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Biography

Ahmed Shamsul Arefin, Postgraduate Prize winner, Faculty of Engineering and Built Environment (FEBE) News- Issue 5

Image courtesy: FEBE News, UoN: Postgraduate Poster Prizewinners Announced, Oct 24, 2011

I am a Research Academic at the Priority Research Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine (CIBM), University of Newcastle. I have graduated with a PhD in Computer Science  from the University of Newcastle in 2013. Prior to that I completed my MSc in Information and Communication Technology from the Institute of Information and Communication Technology, Bangladesh University of Engineering and Technology (BUET), Dhaka, Bangladesh, in 2008.

My areas of research expertise include: graph based data mining, network analysis, high performance computing (HPC), GPU-based computing, and bioinformatics.

For a more detailed description of my recent research and software codes, please refer to http://ahmedshamsularefin.id.au.</p>

Qualifications

  • PhD (Computer Science), University of Newcastle, 04/03/2013
  • Master of Science (Information&Communication Tech), Bangladesh University of Engineering & Technology, 12/01/2008
  • Bachelor of Science (Computer Science&Engineering), Chittagong University of Eng & Tech - Bangladesh, 01/07/2004
  • Teachers Certificate, University of Newcastle, 11/08/2014
  • Professional Certificate, University of Newcastle, 11/08/2014

Research

Research keywords

  • Bioinformatics
  • Combinatorial Optimization
  • Data Mining
  • GPU-based Computing
  • Graph Theory
  • Network Analysis
  • Parallel and Distributed Computing
  • Programming Languages

Research expertise

My current research stand point is at the intersection of graph based data mining and high performance/ distributed computing. I am also fascinated by network analysis (including social networks) and I aim to incorporate parallel data mining in network analysis. During my PhD research, I worked with a set of GPU-based methods for constructing minimum spanning trees and k-nearest neighbor graphs (GPU-FS-kNN, PLoS ONE 7(8): e44000), and an external memory-based highly scalable data clustering method for clustering large data sets. The methods guided to uncover some important genes from a well-known breast cancer microarray study. Furthermore, in a different application, it helped to identify a small number (out of a relatively large molecular signature) of transcripts recurrently clustering with different markers of Alzheimer’s disease progression.

I also worked with graph theory. During my MSc. research, I proved that the minimum edge-ranking spanning tree (MERST) problem for general Series-Parallel (SP) graphs is NP-Complete and designed an efficient approximation algorithm which gives a near-optimal solution for the problem. The MERST problem of graphs has important applications such as scheduling the parallel assembly of a complex multi-part product from its components and relational databases.

In short, I do a great deal work and research in big data, data mining, clustering, graphs and visualization. I am an enthusiastic computer programmer with demonstrated abilities in C++, Java, C#, Python, R, OpenMP, MPI and CUDA based application developments.

Languages

  • Bengali
  • English

Fields of Research

CodeDescriptionPercentage
080299Computation Theory And Mathematics Not Elsewhere Classified50
080199Artificial Intelligence And Image Processing Not Elsewhere Classified25
080309Software Engineering25

Memberships

Committee/Associations (relevant to research).

  • Member - University de Valladolid Online Judge Algorithmic Team

Awards

Best Paper in International Conference.

2012Best Paper Award Nominee- ICCSA 2012
International Conference on Computational Science and Its Applications (Brazil)
Best paper award nominee certificate in International Conference on Computational Science and Its Applications 2012 for the research titled kNN-Boruvka-GPU: a fast and scalable MST construction from kNN graphs on GPU

Research Award.

2011Postgraduate Research Prize 2011 (CSSE category, from FEBE, UoN)
The University of Newcastle (Australia)
For the following research (Poster Presentation): " A Fast and Scalable k Nearest Neighbors Search Technique using GPU and Applications" (Relevant publication: Arefin, A. S., Riveros C., Berretta, R., and Moscato, P. (2012). “GPU-FS-kNN: A software tool for fast and scalable kNN computation technique using GPU”, PLoS ONE 7(8): e44000. doi:10.1371/journal.pone.0044000).
2011Postgraduate Research Student Support Scholarship 2011-2013
The University of Newcastle, Australia. (Australia)
University of Newcastle (Merit scholarship based on the quality of research in order to participate in international and/or local conferences). The scholarship includes a lump sum amount (total: $6000 AUD) to spend on conference travels.
2009Endeavour International Postgraduate Research Scholarships (EIPRS) 2009 - 2012
The University of Newcastle, Australia. (Australia)
For pursuing post-graduate studies, tuition fee scholarship.
2009University of Newcastle Research Scholarship (UNRS) - Central, 2009-2012
The University of Newcastle, Australia. (Australia)
For pursuing post-graduate studies, living allowance.

Collaboration

My current research collaborators are:

  • Professor Hugh Craig, Director of the Centre for Linguistic and Literary Computing, University of Newcastle.
  • Professor Manuel Graeber, Barnet-Cropper Chair of Brain Tumor Research, Brain & Mind Research Institute, Sydney Medical School, University of Sydney (Neurogenetics, Volume 15, Issue 3, pp 201-212 ).
  • Dr. Daniel Johnstone, NHMRC Early Career Fellow, Bosch Institute, School of Medical Sciences, University of Sydney (PLoS ONE 7(9): e45535).

Teaching

Teaching keywords

  • Algorithms
  • Computer Graphics
  • Computer Programming Languages
  • Data Structures
  • Operating Systems
  • Software Development

Teaching expertise

I completed two teaching related qualifications: ‘Professional Certificate Course in University Assessment’ and ‘Fundamentals in University Teaching Certificate’ from the Center for Teaching and Learning (CTL), University of Newcastle, Australia in 2014. Further in July 2013, I participated in a 'Sessional Academic Development Workshop', offered by the CTL, University of Newcastle. I am also completing a 'Post Graduate Certificate in Higher Education' (with specialization in Teaching and Learning), from the Macquarie University, Sydney, Australia.

I have taught/tutored the following units at the School of EECS, FEBE, University of Newcastle, Australia:

  • Lecturer, SENG 1120 Introduction to Software Engineering II (Semester 2, 2013)
  • Tutor (principle), SENG 1110 Introduction to Software Engineering I (Semester 1, 2013)
  • Tutor, SENG 2130 Software Development, (Semester 1, 2012)
  • Tutor, COMP 2240 Operating Systems, (Semester 2, 2011)

Furthermore, I performed the following programming contest related (extra-curricular) activities in my discipline:

  • Coached one of the University of Newcastle ACM-ICPC teams ("UoN Stu and Arts") for participating in the 2013 South Pacific Regional Contest, Sept. 21, 2013 (University of Sydney Site).
  • Worked as a trainer for the first University of Newcastle ACM-ICPC teams for participating the 2012 South Pacific Regional Contest, 2012 (University of Sydney Site).

I also worked as a successful programming contest problem setter, judge and organizer for local and international contests (e.g., University of Valladolid (UVa) online contests, problem numbers: 10219-10222).

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Publications

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

Click on a category title below to expand the list of citations for that specific category.

Journal article (4 outputs)

YearCitationAltmetricsLink
2014Filiou MD, Arefin AS, Moscato P, Graeber MB, ''Neuroinflammation' differs categorically from inflammation: transcriptomes of Alzheimer's disease, Parkinson's disease, schizophrenia and inflammatory diseases compared', neurogenetics, (2014)

DOI: 10.1007/s10048-014-0409-x

Citations: Scopus - 0

2012Arefin AS, Mathieson L, Johnstone DM, Berretta RE, Moscato PA, 'Unveiling clusters of RNA transcript pairs associated with markers of Alzheimer's disease progression', PLOS One, 7 1-25 (2012) [C1]

Citations: Scopus - 7 | Web of Science - 6

Co-authors: Pablo Moscato, Regina Berretta

2012Arefin 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 - 7 | Web of Science - 5

Co-authors: Pablo Moscato, Regina Berretta

2005Arefin AS, Hasan MA, 'An improvement of bitonic sorting for parallel computing', WSEAS Transactions on Information Science and Applications, 2 964-967 (2005)

Citations: Scopus - 3

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Conference (7 outputs)

YearCitationAltmetricsLink
2013Arefin AS, Berretta R, Moscato P, 'A GPU-based Method for Computing Eigenvector Centrality of Gene-expression Networks', Proceedings of the Eleventh Australasian Symposium on Parallel and Distributed Computing (AusPDC 2013), Adelaide (2013) [E1]
2012Arefin 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, Melbourne (2012) [E1]

Citations: Scopus - 0

Co-authors: Pablo Moscato, Regina Berretta

2012Arefin 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, Salvador de Bahia, Brazil (2012) [E1]

Citations: Scopus - 1 | Web of Science - 1

Co-authors: Pablo Moscato, Regina Berretta

2012Arefin AS, Riveros RC, Berretta RE, Moscato PA, 'Computing large-scale distance matrices on GPU', Proceedings of 2012 7th International Conference on Computer Science & Education, Melbourne (2012) [E1]

Citations: Scopus - 0

Co-authors: Pablo Moscato, Regina Berretta

2011Arefin AS, Inostroza-Ponta M, Mathieson L, Berretta RE, Moscato PA, 'Clustering nodes in large-scale biological networks using external memory algorithms', Algorithms and Architectures for Parallel Processing, Melbourne, Australia (2011) [E1]

DOI: 10.1007/978-3-642-24669-2_36

Citations: Scopus - 3 | Web of Science - 2

Co-authors: Pablo Moscato, Regina Berretta

2007Arefin AS, Habib KMM, Sultana R, Kabir SML, 'Designing a low cost microcontroller-based device for multipurpose learning', PROCEEDINGS OF 10TH INTERNATIONAL CONFERENCE ON COMPUTER AND INFORMATION TECHNOLOGY (ICCIT 2007), United Int Univ, Dhanmondi, BANGLADESH (2007)

Author URL

Citations: Scopus - 0

2007Arefin AS, Mia MAK, 'NP-Completeness of the minimum edge-ranking spanning tree problem on series-parallel graphs', PROCEEDINGS OF 10TH INTERNATIONAL CONFERENCE ON COMPUTER AND INFORMATION TECHNOLOGY (ICCIT 2007), United Int Univ, Dhanmondi, BANGLADESH (2007)

Author URL

Citations: Scopus - 0

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Grants and Funding

No funding.

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Research Supervision

Number of current supervisions0

No Supervisions.

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Research Collaborations

The map is a representation of a researchers co-authorship with collaborators across the globe. The map displays the number of publications against a country, where there is at least one co-author based in that country. Data is sourced from the University of Newcastle research publication management system (NURO) and may not fully represent the authors complete body of work.

CountryCount of Publications
Australia7
Bangladesh2
Germany1
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Dr Ahmed Shamsul Arefin

Work Phone40420476
Email
PositionResearch Academic
Centre for Bioinformatics, Biomarker Discovery & Information-Based Medicine (CIBM)
School of Elect Engineering and Computer Science
Faculty of Engineering and Built Environment
The University of Newcastle, Australia
Office
3020,
HMRI Building,
Hunter Medical Research Institute Kookaburra Circuit 1, New Lambton Heights, NSW, 2305, AUSTRALIA
URL:www.newcastle.edu.au/profile/ahmed-arefin