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Ronnie Alves received his PhD in Computer Science (Artificial Intelligence) from the University of Minho at Braga (Portugal) in April'2008, under the supervision of Prof. Dr. Orlando Belo. While pursuing his PhD studies, he also served as a Visiting Researcher in the Data Mining Group at DAIS Lab in the University of Illinois at Urbana-Champaign, USA) led by Prof. Dr. Jiawei Han and in the Bioinformatics Research Group at Pablo de Olavide University – Sevilla, Spain) led by Prof. Dr. Jesus Aguilar-Ruiz.

Before starting his Ph.D, he also worked as IT Consultant on several industrial data mining projects (From Retail to Telecommunications) in Brazil and Portugal. He was awarded a Postdoctoral Fellowship (Transcriptomics) from the French National Center for Scientific Research (CNRS) in the Virtual Biology Lab at the Institute of Biology Valrose (iBV) at Nice from September'2008 to March'2010. Followed by another two-year postdoc position on Machine Learning and Bioinformatics at the Institute of Informatics at the Federal University of Rio Grande do Sul (UFRGS). Being also a Collaborating Professor in the Department of Theoretical Informatics.

He worked as Researcher Fellow (Jeune Chercheur) in the Lab. of Computer Science, Robotics and Microelectronics of Montpellier (LIRMM), being a member of the Computational Biology Institute (IBC) at the Université Montpellier (UM) and the Institute for Regenerative Medicine and Biotherapy - CHRU de Montpellier (with the bioinformatics team led by Prof. Thérèse Commes) from September'2014 to February'2016.

He is a Full Researcher & Head of Data Science at the Instituto Tecnologico Vale (ITV).

He is an Associate Editor (section Machine Learning and Artificial Intelligence) of BMC Bioinformatics.

He is a council member in the AI for Good initiative.

He holds the position of Collaborating Professor in the Computer Science Graduate's Program of UFPA (PPGCC-UFPA). He supervises Ph.D and MSc students in the research area of Intelligent Systems, focusing on machine learning and bioinformatics.

He is also a member of the Special Committee on Computational Biology (CE-BioComp) of the Brazilian Computer Society (SBC).

My research interests include: machine learning and bioinformatics.

Teaching: Machine Learning (at PPGCC-UFPA), Applied Statistics , Genomics & Bioinformatics (at ITV)

CV: Lattes, Linkedin, ORCHID, ResearchGate, MIT_Sloan_AI

NEWs: ML-News, Brazilian Symposium on Bioinformatics (BSB) 2020

Conferences [Qualis-CC] [WikiCFP] [TopCS] [MyConf]


NEW!! Reinforcement Learning Course [2/2020 | 1/2021]

  • Videos (available in PT); Slides & GoogleColab [available in EN]

Tutorial at ECML-PKDD'2014: The Pervasiveness of Machine Learning in Omics Science,

Publications [log]

geneRFinder: gene finding in distinct metagenomic data complexities. BMC BIOINFORMATICS, v. 22, p. SILVA, RAÍSSA ; Padovani, Kleber ; GÓES, FABIANA ; Alves, Ronnie . 87, 2021. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-03997-w

Polygonal Coordinate System: Visualizing high-dimensional data using geometric DR, and a deterministic version of t-SNE. EXPERT SYSTEMS WITH APPLICATIONS. FLEXA, CAIO ; GOMES, WALISSON ; MOREIRA, IGOR ; Alves, Ronnie ; SALES, CLAUDOMIRO. 2021 https://doi.org/10.1016/j.eswa.2021.114741

Decoding Machine Learning Benchmarks. CARDOSO, L. F. F. ; SANTOS, V. ; FRANCES, R. S. K. ; Prudêncio, Ricardo B. C. ; ALVES, R. In: Brazilian Conference on Intelligent Systems (BRACIS), 2020, Rio Grande. Intelligent Systems, 2020. v. 12320. p. 412-425. https://link.springer.com/chapter/10.1007/978-3-030-61380-8_28

On the utilization of deep and ensemble learning to detect milk adulteration. NETO, HABIB ASSEISS ; TAVARES, WANESSA L.F. ; RIBEIRO, DANIELA C.S.Z. ; ALVES, RONNIE C.O. ; FONSECA, LEORGES M. ; CAMPOS, SÉRGIO V.A. . BioData Mining, v. 12, p. 1-10, 2019. https://biodatamining.biomedcentral.com/articles/10.1186/s13040-019-0200-5

A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining. Markus Gastauer, Mabel Patricia Ortiz Vera, Kleber Padovani de Souza, Eder Soares Pires, Ronnie Alves, Cecílio Frois Caldeira, Silvio Junio Ramos & Guilherme Oliveir. Nature Scientific Data 6:190008 https://doi.org/10.1038/sdata.2019.8 (2019)

Machine learning meets genome assembly. Kleber Padovani de Souza, João Carlos Setubal, André Carlos Ponce de Leon F. de Carvalho, Guilherme Oliveira, Annie Chateau and Ronnie Alves. Briefings in Bioinformatics, bby072, https://doi.org/10.1093/bib/bby072

pipebar

PIPEBAR and OverlapPER: tools for a fast and accurate DNA barcoding analysis and paired-end assembly. Renato Renison Moreira Oliveira, Gisele Lopes Nunes, Talvâne Glauber Lopes de Lima, Guilherme Oliveira and Ronnie Alves. BMC Bioinformatics,

https://doi.org/10.1186/s12859-018-2307-y

Influence of water quality on diversity and composition of fungal communities in a tropical river. Mabel Patricia Ortiz-Vera, Luiz Ricardo Olchanheski, Eliane Gonçalves da Silva, Felipe Rezende de Lima, Lina Rocío del Pilar Rada Martinez, Maria Inês Zanoli Sato, Rodolfo Jaffé, Ronnie Alves, Simone Ichiwaki, Gabriel Padilla & Welington Luiz Araújo. Nature Scientific Reports volume 8, Article number: 14799 (2018), https://www.nature.com/articles/s41598-018-33162-y

[DBLP] [Complete List] [Google Scholar] [ResearchGate]

-XAVIER JUNIOR, R. B. ; DE SOUZA, KLEBER PADOVANI ; ALVES, R. . Genome Assembly using Reinforcement Learning. In: In the Brazilian Symposium on Bioinformatics (BSB), 2019, Fortaleza. Lecture Notes in Bioinformatics (LNBI), 2019.

-SILVA, R. L. S. ; SOUZA, K. P. ; Góes, F. R. ; ALVES, R. . A Random Forest Classifier for Prokaryotes Gene Prediction. In: In the Brazilian Conference on Intelligent System (BRACIS), 2019, Salvador. IEEE Xplore Digital Library, 2019.

-FLEXA, C. ; GOMES, W. ; VIADEMONTE, S. ; SALES, C. ; ALVES, R. . A geometry-based approach to visualize high-dimensional data. In: In the Brazilian Conference on Intelligent System (BRACIS), 2019, Salvador. IEEE Xplore Digital Library, 2019.

-SANTOS, V.; Corrêa, L. H. S.; MEIGUINS, B.; OLIVEIRA, G.; ALVES, RONNIE Metagenomics-based signature clustering and interactive visualization analysis In: International Joint Conference on Neural Networks (IJCNN), 2018, Rio de Janeiro. International Joint Conference on Neural Networks (IJCNN). IEEE, 2018.

-NASCIMENTO, SIDNEY VASCONCELOS DO; MAGALHÃES, MARCELO MURAD; CUNHA, ROBERTO LISBOA; COSTA, PAULO HENRIQUE DE OLIVEIRA; ALVES, RONNIE CLEY DE OLIVEIRA; OLIVEIRA, GUILHERME CORRÊA DE; VALADARES, RAFAEL BORGES DA SILVA. Differential accumulation of proteins in oil palms affected by fatal yellowing disease. PLoS One, v.13, p.e0195538 - , 2018.

-LANES, ÉDER C.; POPE, NATHANIEL S.; Alves, Ronnie; CARVALHO FILHO, NELSON M.; GIANNINI, TEREZA C.; GIULIETTI, ANA M.; IMPERATRIZ-FONSECA, VERA L.; MONTEIRO, WALÉRIA; OLIVEIRA, GUILHERME; SILVA, AMANDA R.; SIQUEIRA, JOSÉ O.; SOUZA-FILHO, PEDRO W.; VASCONCELOS, SANTELMO; JAFFÉ, RODOLFO Landscape Genomic Conservation Assessment of a Narrow-Endemic and a Widespread Morning Glory From Amazonian Savannas. Frontiers in Plant Science, v.9, p.532 - , 2018.

-GUIMARÃES, JOSÉ TASSO FELIX ; CARREIRA, LÉA MARIA MEDEIROS ; ALVES, R ; MARTINS E SOUZA FILHO, PEDRO WALFIR ; GIANNINI, TEREZA CRISTINA ; MACAMBIRA, HIGOR JARDIM ; DA SILVA, EDILSON FREITAS ; DIAS, ANNA CHRISTINA RIO ; DA SILVA, CARLA BASTISTA ; ROMEIRO, LUIZA DE ARAÚJO ; RODRIGUES, TARCÍSIO MAGEVSKI . Pollen morphology of the Poaceae: implications of the palynological and paleoecological records of the southeastern Amazon in Brazil. PALYNOLOGY, v. 1, p. 1-13, 2017.

-RUFFLE, FLORENCE ; AUDOUX, JEROME ; BOUREUX, ANTHONY ; BEAUMEUNIER, SACHA ; GAILLARD, JEAN-BAPTISTE ; BOU SAMRA, ELIAS ; MEGARBANE, ANDRE ; CASSINAT, BRUNO ; CHOMIENNE, CHRISTINE ; ALVES, R ; RIQUIER, SEBASTIEN ; GILBERT, NICOLAS ; LEMAITRE, JEAN-MARC ; BACQ-DAIAN, DELPHINE ; BOUGÉ, ANNE LAURE ; PHILIPPE, NICOLAS ; COMMES, THERESE . New chimeric RNAs in acute myeloid leukemia. F1000RESEARCH, v. 6, p. 1302, 2017.

-GUIMARAES, J. T. F. ; REIS, L. ; FIGUEIREDO, M. ; RODRIGUES, T. ; Alves, Ronnie ; SOUZA, P. M. ; SILVA, M. S. ; SAHOO, PRAFULLA KUMAR ; GIANNINI, T. C. ; CARREIRA, L. . Modern pollen rain as a background for palaeoenvironmental studies in the Serra dos Carajás, southeastern Amazonia. HOLOCENE, p. 095968361668326, 2017.

-BEAUMEUNIER, S.; AUDOUX, J.; BOUREUX, A.; COMMES, T.; FRUFFLE, F.; ALVES, R. On the evaluation of the fidelity of supervised classifiers in the prediction of chimeric RNAs. BioData Mining, 2016.

-RICHARD, F.D.; ALVES, R.; KAJAVA, A.V. A scoring tool for boundary determination between repetitive and non-repetitive protein sequences. Bioinformatics. 2016.

-LIRA, W.P.; GAMA, F.; BARBOSA, H.; ALVES, R.; SOUZA, C.R.B.: VCloud: adding interactiveness to word clouds for knowledge exploration in large unstructured texts. ACM SAC 2016: 193-198

-JUNIOR, J.F.D.; ALVES, R.; COMMES, T. A module-based approach for evaluating differential genome-wide expression profiles. In the 5th Brazilian Conference on Intelligent System (BRACIS). Recife, PE, Brazil, October 9-12, 2016. [pdf]

-CORREA, L., GOES, F.; ALVES, A.; ALVES, R. Functional network-oriented analysis of environmental metagenomics data. In the 3ème Colloque de Génomique Environnementale Montpellier (GE2015). Montpellier, October 26-28, 2015.

-BEAUMEUNIER, S.; AUDOUX, J.; BOUREAUX, A.; COMMES, T.; PHILIPPE, N.; ALVES, R. The Role of Machine Learning in Finding Chimeric RNAs. 6th International Workshop on Biological Knowledge Discovery and Data Mining (BIOKDD 2015), Valencia, Spain, September 1-4, 2015. [site] Best Paper Award at BIOKDD-DEXA'15

-LIRA, W. P. ; ALVES, R.; COSTA, J.M.R. ; PESSIN, G. GALVAO, L.; CARDOSO, A.C. ; DE SOUZA, C.R.B. A Visual-Analytics System for Railway Safety Management. IEEE Computer Graphics and Applications, v. 34, p. 52-57, 2014.

-GUIMARAES, J.T.F; SOUZA-FILHO, P.W.M ; ALVES, R; DE SOUZA, E.B; DA COSTA, F.R; REIS, L. S.; SAHOO, P.K.; DE OLIVEIRA MANES, C-L.; SILVA JUNIOR, R.O.; OTI, D.; DALL'AGNOL, R. Source and distribution of pollen and spores in surface sediments of a plateau lake in southeastern Amazonia. Quaternary International, v. xx, p. 1-16, 2014.

-LICHTNOW, D.; ALVES, R.; PASTOR, O.; BURRIEL, V.; OLIVEIRA, J.P.M.: BION2SEL: An Ontology-Based Approach for the Selection of Molecular Biology Databases. In the Brazilian Symposium on Bioinformatics (BSB), Belo Horizonte, MG, Brazil, October 28-30, 2014. To appear in the Lecture Notes in Bioinformatics (LNBI), vol. 8826 Springer. 83-90.

-GOES, F.; ALVES, R.; CORREA, L.; CHAPARRO, C; and THOM, L. A comparison of classification methods for gene prediction in metagenomics. In the International Workshop on New Frontiers in Mining Complex Patterns (NFmcp). The European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD), Nancy, France, September 15-19, 2014.

-CORREA, L.; ALVES, R.; GOES, F.; CHAPARRO, C; and THOM, L. A pipeline for functional and visual analytics of microbial genetic networks. In the 2nd International Workshop on Dynamic Networks and Knowledge Discovery (DyNaK). The European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD), Nancy, France, September 15-19, 2014.

-ALVES, R.; MENDES, MARCUS; BONNATO, DIEGO. A Network-Based Meta-analysis Strategy for the Selection of Potential Gene Modules in Type 2 Diabetes. In: 8th Brazilian Symposium on Bioinformatics, 2013, Recife. Advances in Bioinformatics and Computational Biology - Lecture Notes in Computer Science. New York: Springer International Publishing, 2013. v. 8213. p. 160-169.

-MENDOZA, MARIANA R. ; DA FONSECA, GUILHERME C. ; LOSS-MORAIS, GUILHERME ; ALVES, R; MARGIS, ROGERIO ; BAZZAN, ANA L. C. . RFMirTarget: Predicting Human MicroRNA Target Genes with a Random Forest Classifier. Plos One, v. 8, p. e70153, 2013.

-ALVES, R.; FERREIRA, P.; RIBEIRO, J.; BELO, O. Detecting Abnormal Patterns in Call Graphs based on the Aggregation of Relevant Vertex Measures In: 12th Industrial Conference on Data Mining, 2012, Berlin.

-SIMAO, E.M.; SINIGAGLIA, M.; BUGS, C.A., CASTRO, M.A.A.; LIBRELOTTO, G. R.; ALVES, R.; MOMBACH, J. C. M. Induced genome maintenance pathways in pre-cancer tissues describe an anti-cancer barrier in tumor development. Molecular Biosystems (Print), 2012.

-ALVES, R. ; RODRIGUEZ-BAENA, D. S. ; AGUILAR-RUIZ, J. S. Gene Association Analysis: A Survey of Frequent Pattern Mining from Gene Expression Data. Briefings in Bioinformatics, p. 210-224, 2010.