Representation, characterization and modeling of biological images using complex networks

• Grant number: 18/09125-4
• Support Opportunities: Regular Research Grants
• Start date: December 01, 2018
• End date: November 30, 2020
• Field of knowledge: Physical Sciences and Mathematics - Computer Science
• Principal Investigator: Cesar Henrique Comin
• Grantee: Cesar Henrique Comin
• Host Institution: Centro de Ciências Exatas e de Tecnologia (CCET). Universidade Federal de São Carlos (UFSCAR). São Carlos , SP, Brazil
• City of the host institution: São Carlos

Abstract

The representation of natural and artificial systems according to their respective topology, using networks or graphs, has attracted increasing attention over the past years. The large body of work produced on the subject originated a new research area known as network theory. The objective of this project is to apply a series of recent results from network theory on biological images, aiming at revealing relevant properties about these images that are usually not observed using traditional methods. This objective entails three main fundamental aspects, given by i) the definition of adequate image representations using networks, ii) the selection of appropriate network features for characterizing the data and iii) the definition of relevant models for explaining the observed network topology. In the following, we describe the expected challenges for each considered aspect, as well as possible approaches that will be used for overcoming them. We will show that many methods from network theory can be used for analyzing images from different types of biological systems. Special focus will be given to biological systems having natural representations as networks, such as blood vessels and neurons, but other applications will also be considered. We aim at applying the newly developed methods on state-of-the-art research topics in biology, which will be done by means of collaborations with researches from the area. (AU)

Scientific publications

(23)

(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)

BRITO, ANA C. M.; SILVA, FILIPI N.; DE ARRUDA, HENRIQUE F.; COMIN, CESAR H.; AMANCIO, DIEGO R.; COSTA, LUCIANO DA F.. lassification of abrupt changes along viewing profiles of scientific article. Journal of Informetrics, v. 15, n. 2, MAY 2021. (18/10489-0, 19/16223-5, 15/08003-4, 16/19069-9, 18/09125-4, 15/22308-2)

MENDES, RODRIGO DE P.; YUAN, XIN; GENEGA, ELIZABETH M.; XU, XIAOYIN; COSTA, LUCIANO DA F.; COMIN, CESAR H.. Gland context networks: A novel approach for improving prostate cancer identification. Computerized Medical Imaging and Graphics, v. 94, DEC 2021. (21/12354-8, 18/09125-4, 15/22308-2)

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. (16/19069-9, 14/20830-0, 15/18942-8, 15/22308-2, 14/08026-1, 18/09125-4, 11/50761-2)

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. (13/07375-0, 15/22308-2, 11/50761-2, 18/09125-4)

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. (15/22308-2, 11/50761-2, 18/09125-4)

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. (15/22308-2, 11/50761-2, 18/09125-4, 18/10489-0)

TOKUDA, ERIC K.; COMIN, CESAR H.; COSTA, LUCIANO DA F.. Revisiting agglomerative clustering. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, v. 585, JAN 1 2022. (19/01077-3, 15/22308-2, 18/09125-4)

TOKUDA, ERIC K.; DE ARRUDA, HENRIQUE F.; DOMINGUES, GUILHERME S.; COSTA, LUCIANO DA F.; SHIBATA, FLORENCE AS; CESAR-JR, ROBERTO M.; COMIN, CESAR H.. Estimating the effects of urban green regions in terms of diffusion. ENVIRONMENT AND PLANNING B-URBAN ANALYTICS AND CITY SCIENCE, v. N/A, p. 16-pg., 2022-10-05. (15/22308-2, 18/09125-4, 18/10489-0, 19/01077-3)

BORDELEAU, MAUDE; COMIN, CESAR H.; DE COSSIO, LOURDES FERNANDEZ; LACABANNE, CHLOE; FREITAS-ANDRADE, MOISES; IBANEZ, FERNANDO GONZALEZ; RAMAN-NAIR, JOANNA; WAKEM, MICHAEL; CHAKRAVARTY, MALLAR; COSTA, LUCIANO DA F.; et al. aternal high-fat diet in mice induces cerebrovascular, microglial and long-term behavioural alterations in offsprin. COMMUNICATIONS BIOLOGY, v. 5, n. 1, JAN 11 2022. (15/22308-2, 18/09125-4)

DA SILVA, MATHEUS V.; OUELLETTE, JULIE; LACOSTE, BAPTISTE; COMIN, CESAR H.. An analysis of the influence of transfer learning when measuring the tortuosity of blood vessels. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE, v. 225, p. 11-pg., 2022-07-29. (18/09125-4, 21/12354-8)

LITHOPOULOS, MARISSA A.; TOUSSAY, XAVIER; ZHONG, SHUMEI; XU, LIQUN; MUSTAFA, SHAMIMUNISA B.; OUELLETTE, JULIE; FREITAS-ANDRADE, MOISES; COMIN, CESAR H.; BASSAM, HAYAM A.; BAKER, ADAM N.; et al. Neonatal hyperoxia in mice triggers long-term cognitive deficits via impairments in cerebrovascular function and neurogenesis. Journal of Clinical Investigation, v. 132, n. 22, p. 21-pg., 2022-11-15. (21/12354-8, 18/09125-4)

SILVA, FILIPI N.; COMIN, CESAR H.; COSTA, LUCIANO DA F.. Malleability of complex networks. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, v. N/A, p. 15-pg., 2019-08-01. (18/09125-4, 15/22308-2, 17/09280-7, 13/07375-0, 15/18942-8, 11/50761-2, 15/08003-4)

DE ARRUDA, HENRIQUE FERRAZ; BENATTI, ALEXANDRE; SILVA, FILIPI NASCIMENTO; COMIN, CESAR HENRIQUE; COSTA, LUCIANO DA FONTOURA. Contrarian effects and echo chamber formation in opinion dynamics. JOURNAL OF PHYSICS-COMPLEXITY, v. 2, n. 1, p. 12-pg., 2021-06-01. (19/16223-5, 15/22308-2, 18/10489-0, 11/50761-2, 18/09125-4)

SILVA, FILIPI N.; COMIN, CESAR H.; COSTA, LUCIANO DA F.. Malleability of complex networks. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, AUG 2019. (15/22308-2, 15/08003-4, 17/09280-7, 15/18942-8, 13/07375-0, 18/09125-4, 11/50761-2)

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. (15/22308-2, 15/08003-4, 16/23827-6, 18/09125-4, 16/19069-9, 14/20830-0, 13/26416-9)

GEWERS, FELIPE L.; FERREIRA, GUSTAVO R.; DE ARRUDA, HENRIQUE F.; SILVA, FILIPI N.; COMIN, CESAR H.; AMANCIO, DIEGO R.; COSTA, LUCIANO DA F.. Principal Component Analysis: A Natural Approach to Data Exploration. ACM COMPUTING SURVEYS, v. 54, n. 4, JUL 2021. (17/13464-6, 18/09125-4, 15/22308-2, 16/19069-9, 18/10489-0, 11/50761-2, 19/16223-5)

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. (15/22308-2, 16/23827-6, 18/09125-4, 13/26416-9, 12/51301-8, 12/25219-2)

TOKUDA, ERIC K.; DE ARRUDA, HENRIQUE F.; COMIN, CESAR H.; JR, ROBERTO M. CESAR; SILVA, CLAUDIO T.; COSTA, LUCIANO DA F.. Spatial distribution of graffiti types: a complex network approach. European Physical Journal B, v. 94, n. 9, SEP 2021. (19/01077-3, 19/16223-5, 18/09125-4, 15/22308-2, 18/10489-0)

RIBEIRO PRIST, PAULA; REVERBERI TAMBOSI, LEANDRO; FILIPE MUCCI, LUIS; PINTER, ADRIANO; PEREIRA DE SOUZA, RENATO; DE LARA MUYLAERT, RENATA; ROGER RHODES, JONATHAN; HENRIQUE COMIN, CESAR; DA FONTOURA COSTA, LUCIANDO; LANG D'AGOSTINI, TATIANA; et al. Roads and forest edges facilitate yellow fever virus dispersion. JOURNAL OF APPLIED ECOLOGY, v. 59, n. 1, OCT 2021. (18/09125-4, 18/14389-0, 15/22308-2, 18/23364-1, 17/11666-0)

COMIN, CESAR H.; TSIRUKIS, I, DEMETRIOS; SUN, YE; XU, XIAOYIN. Quantification of retinal blood leakage in fundus fluorescein angiography in a retinal angiogenesis model. SCIENTIFIC REPORTS, v. 11, n. 1, OCT 6 2021. (15/22308-2, 18/09125-4)

TOKUDA, ERIC K.; COMIN, CESAR H.; COSTA, LUCIANO DA F.. Impact of the topology of urban streets on mobility optimization. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, v. 2022, n. 10, p. 20-pg., 2022-10-01. (18/09125-4, 21/12354-8, 19/01077-3, 15/22308-2)

BENATTI, ALEXANDRE; DE ARRUDA, HENRIQUE FERRAZ; COMIN, CESAR HENRIQUE; SILVA, FILIPI NASCIMENTO; COSTA, LUCIANO DA FONTOURA; GLANZEL, W; HEEFFER, S; CHI, PS; ROUSSEAU, R. Robustness of citation networks retrieved from queries. 18TH INTERNATIONAL CONFERENCE ON SCIENTOMETRICS & INFORMETRICS (ISSI2021), v. N/A, p. 2-pg., 2021-01-01. (18/09125-4, 19/16223-5, 15/22308-2, 18/10489-0)

BRITO, ANA C. M.; SILVA, FILIPI N.; DE ARRUDA, HENRIQUE F.; COMIN, CESAR H.; AMANCIO, DIEGO R.; COSTA, LUCIANO DA F.. Classification of abrupt changes along viewing profiles of scientific articles. Journal of Informetrics, v. 15, n. 2, p. 15-pg., 2021-03-18. (18/09125-4, 18/10489-0, 15/22308-2, 16/19069-9, 15/08003-4)