOEXTER HELENA BRENTANI, MARCELO QUEIROZ; BRENTANI, HELENA. Initial findings of striatum tripartite model in OCD brain samples based on transcriptome analysis. SCIENTIFIC REPORTS, v. 9, FEB 28 2019. Web of Science Citations: 1.

SILVA REIS, WILLY ARTHUR; DE BARROS, LELIANE NUNES; DELGADO, KARINA VALDIVIA. Robust topological policy iteration for infinite horizon bounded Markov Decision Processes. INTERNATIONAL JOURNAL OF APPROXIMATE REASONING, v. 105, p. 287-304, FEB 2019. Web of Science Citations: 0.

FELTRIN, ARTHUR SANT'ANNA; TAHIRA, ANA CAROLINA; SIMOES, SERGIO NERY; BRENTANI, HELENA; MARTINS, JR., DAVID CORREA. Assessment of complementarity of WGCNA and NERI results for identification of modules associated to schizophrenia spectrum disorders. PLoS One, v. 14, n. 1 JAN 15 2019. Web of Science Citations: 0.

RAMOS, TAIANE COELHO; BALARDIN, JOANA BISOL; SATO, JOAO RICARDO; FUJITA, ANDRE. Abnormal Cortico-Cerebellar Functional Connectivity in Autism Spectrum Disorder. FRONTIERS IN SYSTEMS NEUROSCIENCE, v. 12, JAN 15 2019. Web of Science Citations: 4.

SANCHES, GUILHERME M.; GRAZIANO MAGALHAES, PAULO S.; JUNQUEIRA FRANCO, HENRIQUE C. Site-specific assessment of spatial and temporal variability of sugarcane yield related to soil attributes. Geoderma, v. 334, p. 90-98, JAN 15 2019. Web of Science Citations: 1.

DRIEMEIER, CARLOS E.; LING, LIU Y.; YANCY-CABALLERO, DAISON; MANTELATTO, PAULO E.; DIAS, CARLOS S. B.; ARCHILHA, NATHALY L. Location of water in fresh sugarcane bagasse observed by synchrotron X-ray microtomography. PLoS One, v. 13, n. 12 DEC 6 2018. Web of Science Citations: 2.

BANDIERA PAIVA, THALES; TERADA, ROUTO. Improving the Efficiency of a Reaction Attack on the QC-MDPC McEliece. IEICE TRANSACTIONS ON FUNDAMENTALS OF ELECTRONICS COMMUNICATIONS AND COMPUTER SCIENCES, v. E101A, n. 10, p. 1676-1686, OCT 2018. Web of Science Citations: 0.

GUZMAN, GROVER E. C.; SATO, JOAO R.; VIDAL, MACIEL C.; FUJITA, ANDRE. Identification of alterations associated with age in the clustering structure of functional bra in networks. PLoS One, v. 13, n. 5 MAY 24 2018. Web of Science Citations: 1.

LAMAS, LEONARDO; DREZNER, RENE; OTRANTO, GUILHERME; BARRERA, JUNIOR. Analytic method for evaluating players' decisions in team sports: Applications to the soccer goalkeeper. PLoS One, v. 13, n. 2 FEB 6 2018. Web of Science Citations: 1.

ATASHPAZ-GARGARI, ESMAEIL; REIS, MARCELO S.; BRAGA-NETO, ULISSES M.; BARRERA, JUNIOR; DOUGHERTY, EDWARD R. A fast Branch-and-Bound algorithm for U-curve feature selection. PATTERN RECOGNITION, v. 73, p. 172-188, JAN 2018. Web of Science Citations: 3.

LIMA, WANIA REZENDE; MARTINS, DAVID CORREA; PARREIRA, KLEBER SIMONIO; SCARPELLI, PEDRO; DE MORAES, MIRIAM SANTOS; TOPALIS, PANTELIS; HASHIMOTO, RONALDO FUMIO; GARCIA, CELIA R. S. Genome-wide analysis of the human malaria parasite Plasmodium falciparum transcription factor PfNF-YB shows interaction with a CCAAT motif. ONCOTARGET, v. 8, n. 69, p. 113987-114001, DEC 26 2017. Web of Science Citations: 1.

YANCY-CABALLERO, DAISON; LING, LIU Y.; ARCHILHA, NATHALY L.; FERREIRA, JOAO E.; DRIEMEIER, CARLOS. Mineral Particles in Sugar Cane Bagasse: Localization and Morphometry Using Microtomography Analysis. ENERGY & FUELS, v. 31, n. 11, p. 12288-12296, NOV 2017. Web of Science Citations: 4.

JACOMINI, RICARDO DE SOUZA; MARTINS, JR., DAVID CORREA; DA SILVA, FELIPE LENO; REALI COSTA, ANNA HELENA. GeNICE: A Novel Framework for Gene Network Inference by Clustering, Exhaustive Search, and Multivariate Analysis. JOURNAL OF COMPUTATIONAL BIOLOGY, v. 24, n. 8, p. 809-830, AUG 2017. Web of Science Citations: 0.

FUJITA, ANDRE; TAKAHASHI, DANIEL YASUMASA; BALARDIN, JOANA BISOL; VIDAL, MACIEL CALEBE; SATO, JOAO RICARDO. Correlation between graphs with an application to brain network analysis. COMPUTATIONAL STATISTICS & DATA ANALYSIS, v. 109, p. 76-92, MAY 2017. Web of Science Citations: 0.

FUJITA, ANDRE; VIDAL, MACIEL C.; TAKAHASHI, DANIEL Y. A Statistical Method to Distinguish Functional Brain Networks. FRONTIERS IN NEUROSCIENCE, v. 11, FEB 14 2017. Web of Science Citations: 8.

VIDAL, MACIEL C.; SATO, JOAO R.; BALARDIN, JOANA B.; TAKAHASHI, DANIEL Y.; FUJITA, ANDRE. ANOCVA in R: A Software to Compare Clusters between Groups and Its Application to the Study of Autism Spectrum Disorder. FRONTIERS IN NEUROSCIENCE, v. 11, JAN 24 2017. Web of Science Citations: 1.

REIS, MARCELO S.; ESTRELA, GUSTAVO; FERREIRA, CARLOS EDUARDO; BARRERA, JUNIOR. featsel: A framework for benchmarking of feature selection algorithms and cost functions. SOFTWAREX, v. 6, p. 193-197, 2017. Web of Science Citations: 1.

DRIEMEIER, CARLOS; LING, LIU YI; SANCHES, GUILHERME M.; PONTES, ANGELICA O.; GRAZIANO MAGALHAES, PAULO S.; FERREIRA, JOAO E. A computational environment to support research in sugarcane agriculture. COMPUTERS AND ELECTRONICS IN AGRICULTURE, v. 130, p. 13-19, NOV 15 2016. Web of Science Citations: 7.

GOYA, DENISE H.; NAKAMURA, DIONATHAN; TERADA, ROUTO. Certificateless Key Agreement Protocols under Strong Models. IEICE TRANSACTIONS ON FUNDAMENTALS OF ELECTRONICS COMMUNICATIONS AND COMPUTER SCIENCES, v. E99A, n. 10, p. 1822-1832, OCT 2016. Web of Science Citations: 0.

MOREIRA, DANIEL A. M.; DELGADO, KARINA VALDIVIA; DE BARROS, LELIANE NUNES. Robust probabilistic planning with ilao. APPLIED INTELLIGENCE, v. 45, n. 3, p. 662-672, OCT 2016. Web of Science Citations: 0.

KINKER, GABRIELA SARTI; THOMAS, ANDREW MALTEZ; CARVALHO, VINICIUS JARDIM; LIMA, FELIPE PRATA; FUJITA, ANDRE. Deletion and low expression of NFKBIA are associated with poor prognosis in lower-grade glioma patients. SCIENTIFIC REPORTS, v. 6, APR 7 2016. Web of Science Citations: 4.

MEKKAOUI, CHOUKRI; METELLUS, PHILIPPE; KOSTIS, WILLIAM J.; MARTUZZI, ROBERTO; PEREIRA, FABRICIO R.; BEREGI, JEAN-PAUL; REESE, TIMOTHY G.; CONSTABLE, TODD R.; JACKOWSKI, MARCEL P. Diffusion Tensor Imaging in Patients with Glioblastoma Multiforme Using the Supertoroidal Model. PLoS One, v. 11, n. 1 JAN 13 2016. Web of Science Citations: 3.