Dr Carlos Riveros
Casual Academic
School of Electrical Engineering and Computing (Computer Science and Software Engineering)
- Email:carlos.riveros@newcastle.edu.au
- Phone:(02) 4042 0478
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
UON Appointment
| Title | Organisation / Department |
|---|---|
| Casual Academic | University of Newcastle School of Electrical Engineering and Computing Australia |
Professional appointment
| Dates | Title | Organisation / Department |
|---|---|---|
| 1/02/2016 - | HMRI Bioinformatics Fellow | Hunter Medical Research Institute (HMRI) Australia |
| 1/02/2008 - 6/01/2016 |
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 |
Publications
For publications that are currently unpublished or in-press, details are shown in italics.
Chapter (1 outputs)
| Year | Citation | Altmetrics | Link | ||||||||
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| 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]
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Journal article (25 outputs)
| Year | Citation | Altmetrics | Link | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2017 |
Milioli HH, Tishchenko I, Riveros C, Berretta R, Moscato P, 'Basal-like breast cancer: molecular profiles, clinical features and survival outcomes.', BMC Med Genomics, 10 19 (2017)
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| 2016 |
Tishchenko I, Riveros C, Moscato P, 'Alzheimer¿s disease patient groups derived from a multivariate analysis of cognitive test outcomes in the Coalition Against Major Diseases dataset', Future Science OA, 2 FSO140-FSO140 (2016) [C1]
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| 2016 |
Tishchenko I, Milioli HH, Riveros C, Moscato P, 'Extensive Transcriptomic and Genomic Analysis Provides New Insights about Luminal Breast Cancers', PLOS ONE, 11 (2016) [C1]
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| 2016 |
Casanova R, Varma S, Simpson B, Kim M, An Y, Saldana S, et al., 'Blood metabolite markers of preclinical Alzheimer's disease in two longitudinally followed cohorts of older individuals', Alzheimers & Dementia, 12 815-822 (2016) [C1]
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| 2016 |
Puthiyedth N, Riveros C, Berretta R, Moscato P, 'Identification of Differentially Expressed Genes through Integrated Study of Alzheimer's Disease Affected Brain Regions', PLOS ONE, 11 (2016) [C1]
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| 2016 |
Riveros C, Ujaldón M, Moscato P, 'GPU Acceleration of an Entropy-based Model to Quantify Epistatic Interactions Between SNPs', Current Bioinformatics, 11 396-407 (2016) [C1]
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| 2016 |
Milioli HH, Vimieiro R, Tishchenko I, Riveros C, Berretta R, Moscato P, 'Iteratively refining breast cancer intrinsic subtypes in the METABRIC dataset.', BioData Min, 9 2 (2016) [C1]
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| 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]
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| 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]
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| 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]
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| 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]
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| 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]
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| 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]
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| 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]
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| 2012 |
Johnstone DM, Graham RM, Trinder D, Delima RD, Riveros RC, Olynyk JK, et al., 'Brain transcriptome perturbations in the Hfe(-/-) mouse model of genetic iron loading', Brain Research, 1448 144-152 (2012) [C1]
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| 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]
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| 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]
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| 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 (2012) [C1]
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| 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]
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| 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]
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| 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]
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| 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]
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| Show 22 more journal articles | |||||||||||
Conference (25 outputs)
| Year | Citation | Altmetrics | Link | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2017 | English C, Hendrickx W, Riveros C, 'Slow walking speed is associated with high sitting time in stroke survivors: a data pooling study', INTERNATIONAL JOURNAL OF STROKE (2017) | ||||||||||
| 2017 |
Ly SL, Riveros C, Heidari M, Johnstone D, Milward E, 'SINGLE CELL RNASEQ ANALYSIS PROVIDES EVIDENCE FOR RELATIONSHIPS BETWEEN IRON-RELATED GENE EXPRESSION AND BRAIN OLIGODENDROGLIAL MYELINATING CAPABILITY', AMERICAN JOURNAL OF HEMATOLOGY (2017)
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| 2016 |
Wong-Brown M, Riveros C, Scott R, 'TARGETED RESEQUENCING OF BRCA1 AND BRCA2 IN FAMILIAL BREAST CANCER', ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY (2016)
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| 2015 |
Milioli H, Tishchenko I, Riveros C, Berretta R, Moscato P, 'BASAL-LIKE BREAST CANCER SUBGROUPS UNCOVERED BY GENOMIC AND TRANSCRIPTOMIC PROFILES AND OVERALL SURVIVAL OUTCOMES', ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY (2015) [E3]
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| 2015 |
Tishchenko I, Milioli H, Riveros C, Moscato P, 'HOW INTRINSIC ARE LUMINAL BREAST CANCER SUBTYPES?', ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY (2015) [E3]
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| 2015 |
Tishchenko I, Riveros C, Moscato P, 'REVISION OF MOLECULAR BREAST CANCER SUBTYPES', ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY (2015) [E3]
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| 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) [E1] © 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.
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| 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) [E3]
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| 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) [E3]
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| 2015 |
Puthiyedth N, Riveros C, Berretta R, Moscato P, 'A NOVEL COMBINATORIAL OPTIMISATION APPROACH FOR FEATURE SELECTION VIA INTEGRATION OF INFORMATION FROM MULTIPLE DATASETS', ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY (2015) [E3]
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| 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]
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| 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]
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| 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]
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| 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]
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| 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]
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| 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]
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| 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]
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| Show 22 more conferences | |||||||||||
Report (1 outputs)
| Year | Citation | Altmetrics | Link | ||
|---|---|---|---|---|---|
| 1989 |
Moscato PA, Riveros C, 't-expansion and the Mathieu equation', . (1989)
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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 FÃsica, SeDiCI - Universidad Nacional de La Plata, (1990) |
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, Professor Regina Berretta, Doctor 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 |
Research Supervision
Number of supervisions
Completed2
Current0
Past Supervision
| Year | Level of Study | Research Title | Program | Supervisor Type |
|---|---|---|---|---|
| 2016 | PhD | A Novel Feature Selection Approach for Data Integration Analysis: Applications to Transcriptomics Study | PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle | Co-Supervisor |
| 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 |
Dr Carlos Riveros
Position
Casual Academic
School of Electrical Engineering and Computing
Faculty of Engineering and Built Environment
Focus area
Computer Science and Software Engineering
Contact Details
| 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 , |
