Dr Carlos Riveros

Dr Carlos Riveros

Computational Scientist - CIBM

School of Elect Engineering and Computer Science (Computer Science and Software Engineering)

Career Summary

Biography

I am a computing scientist with more than twenty five years of experience in academic, scientific and industrial software development, the last seven in research and development in the area of High-Performance Computing applied to Bioinformatics and Information-Based Medicine. I obtained my PhD in Physics in 1990 and have since worked in the public and private sectors for multinational companies and research institutions, as well as managed
my own boutique software development company for almost eight years.

My current research interests are in optimisation problems, in particular applied to multi-dimensional clustering and classification in large to very large datasets, such as those arising from bioinformatics.  I am interested in exact and heuristics methods, influence of outliers and noise, and aggregation of data from multiple domains.  Application of high performance computing techniques, massively parallel systems (in particular GPUs), and heterogeneous distributed computing is central for the practical and efficient solution of these problems in the very large datasets of today.


Qualifications

  • PhD (Physics), Universidad Nacional de la Plata - Argentina
  • Bachelor of Physics, Universidad Nacional de la Plata - Argentina

Keywords

  • Algorithms
  • Bioinformatics
  • GPU
  • High Performance Computing
  • Software Development

Languages

  • English (Fluent)
  • Spanish (Fluent)

Fields of Research

Code Description Percentage
010299 Applied Mathematics not elsewhere classified 35
060499 Genetics not elsewhere classified 35
080299 Computation Theory and Mathematics not elsewhere classified 30

Professional Experience

Professional appointment

Dates Title Organisation / Department
1/02/2008 -  Computing Scientist - Sr. SW Developer

Research and support in systems and algorithms for metabolomics, proteomics and genotyping.  Graph-based methods, information-based methods, evolutionary algorithms, data mining.

High-Performance Computing support and expertise consulting.  Systems definition, requisition, configuration and monitoring.

Applied GPU computing research.

RhD student co-supervision.

The University of Newcastle
Priority Research Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine
Australia
1/08/2006 - 1/01/2008 I&C Senior Engineer / Chief of Engineering Termoelectrica San Martin, Argentina
Engineering
Argentina
1/08/2001 - 1/08/2006 Contract Performance Manager General Electric
Argentina
1/09/1994 - 1/08/2001 CEO / Principal Software Engineer VFlops Informatica, Argentina
Industrial Software Development
Argentina
1/04/1992 - 1/08/1993 Visiting PostDoc Research Associate

R&D in advanced geophysical data processing algorithms: multi-layer wave decomposition and propagation, experimental anisotropic wave propagation, cross-borehole and surface-to-borehole diffraction tomography for reservoir characterisation.

Design and implementation of data management and conversion front-ends for large 3D geophysical exploration datasets for the Lab’s Convex supercomputer.

University of Houston
Allied Geophysical Labs
United States
1/01/1991 - 1/09/1994 Chief Geophysical Researcher

Principal software architect and algorithm designer of a real-time 2D & 3D ruggedized geophysical array multiprocessor system.

Development of active and passive sonar detection and ranging with hydrophone aperture arrays for military application.

R&D of adaptive filtering and signal recognition algorithms for deep-well oil pump predictive maintenance characterisation.

Development and vectorisation of geophysical data processing algorithms for geophysical prospecting.

Sismos Geophysical Company
Geophysics R&D
Argentina

Teaching

Code Course Role Duration
SENG3100 Personal Software Process
Faculty of Engineering and Built Environment - The University of Newcastle (Australia)
Lecturer 1/03/2008 - 31/07/2008
COMP3320 Computer Graphics
Faculty of Engineering and Built Environment - The University of Newcastle (Australia)
Lecturer 1/08/2008 - 30/11/2008
COMP3320 Computer Graphics
Faculty of Engineering and Built Environment - The University of Newcastle (Australia)
Tutorial demonstrator 1/08/2008 - 30/11/2008
SENG4800 A/B Final Year Project (Embedded Honors)
Faculty of Engineering and Built Environment - The University of Newcastle (Australia)
Teaching Assistant 1/03/2012 - 30/11/2012
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Publications

For publications that are currently unpublished or in-press, details are shown in italics.


Chapter (1 outputs)

Year Citation Altmetrics Link
2015 Riveros C, Vimieiro R, Holliday EG, Oldmeadow C, Wang JJ, Mitchell P, et al., 'Identification of genome-wide SNP-SNP and SNP-clinical Boolean interactions in Age-related Macular Degeneration', Epistasis: Methods and Protocols, Springer, New York 217-255 (2015) [B1]
DOI 10.1007/978-1-4939-2155-3_12
Co-authors Christopher Oldmeadow, Rodney Scott, Liz Holliday, Pablo Moscato, John Attia

Journal article (19 outputs)

Year Citation Altmetrics Link
2015 Puthiyedth N, Riveros C, Berretta R, Moscato P, 'A New Combinatorial Optimization Approach for Integrated Feature Selection Using Different Datasets: A Prostate Cancer Transcriptomic Study.', PLoS One, 10 e0127702 (2015) [C1]
DOI 10.1371/journal.pone.0127702
Co-authors Regina Berretta, Pablo Moscato
2015 Riveros C, Ujaldón M, Moscato P, 'GPU Acceleration of an Entropy-based Model to Quantify Epistatic Interactions Between SNPs', Current Bioinformatics, [In Press] 1-8 (2015)
Co-authors Pablo Moscato
2015 Milioli HH, Vimieiro R, Riveros C, Tishchenko I, Berretta R, Moscato P, 'The Discovery of Novel Biomarkers Improves Breast Cancer Intrinsic Subtype Prediction and Reconciles the Labels in the METABRIC Data Set.', PLoS One, 10 e0129711 (2015) [C1]
DOI 10.1371/journal.pone.0129711
Co-authors Regina Berretta, Pablo Moscato, Inna Tishchenko
2014 Arefin AS, Vimieiro R, Riveros C, Craig H, Moscato P, 'An information theoretic clustering approach for unveiling authorship affinities in Shakespearean era plays and poems.', PloS one, 9 e111445 (2014) [C1]
DOI 10.1371/journal.pone.0111445
Citations Scopus - 1Web of Science - 1
Co-authors Hugh Craig, Pablo Moscato
2014 Milward EA, Moscato P, Riveros C, Johnstone DM, 'Beyond Statistics: A New Combinatorial Approach to Identifying Biomarker Panels for the Early Detection and Diagnosis of Alzheimer's Disease', JOURNAL OF ALZHEIMERS DISEASE, 39 211-217 (2014) [C1]
DOI 10.3233/JAD-131424
Citations Scopus - 1Web of Science - 1
Co-authors Pablo Moscato, Liz Milward
2014 Mate K, Riveros C, Weidenhofer J, Goldie B, Scott J, Moscato P, et al., 'Strategies for Enhancing Communication between Students, Academics and Researchers participating in Large-Scale Undergraduate Research Projects', International Journal of Innovation in Science and Mathematics Education, 22 14-29 (2014) [C1]
Co-authors Karen Mate, Liz Milward, Judith Weidenhofer, Pablo Moscato
2013 Mendes A, Boland N, Guiney P, Riveros C, 'Switch and Tap-Changer Reconfiguration of Distribution Networks Using Evolutionary Algorithms', IEEE TRANSACTIONS ON POWER SYSTEMS, 28 85-92 (2013) [C1]
DOI 10.1109/TPWRS.2012.2194516
Citations Scopus - 10Web of Science - 6
Co-authors Alexandre Mendes, Natashia Boland
2013 Johnstone DM, Riveros C, Heidari M, Graham RM, Trinder D, Berretta R, et al., 'Evaluation of Different Normalization and Analysis Procedures for Illumina Gene Expression Microarray Data Involving Small Changes', Microarrays, 2 131-152 (2013) [C1]
Co-authors Regina Berretta, Rodney Scott, Pablo Moscato, Liz Milward
2012 Delima RD, Riveros RC, Olynyk JK, Scott R, Moscato PA, Milward AE, et al., 'Brain transcriptome perturbations in the Hfe(-/-) mouse model of genetic iron loading', Brain Research, 1448 144-152 (2012) [C1]
Citations Scopus - 7Web of Science - 7
Co-authors Liz Milward, Pablo Moscato, Rodney Scott
2012 Ravetti MG, Riveros RC, Mendes ADS, Resende MGC, Pardalos PM, 'Parallel hybrid heuristics for the permutation flow shop problem', Annals of Operations Research, 199 269-284 (2012) [C1]
Citations Scopus - 3Web of Science - 3
Co-authors Alexandre Mendes
2012 Johnstone DM, Graham RM, Trinder D, Riveros RC, Olynyk JK, Scott R, et al., 'Changes in brain transcripts related to Alzheimer's disease in a model of HFE hemochromatosis are not consistent with increased Alzheimer's disease risk', Journal of Alzheimers Disease, 30 791-803 (2012) [C1]
Citations Scopus - 3Web of Science - 3
Co-authors Rodney Scott, Pablo Moscato, Liz Milward
2012 Arefin AS, Riveros RC, Berretta RE, Moscato PA, 'GPU-FS-kNN: A software tool for fast and scalable kNN computation using GPUs', PLOS One, 7 e44000 (2012) [C1]
Citations Scopus - 14Web of Science - 6
Co-authors Pablo Moscato, Regina Berretta
2011 Oldmeadow CJ, Riveros RC, Holliday EG, Scott R, Moscato PA, Wang JJ, et al., 'Sifting the wheat from the chaff: Prioritizing GWAS results by identifying consistency across analytical methods', Genetic Epidemiology, 35 745-754 (2011) [C1]
DOI 10.1002/gepi.20622
Citations Scopus - 5Web of Science - 5
Co-authors Rodney Scott, Pablo Moscato, John Attia, Liz Holliday, Christopher Oldmeadow
2010 Riveros RC, Mellor D, Gandhi KS, McKay FC, Cox MB, Berretta RE, et al., 'A transcription factor map as revealed by a genome-wide gene expression analysis of whole-blood mRNA transcriptome in multiple sclerosis', Plos One, 5 1-28 (2010) [C1]
DOI 10.1371/journal.pone.0014176
Citations Scopus - 21Web of Science - 20
Co-authors Regina Berretta, Pablo Moscato, Rodney Scott
2010 Gandhi KS, McKay FC, Cox MB, Riveros RC, Armstrong N, Heard RN, et al., 'The multiple sclerosis whole blood mRNA transcriptome and genetic associations indicate dysregulation of specific T cell pathways in pathogenesis', Human Molecular Genetics, 19 2134-2143 (2010) [C1]
DOI 10.1093/hmg/ddq090
Citations Scopus - 45Web of Science - 43
Co-authors Pablo Moscato, Rodney Scott
2009 Ikin A, Riveros RC, Moscato PA, Mendes ADS, 'The Gene Interaction Miner: A new tool for data mining contextual information for protein-protein interaction analysis', Bioinformatics, 26 283-284 (2009) [C1]
DOI 10.1093/bioinformatics/btp652
Citations Scopus - 4Web of Science - 4
Co-authors Pablo Moscato, Alexandre Mendes
1989 Riveros C, Logiudice EA, Vucetich H, 'On differential fifth force measurements', Physics Letters A, 136 343-347 (1989)
DOI 10.1016/0375-9601(89)90412-X
Citations Scopus - 1Web of Science - 1
1988 Horvath JE, Logiudice EA, Riveros C, Vucetich H, 'Einstein equivalence principle and theories of gravitation: A gravitationally modified standard model', Physical Review D, 38 (1988)
DOI 10.1103/PhysRevD.38.1754
Citations Scopus - 4Web of Science - 4
1986 Riveros C, Vucetich H, 'Bounds on the validity of Newton's gravitational law from electromagnetic solar deflection', Physical Review D, 34 (1986)
DOI 10.1103/PhysRevD.34.321
Citations Scopus - 3Web of Science - 5
Show 16 more journal articles

Conference (18 outputs)

Year Citation Altmetrics Link
2015 Arefin AS, Riveros C, Berretta R, Moscato P, 'The MST-kNN with paracliques', Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (2015)

© Springer International Publishing Switzerland 2015. In this work, we incorporate new edges from a paracliqueidentification approach to the output of theMST-kNN graph partitioni... [more]

© Springer International Publishing Switzerland 2015. In this work, we incorporate new edges from a paracliqueidentification approach to the output of theMST-kNN graph partitioning method. We present a statistical analysis of the results on a dataset originated from a computational linguistic study of 84 Indo-European languages. We also present results from a computational stylistic study of 168 plays of the Shakespearean era. For the latter, results of the Kruskal- Wallis test 1 (observed vs. all permutations) showed a p-value of a 1.62E- 11 and a Wilcoxon test a p-value of 8.1E-12. Overall, our results clearly show in both cases that the modified approach provides statistically more significant results than the use of the MST-kNN alone, thus providing a highly-scalable alternative and statistically sound approach for data clustering.

Co-authors Pablo Moscato, Regina Berretta
2015 Milioli HH, Tishchenko I, Riveros C, Berretta R, Moscato P, 'Molecular classification of basal-like breast cancer subtypes based on predictive survival markers', ANNALS OF ONCOLOGY (2015)
DOI 10.1093/annonc/mdv117.11
Co-authors Regina Berretta, Pablo Moscato, Inna Tishchenko
2015 Milioli HH, Tishchenko I, Riveros C, Sakoff J, Berretta R, Moscato P, 'Consensus on breast cancer cell lines classification for an effective and efficient clinical decision-making', ANNALS OF ONCOLOGY (2015)
DOI 10.1093/annonc/mdv121.8
Co-authors Regina Berretta, Jennette Sakoff, Pablo Moscato
2014 Riveros C, Ujaldon M, Moscato P, 'Entropy-based High Performance Computation of Boolean SNP-SNP Interactions Using GPUs', PROCEEDINGS IWBBIO 2014: INTERNATIONAL WORK-CONFERENCE ON BIOINFORMATICS AND BIOMEDICAL ENGINEERING, VOLS 1 AND 2 (2014) [E1]
Co-authors Pablo Moscato
2014 Riveros C, Milioli H, Vimieiro R, Berretta R, Moscato P, 'Discovery of gene interactions by GPU-enabled computation of pairwise expression level metafeatures', International Conference in Bioinformatics InCoB2014 (2014) [E3]
Co-authors Regina Berretta, Pablo Moscato
2012 Vimieiro R, Riveros C, Moscato P, 'Mining frequent itemset patterns in age-related macular degeneration' (2012)
Co-authors Pablo Moscato
2012 Riveros C, Vimieiro R, Moscato P, 'Cross-association of epistatic interactions in age-related macular degeneration' (2012)
Co-authors Pablo Moscato
2012 Arefin AS, Riveros RC, Berretta RE, Moscato PA, 'Computing large-scale distance matrices on GPU', Proceedings of 2012 7th International Conference on Computer Science & Education (2012) [E1]
Co-authors Pablo Moscato, Regina Berretta
2012 Arefin AS, Riveros RC, Berretta RE, Moscato PA, 'kNN-MST-Agglomerative: A fast and scalable graph-based data clustering approach on GPU', Proceedings of 2012 7th International Conference on Computer Science & Education (2012) [E1]
Citations Scopus - 6
Co-authors Regina Berretta, Pablo Moscato
2012 Arefin AS, Riveros RC, Berretta RE, Moscato PA, 'kNN-Boruvka-GPU: A fast and scalable MST construction from kNN graphs on GPU', Lecture Notes in Computer Science (2012) [E1]
Citations Scopus - 3Web of Science - 3
Co-authors Regina Berretta, Pablo Moscato
2010 Riveros C, 'A new high-performance computing approach to screen all pairs of SNPs for epistatic interactions' (2010)
2010 Mendes ADS, Boland NL, Guiney P, Riveros RC, '(N-1) contingency planning in radial distribution networks using genetic algorithms', 2010 IEEE/PES Transmission and Distribution. Proceedings (2010) [E1]
DOI 10.1109/TDC-LA.2010.5762896
Co-authors Natashia Boland, Alexandre Mendes
2009 Johnstone DM, Ravetti MG, Riveros C, Moscato PA, Hersey P, Scott R, Milward AE, 'Genome-wide microarray analysis of melanoma reveals unexpected anomalies in iron-related gene expression', 2009 International Biolron Society Meeting: Program Book (2009) [E3]
Co-authors Liz Milward, Rodney Scott, Pablo Moscato
2008 Johnstone DM, Riveros C, Moscato P, Milward EA, 'Effects of different normalisation and analysis procedures on illumina gene expression microarray data' (2008)
Co-authors Liz Milward, Pablo Moscato
2008 Riveros C, 'Entropy and Classification' (2008)
1993 Ass'ad J, Riveros C, Kamel MH, McDonald JA, 'Ultrasonic velocity measurements in a cracked solid: Experiment versus theory' (1993)
1993 Riveros C, '3-D wave-equation solution by step marching and layer Eigenmode decomposition' (1993)
1993 Riveros C, Hege L, Ass'ad JM, '2-D migration by layer Eigenmode decomposition' (1993)
Show 15 more conferences

Report (1 outputs)

Year Citation Altmetrics Link
1989 Moscato PA, Riveros C, 't-expansion and the Mathieu equation', . (1989)
Co-authors Pablo Moscato

Thesis / Dissertation (1 outputs)

Year Citation Altmetrics Link
1990 Riveros C, El principio de equivalencia, su verificación experimental y su relación con las fuerzas fundamentales - Facultad de Ciencias Exactas - Tesis de Postgrado - ARG-UNLP-TPG-0000000079 - Departamento de Física, SeDiCI - Universidad Nacional de La Plata, (1990)
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Grants and Funding

Summary

Number of grants 1
Total funding $27,000

Click on a grant title below to expand the full details for that specific grant.


20111 grants / $27,000

The Pierre and Marie Curie GPU computing servers$27,000

Funding body: NHMRC (National Health & Medical Research Council)

Funding body NHMRC (National Health & Medical Research Council)
Project Team Professor Pablo Moscato, Conjoint Professor Peter Greer, Associate Professor Regina Berretta, Dr CARLOS Riveros
Scheme Equipment Grant
Role Investigator
Funding Start 2011
Funding Finish 2011
GNo G1100032
Type Of Funding Other Public Sector - Commonwealth
Category 2OPC
UON Y
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Research Supervision

Number of supervisions

Completed1
Current3

Total current UON EFTSL

PhD0.3

Current Supervision

Commenced Level of Study Research Title / Program / Supervisor Type
2014 PhD Multiobjective Quadratic Assignment Problem for Functional Genomics Analysis in Oncology and Neuroscience
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Co-Supervisor
2014 PhD The Multiobjective (a,B)-k-Feature Set Problem Using Memetic Algorithms
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Co-Supervisor
2012 PhD Combinational Meta-Analysis of Microarray Gene Expression Data and Applications to Prostate Cancer
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Co-Supervisor

Past Supervision

Year Level of Study Research Title / Program / Supervisor Type
2013 PhD An Integrated, Fast and Scalable Approach for Large-Scale Biological Network Analysis
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Co-Supervisor
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Dr Carlos Riveros

Position

Computational Scientist - CIBM
Centre for Bioinformatics, Biomarker Discovery and Information-based Medicine
School of Elect Engineering and Computer Science
Faculty of Engineering and Built Environment

Focus area

Computer Science and Software Engineering

Contact Details

Email carlos.riveros@newcastle.edu.au
Phone (02) 4042 0478
Fax (02) 4042 0037

Office

Room Level 3 Pod - 3020
Building HMRI Building
Location Lot 1, Kookaburra Circuit New Lambton Heights, NSW 2305

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