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Intermediate representations in Computational Science for knowledge discovery

Grant number: 15/22308-2
Support type:Research Projects - Thematic Grants
Duration: November 01, 2017 - October 31, 2022
Field of knowledge:Physical Sciences and Mathematics - Computer Science - Computing Methodologies and Techniques
Principal researcher:Roberto Marcondes Cesar Junior
Grantee:Roberto Marcondes Cesar Junior
Home Institution: Instituto de Matemática e Estatística (IME). Universidade de São Paulo (USP). São Paulo , SP, Brazil
Principal researchers:Carlos Alberto Moreira Filho ; Luciano da Fontoura Costa ; Nina Sumiko Tomita Hirata ; Ronaldo Fumio Hashimoto
Assoc. researchers:Cesar Henrique Comin ; Edson Amaro Junior ; Fernanda Bernardi Bertonha ; Marcel Parolin Jackowski ; Maria da Graca Campos Pimentel ; Roberto Hirata Junior ; Ronaldo Fumio Hashimoto ; Silvia Yumi Bando Takahara ; Valeria Meirelles Carril Elui
Associated grant(s):20/06160-3 - Human leukocyte transcriptional response to SARS-CoV-2 infection, AP.R
18/17421-2 - 2018 IEEE International Conference on Image Processing, AR.EXT
Associated scholarship(s):20/13255-0 - Algorithms for the acquisition, formation and annotation of remote sensing images, BP.TT
20/13275-1 - Projects cyberinfrastructure administrator, BP.TT
20/06744-5 - Deep learning and intermediate representations for pediatric image analysis, BP.PD
+ associated scholarships 19/23343-7 - Temporal analysis of gene expression, BP.PD
19/01077-3 - Integrating computer vision and complex networks for urban analysis, BP.PD
19/06280-1 - Integration, transformation, dataset augmentation and quality control for intermediate representation, BP.PD
19/06254-0 - Structural pattern recognition and intermediate representations, BP.PD
19/04219-3 - Project cyberinfrasctruture administration, BP.TT
18/10489-0 - Transformations of complex networks and their implication in topology and dynamics of complex systems, BP.PD
18/00390-7 - QR code detection using deep learning models, BP.MS
18/00477-5 - Learning image-to-image transformations, BP.MS
18/07386-5 - Segmentation of neonatal magnetic resonance imaging: a structural approach, BP.MS - associated scholarships

Abstract

This project focuses on a unified strategy for knowledge and emerging dynamics discovery in Computational Science using intermediate representations. The intended applications are in areas characterized by large volumes of data in which knowledge discovery implies the transition from raw data bases for intermediate representations (usually feature vectors and graphs), thus allowing for the subsequent use of different analytical methods. In this context, integration and transformation methods to be used in the generation of intermediate data should also ensure the quality and reliability of data generated for the intermediate representation. The results of the analysis phase may influence both experiments and the integration methods for generating new data by feedback mechanisms. This project has two general goals: 1) to develop methodologies to solve Computational Science problems based on a common approach of intermediate mathematical-computational representations; 2) to apply the developed methodologies to different scientific problems, thus creating specific solutions to each problem. This methodological strategy will be used to address specific problems in areas which our group has been working in recent years: intermediate representations in computer vision and urban informatics; study of biological networks dynamics to characterize the mechanisms of the health-disease transition; development of computational tools for processing of MRI images high field and their integration with biological data; development of new techniques for characterization and visualization of intermediate representations in complex dynamic networks, with applications in Systems Biology. (AU)

Articles published in Agência FAPESP Newsletter about the research grant:
Estudo explica por que bactéria que contamina alimentos causa doença grave no exterior e não no Brasil 
Study explains why bacteria that contaminate food do not always cause serious disease in Brazil 
Articles published in other media outlets (22 total):
More itemsLess items
UOL: Resposta imune ajuda a identificar bactéria que causa problema renal (06/Oct/2019)
Saense: Modelo estatístico mostra atribulada vida dos imperadores romanos (12/Apr/2021)
NCYT Amazings (Espanha): Revelan por qué una cepa bacteriana es una amenaza en muchos países pero no en Brasil (30/Jan/2020)
Brasil CT&I: Diferença genética impede que bactéria causadora de doença grave no exterior contamine carne brasileira (07/Nov/2019)
Jornal da USP online: Diferença genética impede que bactéria causadora de doença grave no exterior contamine carne brasileira (06/Nov/2019)
Revista Ecológico online: Estudo explica por que bactéria que contamina alimentos causa doença grave no exterior e não no Brasil (05/Nov/2019)
Sou Ecológico: Estudo explica por que bactéria que contamina alimentos causa doença grave no exterior e não no Brasil (05/Nov/2019)
ABIPTI - Associação Brasileira das Instituições de Pesquisa Tecnológica e Inovação: Estudo explica por que bactéria que contamina alimentos causa doença grave no exterior e não no Brasil (05/Nov/2019)
Brasil CT&I: Estudo explica por que bactéria que contamina alimentos causa doença grave no exterior e não no Brasil (05/Nov/2019)
Agrosoft: Bactéria que contamina alimentos causa doença grave no exterior e não no brasil (04/Nov/2019)
Confap - Conselho Nacional das Fundações Estaduais de Amparo à Pesquisa: Estudo explica por que bactéria que contamina alimentos causa doença grave no exterior e não no Brasil (04/Nov/2019)
Espaço Ecológico no Ar: Estudo explica por que bactéria que contamina alimentos causa doença grave no exterior e não no Brasil (04/Nov/2019)
Esteta : Estudo explica por que bactéria que contamina alimentos causa doença grave no exterior e não no Brasil (04/Nov/2019)
LabNetwork: Estudo explica por que bactéria que contamina alimentos causa doença grave no exterior e não no Brasil (04/Nov/2019)
Jornal da Ciência online: Estudo explica por que bactéria que contamina alimentos causa doença grave no exterior e não no Brasil (04/Nov/2019)
Blog Jornal da Mulher: Estudo explica por que bactéria que contamina alimentos causa doença grave no exterior e não no Brasil (04/Nov/2019)
Sintracoop: Estudo explica por que bactéria que contamina alimentos causa doença grave no exterior e não no Brasil (04/Nov/2019)
Sociedade Científica: Essa bactéria causa doença grave no exterior, mas não no Brasil (04/Nov/2019)
W Rádio Brasil: Estudo explica por que bactéria que contamina alimentos causa doença grave no exterior e não no Brasil (04/Nov/2019)
Portal da Enfermagem: Estudo explica por que bactéria que contamina alimentos causa doença grave no exterior e não no Brasil (04/Nov/2019)
Jornal Integração: Estudo explica por que bactéria que contamina alimentos causa doença grave no exterior e não no Brasil (04/Nov/2019)
Brasil CT&I: Resposta imune ajuda a identificar bactéria que causa problema renal (07/Oct/2019)

Scientific publications (37)
(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)
CERIBELI, CAROLINE; FERRAZ DE ARRUDA, HENRIQUE; DA FONTOURA COSTA, LUCIANO. How coupled are capillary electrophoresis and mass spectrometry?. SCIENTOMETRICS, MAR 2021. Web of Science Citations: 0.
LIM, MARKUS V. S.; DINIZ, PAULO S. R.; YAZDANPANAH, HAMED. Set-Membership Constrained Frequency-Domain Algorithm. IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS II-EXPRESS BRIEFS, v. 68, n. 2, p. 797-801, FEB 2021. Web of Science Citations: 0.
LI, SIYUAN; REN, WENQI; WANG, FENG; ARAUJO, IAGO BRENO; TOKUDA, ERIC K.; JUNIOR, ROBERTO HIRATA; CESAR-JR., ROBERTO M.; WANG, ZHANGYANG; CAO, XIAOCHUN. A Comprehensive Benchmark Analysis of Single Image Deraining: Current Challenges and Future Perspectives. INTERNATIONAL JOURNAL OF COMPUTER VISION, v. 129, n. 4 JAN 2021. Web of Science Citations: 0.
PERON, THOMAS; DE RESENDE, BRUNO MESSIAS F.; RODRIGUES, FRANCISCO A.; COSTA, LUCIANO DA F.; MENDEZ-BERMUDEZ, J. A. Spacing ratio characterization of the spectra of directed random networks. Physical Review E, v. 102, n. 6 DEC 10 2020. Web of Science Citations: 2.
COSTA, LUCIANO DA FONTOURA; DE ARRUDA, HENRIQUE FERRAZ. Syntonets: toward a harmony-inspired general model of complex networks. European Physical Journal B, v. 93, n. 12 DEC 7 2020. Web of Science Citations: 0.
CARNEIRO-SAMPAIO, MAGDA; MOREIRA-FILHO, CARLOS ALBERTO; BANDO, SILVIA YUMI; DEMENGEOT, JOCELYNE; COUTINHO, ANTONIO. Intrauterine IPEX. FRONTIERS IN PEDIATRICS, v. 8, NOV 20 2020. Web of Science Citations: 0.
TOKUDA, ERIC K.; LOCKERMAN, YITZCHAK; FERREIRA, GABRIEL B. A.; SORRELGREEN, ETHAN; BOYLE, DAVID; CESAR-JR, ROBERTO M.; SILVA, CLAUDIO T. A New Approach for Pedestrian Density Estimation Using Moving Sensors and Computer Vision Sensing the city. ACM TRANSACTIONS ON SPATIAL ALGORITHMS AND SYSTEMS, v. 6, n. 4 AUG 2020. Web of Science Citations: 0.
DE RESENDE, BRUNO MESSIAS F.; COSTA, LUCIANO DA F. Characterization and comparison of large directed networks through the spectra of the magnetic Laplacian. Chaos, v. 30, n. 7 JUL 2020. Web of Science Citations: 0.
OUELLETTE, JULIE; TOUSSAY, XAVIER; COMIN, CESAR H.; COSTA, LUCIANO DA F.; HO, MIRABELLE; LACALLE-AURIOLES, MARIA; FREITAS-ANDRADE, MOISES; LIU, QING YAN; LECLERC, SONIA; PAN, YOULIAN; LIU, ZIYING; THIBODEAU, JEAN-FRANCOIS; YIN, MELISSA; CARRIER, MICAEL; MORSE, CAMERON J.; VAN DYKEN, PETER; BERGIN, CHRISTOPHER J.; BAILLET, SYLVAIN; KENNEDY, CHRISTOPHER R.; TREMBLAY, MARIE-EVE; BENOIT, YANNICK D.; STANFORD, WILLIAM L.; BURGER, DYLAN; STEWART, DUNCAN J.; LACOSTE, BAPTISTE. Vascular contributions to 16p11.2 deletion autism syndrome modeled in mice. NATURE NEUROSCIENCE, v. 23, n. 9 JUL 2020. Web of Science Citations: 0.
YAZDANPANAH, HAMED; DINIZ, PAULO S. R.; LIMA, MARKUS V. S. Feature Adaptive Filtering: Exploiting Hidden Sparsity. IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS I-REGULAR PAPERS, v. 67, n. 7, p. 2358-2371, JUL 2020. Web of Science Citations: 1.
YAZDANPANAH, HAMED; APOLINARIO JR, JOSE A. The Extended Feature LMS Algorithm: Exploiting Hidden Sparsity for Systems with Unknown Spectrum. CIRCUITS SYSTEMS AND SIGNAL PROCESSING, v. 40, n. 1 JUN 2020. Web of Science Citations: 0.
COMIN, CESAR H.; PERON, THOMAS; SILVA, FILIPI N.; AMANCIO, DIEGO R.; RODRIGUES, FRANCISCO A.; COSTA, LUCIANO DA F. Complex systems: Features, similarity and connectivity. PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS, v. 861, p. 1-41, MAY 25 2020. Web of Science Citations: 0.
CIBA, MANUEL; BESTEL, ROBERT; NICK, CHRISTOPH; DE ARRUDA, GUILHERME FERRAZ; PERON, THOMAS; HENRIQUE, COMIN CESAR; COSTA, LUCIANO DA FONTOURA; RODRIGUES, FRANCISCO APARECIDO; THIELEMANN, CHRISTIANE. Comparison of Different Spike Train Synchrony Measures Regarding Their Robustness to Erroneous Data From Bicuculline-Induced Epileptiform Activity. NEURAL COMPUTATION, v. 32, n. 5, p. 887-911, MAY 2020. Web of Science Citations: 0.
COMIN, CESAR H.; TAYLOR, GAVIN J.; COSTA, LUCIANO DA F. Quantifying the regularity of a 3D set of points on the surface of an ellipsoidal object. PATTERN RECOGNITION LETTERS, v. 133, p. 1-7, MAY 2020. Web of Science Citations: 0.
VEGA-OLIVEROS, DIDIER A.; COSTA, LUCIANO DA FONTOURA; RODRIGUES, FRANCISCO APARECIDO. Influence maximization by rumor spreading on correlated networks through community identification. COMMUNICATIONS IN NONLINEAR SCIENCE AND NUMERICAL SIMULATION, v. 83, APR 2020. Web of Science Citations: 0.
YAZDANPANAH, HAMED; DINIZ, PAULO S. R.; LIMA, MARKUS V. S. Improved simple set-membership affine projection algorithm for sparse system modelling: Analysis and implementation. IET SIGNAL PROCESSING, v. 14, n. 2, p. 81-88, APR 2020. Web of Science Citations: 0.
BENATTI, ALEXANDRE; DE ARRUDA, HENRIQUE F.; SILVA, FILIPI NASCIMENTO; COMIN, CESAR HENRIQUE; COSTA, LUCIANO DA FONTOURA. Opinion diversity and social bubbles in adaptive Sznajd networks. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, v. 2020, n. 2 FEB 2020. Web of Science Citations: 0.
SANDRA ELISABETE VIEIRA; SILVIA YUMI BANDO; GERHARD DA PAZ LAUTERBACH; CARLOS ALBERTO MOREIRA-FILHO. Human Leukocyte Transcriptional Response to SARS-CoV-2 Infection. Clinics, v. 75, p. -, 2020.
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.
SILVA, FILIPI N.; COMIN, CESAR H.; COSTA, LUCIANO DA F. Malleability of complex networks. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, AUG 2019. Web of Science Citations: 0.
BANDO, SILVIA Y.; IAMASHITA, PRISCILA; SILVA, FILIPI N.; COSTA, LUCIANO DA F.; ABE, CECILIA M.; BERTONHA, FERNANDA B.; GUTH, BEATRIZ E. C.; FUJITA, ANDRE; MOREIRA-FILHO, CARLOS A. Dynamic Gene Network Analysis of Caco-2 Cell Response to Shiga Toxin-Producing Escherichia coli-Associated Hemolytic-Uremic Syndrome. MICROORGANISMS, v. 7, n. 7 JUL 2019. Web of Science Citations: 0.
DE ARRUDA, HENRIQUE F.; COMIN, CESAR H.; COSTA, LUCIANO DA F. Problem-solving using complex networks. European Physical Journal B, v. 92, n. 6 JUN 2019. Web of Science Citations: 0.
DE ARRUDA, HENRIQUE F.; MARINHO, VANESSA Q.; COSTA, LUCIANO DA F.; AMANCIO, DIEGO R. Paragraph-based representation of texts: A complex networks approach. INFORMATION PROCESSING & MANAGEMENT, v. 56, n. 3, p. 479-494, MAY 2019. Web of Science Citations: 1.
VIEIRA, SANDRA E.; BANDO, SILVIA Y.; DE PAULIS, MILENA; OLIVEIRA, DANIELLE B. L.; THOMAZELLI, LUCIANO M.; DURIGON, EDISON L.; MARTINEZ, MARINA B.; MOREIRA-FILHO, CARLOS ALBERTO. Distinct transcriptional modules in the peripheral blood mononuclear cells response to human respiratory syncytial virus or to human rhinovirus in hospitalized infants with bronchiolitis. PLoS One, v. 14, n. 3 MAR 7 2019. Web of Science Citations: 0.
RODRIGUEZ, MAYRA Z.; COMIN, CESAR H.; CASANOVA, DALCIMAR; BRUNO, ODEMIR M.; AMANCIO, DIEGO R.; COSTA, LUCIANO DA F.; RODRIGUES, FRANCISCO A. Clustering algorithms: A comparative approach. PLoS One, v. 14, n. 1 JAN 15 2019. Web of Science Citations: 8.
CERVANTES, EVELYN PEREZ; COMIN, CESAR HENRIQUE; CESAR JUNIOR, ROBERTO MARCONDES; COSTA, LUCIANO DA FONTOURA. Morphological Neuron Classification Based on Dendritic Tree Hierarchy. NEUROINFORMATICS, v. 17, n. 1, p. 147-161, JAN 2019. Web of Science Citations: 1.
YAZDANPANAH, HAMED; DINIZ, PAULO S. R.; LIMA, MARKUS V. S. Low-Complexity Feature Stochastic Gradient Algorithm for Block-Lowpass Systems. IEEE ACCESS, v. 7, p. 141587-141593, 2019. Web of Science Citations: 0.
DE ARRUDA, HENRIQUE F.; MARINHO, VANESSA Q.; LIMA, THALES S.; AMANCIO, DIEGO R.; COSTA, LUCIANO DA F. An image analysis approach to text analytics based on complex networks. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, v. 510, p. 110-120, NOV 15 2018. Web of Science Citations: 2.
DAZZI, ESTEPHAN; DE CAMPOS, TEOFILO; HILTON, ADRIAN; CESAR JR, ROBERTO M. Scalable object instance recognition based on keygraph matching. PATTERN RECOGNITION LETTERS, v. 114, n. SI, p. 53-62, OCT 15 2018. Web of Science Citations: 0.
MOREIRA-FILHO, CARLOS ALBERTO; BANDO, SILVIA YUMI; BERTONHA, FERNANDA BERNARDI; FERREIRA, LEANDRO RODRIGUES; VINHAS, CHRISTIANA DE FREITAS; BOURGUIGNON OLIVEIRA, LUCILA HABIB; NOGUEIRA ZERBINI, MARIA CLAUDIA; FURLANETTO, GLAUCIO; CHACCUR, PAULO; CARNEIRO-SAMPAIO, MAGDA. Minipuberty and Sexual Dimorphism in the Infant Human Thymus. SCIENTIFIC REPORTS, v. 8, SEP 3 2018. Web of Science Citations: 2.
DE ARRUDA, HENRIQUE F.; COMIN, CESAR H.; COSTA, LUCIANO DA F. How integrated are theoretical and applied physics?. SCIENTOMETRICS, v. 116, n. 2, p. 1113-1121, AUG 2018. Web of Science Citations: 0.
DOMINGUES, G. S.; SILVA, F. N.; COMIN, C. H.; COSTA, L. DA F. Topological characterization of world cities. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, AUG 2018. Web of Science Citations: 2.
LIMA, THALES S.; DE ARRUDA, HENRIQUE F.; SILVA, FILIPI N.; COMIN, CESAR H.; AMANCIO, DIEGO R.; COSTA, LUCIANO DA F. The dynamics of knowledge acquisition via self-learning in complex networks. Chaos, v. 28, n. 8 AUG 2018. Web of Science Citations: 2.
COSTA, LUCIANO DA F.; SILVA, FILIPI N.; COMIN, CESAR H. A pattern recognition approach to transistor array parameter variance. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, v. 499, p. 176-185, JUN 1 2018. Web of Science Citations: 0.
FERREIRA, GUSTAVO RODRIGUES; NAKAYA, HELDER IMOTO; COSTA, LUCIANO DA FONTOURA. Gene regulatory and signaling networks exhibit distinct topological distributions of motifs. Physical Review E, v. 97, n. 4 APR 27 2018. Web of Science Citations: 0.
SOUZA, PAULO J. P.; COMIN, CESAR H.; COSTA, LUCIANO DA F. Topology and dynamics in complex networks: The role of edge reciprocity. EPL, v. 122, n. 2 APR 2018. Web of Science Citations: 1.
BANDO, SILVIA YUMI; IAMASHITA, PRISCILA; GUTH, BEATRIZ E.; DOS SANTOS, LUIS F.; FUJITA, ANDRE; ABE, CECILIA M.; FERREIRA, LEANDRO R.; MOREIRA-FILHO, CARLOS ALBERTO. A hemolytic-uremic syndrome-associated strain O113:H21 Shiga toxin-producing Escherichia coli specifically expresses a transcriptional module containing dicA and is related to gene network dysregulation in Caco-2 cells. PLoS One, v. 12, n. 12 DEC 18 2017. Web of Science Citations: 2.

Please report errors in scientific publications list by writing to: cdi@fapesp.br.