ORCID Profile
0000-0002-4420-3446
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Artificial Intelligence and Image Processing | Neural, Evolutionary and Fuzzy Computation | Analysis Of Algorithms And Complexity | Neural Networks, Genetic Alogrithms And Fuzzy Logic | Operations Research | Logistics and Supply Chain Management | Business and Management | Gene Expression | Post Harvest Horticultural Technologies (incl. Transportation and Storage) |
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Information and Computing Sciences | Processed Fruit and Vegetable Products (incl. Fruit Juices) | Preventive medicine | Cancer and related disorders | Diagnostic methods | Environmentally Sustainable Transport not elsewhere classified
Related Links
Publications
Online support material for Computer Science Honours program using Blackboard
Publisher: IEEE
Date: 2009
Genetic Signatures for a Rodent Model of Parkinson's Disease Using Combinatorial Optimization Methods
Publisher: Humana Press
Date: 2008
DOI: 10.1007/978-1-60327-429-6_20
Abstract: This chapter illustrates the use of the combinatorial optimization models presented in Chapter 19 for the Feature Set selection and Gene Ordering problems to find genetic signatures for diseases using micro-array data. We demonstrate the quality of this approach by using a microarray dataset from a mouse model of Parkinson's disease. The results are accompanied by a description of the currently known molecular functions and biological processes of the genes in the signatures.
Benchmarking a memetic algorithm for ordering microarray data
Publisher: Elsevier BV
Date: 03-2007
DOI: 10.1016/J.BIOSYSTEMS.2006.04.005
Abstract: This work introduces a new algorithm for "gene ordering". Given a matrix of gene expression data values, the task is to find a permutation of the gene names list such that genes with similar expression patterns should be relatively close in the permutation. The algorithm is based on a combined approach that integrates a constructive heuristic with evolutionary and Tabu Search techniques in a single methodology. To evaluate the benefits of this method, we compared our results with the current outputs provided by several widely used algorithms in functional genomics. We also compared the results with our own hierarchical clustering method when used in isolation. We show that the use of images, corrupted with known levels of noise, helps to illustrate some aspects of the performance of the algorithms and provide a complementary benchmark for the analysis. The use of these images, with known high-quality solutions, facilitates in some cases the assessment of the methods and helps the software development, validation and reproducibility of results. We also propose two quantitative measures of performance for gene ordering. Using these measures, we make a comparison with probably the most used algorithm (due to Eisen and collaborators, PNAS 1998) using a microarray dataset available on the public domain (the complete yeast cell cycle dataset).
An Integrated Loss-Based Optimization Model for Apple Supply Chain
Publisher: Springer International Publishing
Date: 2018
MA-Net: A reliable memetic algorithm for community detection by modularity optimization
Publisher: Springer International Publishing
Date: 2014
Optimising weights for heterogeneous ensemble of classifiers with differential evolution
Publisher: IEEE
Date: 07-2016
Multi-warehouse, multi-product inventory control model for agri-fresh products – A case study
Publisher: Elsevier BV
Date: 03-2022
Identifying Communities of Trust and Confidence in the Charity and Not-for-Profit Sector: A Memetic Algorithm Approach
Publisher: IEEE
Date: 12-2014
Novel Biomarkers for Prostate Cancer Revealed by (α,β)-k-Feature Sets
Publisher: Springer Berlin Heidelberg
Date: 2009
Where Does My Brand End? An Overlapping Community Approach
Publisher: Springer International Publishing
Date: 09-11-2016
A Novel Clustering Methodology Based on Modularity Optimisation for Detecting Authorship Affinities in Shakespearean Era Plays
Publisher: Public Library of Science (PLoS)
Date: 29-08-2016
P3‐254: A new approach to tracking progression of molecular pathogenesis in Alzheimer's disease identifies hippocampal iron dyshomeostasis as a novel potential biomarker
Publisher: Wiley
Date: 07-2010
Differences in Abundances of Cell-Signalling Proteins in Blood Reveal Novel Biomarkers for Early Detection Of Clinical Alzheimer's Disease
Publisher: Public Library of Science (PLoS)
Date: 24-03-2011
Evaluation of Different Normalization and Analysis Procedures for Illumina Gene Expression Microarray Data Involving Small Changes.
Publisher: MDPI AG
Date: 21-05-2013
Uncovering Molecular Biomarkers That Correlate Cognitive Decline with the Changes of Hippocampus' Gene Expression Profiles in Alzheimer's Disease
Publisher: Public Library of Science (PLoS)
Date: 13-04-2010
M-Link: a link clustering memetic algorithm for overlapping community detection
Publisher: Springer Science and Business Media LLC
Date: 09-04-2020
Multivariate protein signatures of pre-clinical Alzheimer's disease in the Alzheimer's disease neuroimaging initiative (ADNI) plasma proteome dataset.
Publisher: Public Library of Science (PLoS)
Date: 02-04-2012
Heterogeneous Ensemble Combination Search Using Genetic Algorithm for Class Imbalanced Data Classification
Publisher: Public Library of Science (PLoS)
Date: 14-01-2016
A Transcription Factor Map as Revealed by a Genome- Wide Gene Expression Analysis of Whole-Blood mRNA Transcriptome in Multiple Sclerosis
Publisher: Public Library of Science (PLoS)
Date: 12-2010
Designing a grazing-system experiment for variable native pastures and flexible lamb-production systems
Publisher: CSIRO Publishing
Date: 2017
DOI: 10.1071/AN15856
Abstract: Grazing-system experiments address complex interactions among animals, pastures, soils, climate and management. As part of the national EverGraze program, a grazing-system experiment was designed to determine how the intensity of grazing management, from continuous grazing (P01) to flexible 4- and 20-paddock rotational systems (P04 and P20), influences the profitability and sustainability of a Merino ewe, terminal sire, lamb production system grazed on heterogeneous native pastures. When implementing such an experiment, it is important to understand and characterise landscape variability, and include this in the design of the experiment. A second challenge for grazing-system research is to operate experimental systems with sufficient flexibility to adequately represent commercial production systems and maintain even utilisation across treatments. The present paper addresses the following two issues: (1) the process used to characterise the potential productivity of variable native pastures and the results of this characterisation and (2) the development of flexible systems that adequately represent commercial production within an experiment. This was undertaken with input from a project-steering committee called the EverGraze Regional Group, comprising producers, extension staff and private consultants. Prior to the commencement, the site was mapped into three production zones, namely, high (HPZ), medium (MPZ) and low (LPZ), by visually estimating green herbage mass in late spring and marking boundaries between zones with a GPS. The production zones represented differences in soil properties (gravel, pH and available P) and pasture composition, and were used to balance potential production among plots within the same replication. Grazing-system options were evaluated using the sustainable grazing systems pasture model to help choose an appropriate starting stocking rate. The initial stocking rate chosen for the spring-lambing systems was 5.4 ewes/ha. The modelling predicted large variations in feed availability and quality over summer among years flexible management criteria were therefore developed, including variable sale time for lambs, to utilise the greater feed supply in better seasons. Minimum-pasture benchmarks ( .8 t DM/ha standing herbage mass and % ground cover) and variable green herbage-mass targets were designed to sustain high levels of livestock production and prevent pasture degradation. Criteria for adjusting ewe numbers were developed, but were constrained to pre-joining (March), scanning (July) and post-weaning (December), being consistent with commercial practices. The experiment incorporated flexible management rules as these were considered integral to the successful management of commercial grazing systems.
Optimization of graph based codes for belief propagation decoding
Publisher: IEEE
Date: 11-2014
Unveiling Clusters of RNA Transcript Pairs Associated with Markers of Alzheimer’s Disease Progression
Publisher: Public Library of Science (PLoS)
Date: 21-09-2012
An automatic graph layout procedure to visualize correlated data
Publisher: Springer US
Date: 2006
Genetic biomarkers for brain hemisphere differentiation in Parkinson's Disease
Publisher: AIP
Date: 2007
DOI: 10.1063/1.2816624
The Discovery of Novel Biomarkers Improves Breast Cancer Intrinsic Subtype Prediction and Reconciles the Labels in the METABRIC Data Set
Publisher: Public Library of Science (PLoS)
Date: 22-04-2026
GPU-FS-kNN: A Software Tool for Fast and Scalable kNN Computation Using GPUs
Publisher: Public Library of Science (PLoS)
Date: 28-08-2012
A memetic algorithm for the quadratic assignment problem with parallel local search
Publisher: IEEE
Date: 05-2015
Distinguishing childhood absence epilepsy patients from controls by the analysis of their background brain electrical activity (II): A combinatorial optimization approach for electrode selection
Publisher: Elsevier BV
Date: 07-2009
DOI: 10.1016/J.JNEUMETH.2009.04.028
Abstract: In this sequel to our previous work [Rosso OA, Mendes A, Rostas JA, Hunter M, Moscato P. Distinguishing childhood absence epilepsy patients from controls by the analysis of their background brain electrical activity. J. Neurosci. Methods 2009 :461-68], we extend the analysis of background electroencephalography (EEG), recorded with scalp electrodes in a clinical setting, in children with childhood absence epilepsy (CAE) and control in iduals. The same set of in iduals was considered-five CAE patients, all right-handed females and aged 6-8 years. The EEG was obtained using bipolar connections from a standard 10-20 electrode placement. The functional activity between electrodes was evaluated using a wavelet decomposition in conjunction with the Wootters distance. In the previous study, a Kruskal-Wallis statistical test was used to select the pairs of electrodes with differentiated behavior between CAE and control s les (classes). In this contribution, we present the results for a combinatorial optimization approach to select the pairs of electrodes. The new method produces a better separation between the classes, and at the same time uses a smaller number of features (pairs of electrodes). It managed to almost halve the number of features and also improves the separation between the CAE and control s les. The new results strengthen the hypothesis that mostly fronto-central electrodes carry useful information and patterns that can help to discriminate CAE cases from controls. Finally, we provide a comprehensive set of tests and in-depth explanation of the method and results.
Engagement in Motion: Exploring Short Term Dynamics in Page-Level Social Media Metrics
Publisher: IEEE
Date: 12-2014
Iteratively refining breast cancer intrinsic subtypes in the METABRIC dataset
Publisher: Springer Science and Business Media LLC
Date: 13-01-2016
Clustering nodes in large-scale biological networks using external memory algorithms
Publisher: Springer Berlin Heidelberg
Date: 2011
A Hybrid Simulated Annealing with Kempe Chain Neighborhood for the University Timetabling Problem
Publisher: IEEE
Date: 2007
DOI: 10.1109/ICIS.2007.25
Basal-like breast cancer: molecular profiles, clinical features and survival outcomes
Publisher: Springer Science and Business Media LLC
Date: 28-03-2017
Planning Models to Optimize the Agri-Fresh Food Supply Chain for Loss Minimization: A Review
Publisher: Elsevier
Date: 2016
kNN-Borůvka-GPU: A fast and scalable MST construction from kNN graphs on GPU
Publisher: Springer Berlin Heidelberg
Date: 2012
QAPgrid: A Two Level QAP-Based Approach for Large-Scale Data Analysis and Visualization
Publisher: Public Library of Science (PLoS)
Date: 18-01-2011
Digital technology teachers' perceptions of computer science: It is not all about programming
Publisher: IEEE
Date: 10-2014
kNN-MST-Agglomerative: A fast and scalable graph-based data clustering approach on GPU
Publisher: IEEE
Date: 07-2012
Computing large-scale distance matrices on GPU
Publisher: IEEE
Date: 07-2012
Designing a recycling supply chain network for a bottle manufacturing factory
Publisher: IEEE
Date: 12-2016
Related Organisations
No related organisations have been discovered for Regina Berretta.
Related Funding Activities
Discovery Projects - Grant ID: DP0559755
Start Date: 06-2005
End Date: 09-2008
Amount: $218,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP140104183
Start Date: 06-2014
End Date: 12-2018
Amount: $348,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP120102576
Start Date: 06-2012
End Date: 12-2016
Amount: $320,000.00
Funder: Australian Research Council
View Funded ActivityIndustrial Transformation Training Centres - Grant ID: IC140100032
Start Date: 11-2014
End Date: 12-2019
Amount: $2,119,872.00
Funder: Australian Research Council
View Funded Activity