Research home page
Note regarding Pro-origami
Update (15 February 2019): The Pro-origami server "migration" process is completed and it appears to be working again.
The Pro-origami server has been migrated to a new address and now only http://munk.cis.unimelb.edu.au/pro-origami/ will work, the old address http://munk.csse.unimelb.edu.au/pro-origami will no longer work. (The csse.unimelb.edu.au domain name was actually retired some time ago but was still supported until now).
All of my publications are available for free online (via this website).
You can also find the publications prior to 2018 on the much older site (which I can no longer update, however) http://munk.cis.unimelb.edu.au/~stivalaa/.
Please note: I no longer review for, or submit manuscripts to, journals published by Elsevier. (Also I refuse to fly Cathay Pacific ever again).
Google Scholar profile (this is the best source for up-to-date publication and citation information; I was forced to create ORCID and other accounts by journals/employers, but unlike Google Scholar they do not reliably update automatically and it is difficult or impossible to update them manually, so are just a waste of time given that Google Scholar is what most people actually use anyway).
orcid.org/0000-0002-2442-4743 (as per above, a journal requirement but unlike Google Scholar it is not up to date as it is too difficult to bother with - I was also forced to create ResearcherID and Scopus accounts but I am not even going to bother linking to them).
- M. Byshkin, A. Stivala, A. Mira, G. Robins and A. Lomi 2018 Fast Maximum Likelihood Estimation via Equilibrium Expectation for Large Network Data Sci. Rep. 8:11509 doi:10.1038/s41598-018-29725-8 [view full text] [Supplementary Information]
- A. Stivala 2017 Diversity and community: the role of agent-based modeling Am. J. Commun. Psychol. 59(3-4):261-264 doi: 10.1002/ajcp.12131 [Preprint]
- M. Byshkin, A. Stivala, A. Mira, R. Krause, G. Robins and A. Lomi 2016 Auxiliary Parameter MCMC for Exponential Random Graph Models. J. Stat. Phys. 165(4):740-754. doi: 10.1007/s10955-016-1650-5 [Preprint] [view full text]
- A. Stivala, Y. Kashima and M. Kirley 2016 Culture and cooperation in a spatial public goods game. Phys. Rev. E 94:032303 doi: 10.1103/PhysRevE.94.02303 [Published paper] [Supplemental Material]
- A. Stivala, G. Robins, Y. Kashima and M. Kirley 2016 Diversity and community can coexist Am. J. Commun. Psychol. 57(1-2):243-254 doi: 10.1002/ajcp.12021 [Preprint]
- A. Stivala, J. Koskinen, D. Rolls, P. Wang and G. Robins 2016 Snowball sampling for estimating exponential random graph models for large networks Social Networks 47:167-188 doi: 10.1016/j.socnet.2015.11.003 [Preprint]
- A. Stivala, G. Robins, Y. Kashima and M. Kirley 2014 Ultrametric distribution of culture vectors in an extended Axelrod model of cultural dissemination Sci. Rep. 4:4870 doi:10.1038/srep04870
- A. Stivala, M. Wybrow, A. Wirth, J. Whisstock and P. Stuckey 2011 Automatic generation of protein structure cartoons with Pro-origami Bioinformatics 27(23):3315-3316 doi:10.1093/bioinformatics/btr575
- A. Stivala, P. Stuckey, M. Garcia de la Banda, M. Hermenegildo and A. Wirth 2010 Lock-free parallel dynamic programming J. Parallel Distrib. Comput. 70:839-848 doi:10.1016/j.jpdc.2010.01.004
- A. Stivala, P. Stuckey and A. Wirth 2010 Fast and accurate protein substructure searching with simulated annealing and GPUs BMC Bioinformatics 11:446
- A. Stivala, A. Wirth and P. Stuckey 2009 Tableau-based protein substructure search using quadratic programming BMC Bioinformatics, 10:153
- Y. Kashima, M. Kirley, A. Stivala, and G. Robins 2017. Modeling cultural dynamics. Ch. 13 in R R. Vallacher, S. J. Read, & A. Nowak (Eds.) Computational Social Psychology. New York: Psychology Press.
Supplementary material for publications
Source code, data sets, web server (where applicable) etc. related to the publications above are available via the following links. You can also find source code in my GitHub repositories or for code prior to 2018 on the much older site (which I can no longer update, however) http://munk.cis.unimelb.edu.au/~stivalaa/.
- Equilibrium Expectation (EE) to estimate exponential random graph model (ERGM) parameters for large directed networks
- Another phase transition in the Axelrod model
- Culture and cooperation in a spatial public goods game
- Diversity and Community Can Co-exist
- Ultrametric distribution of culture vectors in an extended Axelrod model of cultural dissemination
- Pro-origami: Protein structure cartoons
- Lock-free parallel dynamic programming
- Fast and accurate protein substructure searching with simulated annealing and GPUs
- Tableau-based protein substructure search using quadratic programming
- Swiss National Research Programme 75 Big Data research grant: The Global Structure of Knowledge Networks: Data, Models and Empirical Results. As named employee (PIs Alessandro Lomi, Fabio Crestani, Garry Robins). 2017 - 2021. [Project details]
- AOARD FA2386-15-1-4020 "Dissemination of opinions and ideas via complex contagion on social networks" 1 July 2015 - 1 July 2016 (with Yoshihisa Kashima, Garry Robins, Michael Kirley)
- PASC "Snowball sampling" 1 April 2015 - 31 March 2017 (with Alessandro Lomi, Rolf Krause, Garry Robins, Alberto Caimo)
- VLSCI VR0261/VR0297 "Co-Evolutionary Dynamics of Culture and Social Structure" / "Modelling large social networks: statistics and cultural dynamics" 1 January 2013 - 31 December 2016 (with Garry Robins, Yoshihisa Kashima, Michael Kirley)
- Source code for user equilibrium traffic assignment and models for scheduling road upgrades (see "Traffic Assignment and Road Network Upgrade Planning" slides for "Mesoscopic modelling of traffic networks" workshop)
- PhD thesis: "Algorithms for the Study of RNA and Protein Structure"
- PhD completion seminar slides: "Algorithms for the Study of RNA and Protein Structure"
- Useful Links for Bioinformatics Research
- In semester 2, 2007 I was the head tutor for 433-253: Algorithms and Data Structures.
- In semester 1, 2007 I was the head tutor for 433-253: Algorithms and Data Structures.
- In semester 2, 2006 I tutored 433-253: Algorithms and Data Structures.
- In 2010, I was the Secretary of the COMBINE ICT for Life Sciences Forum Student Chapter, affiliated as the Australian Regional Student Group in the ISCB Student Council of the International Society for Computational Biology (ISCB)
- In the summer of 2008/2009 I was an intern at The Victorian Partnership for Advanced Computing (VPAC).
- In 2008, I was the President of the CSSE Postgaduate Group.
- In 2007-2008 I was the Department postgraduate seminar coordinator.
Please use my gmail address which should appear somewhere on this page (the new Google Sites seems to place it in some arbitrary position instead of right here where it used to be).
Please note that I can no longer access my old University of Melbourne address firstname.lastname@example.org. Email sent there will be silently lost forever.