Alex Stivala

Research fellow, SoNAR-C Social Network Analysis Research Center and Institute of Computing, Università della Svizzera italiana, Lugano, Switzerland.

Official USI staff page

Source code on GitHub 

Publications

Google Scholar profile 

orcid.org/0000-0002-2442-4743 

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/.

Journal articles

• F. Bianchi, A. Stivala, and A. Lomi 2022 Multiple clocks in network evolution Methodological Innovations 15(1):29-41 doi.org/10.1177/20597991221077877 

• A. Stivala and A. Lomi 2021 Testing biological network motif significance with exponential random graph models. Applied Network Science 6:91. doi.org/10.1007/s41109-021-00434-y 

• A. Stivala 2020 Reply to “Comment on Geodesic Cycle Length Distributions in Delusional and Other Social Networks” Journal of Social Structure 21(1):94-106. doi:10.21307/joss-2020-004

• A. Stivala 2020 Geodesic cycle length distributions in delusional and other social networks Journal of Social Structure 21(1):35-76 . doi:10.21307/joss-2020-002  [Accepted manuscript (CC BY-NC 4.0 license)]

• T. Diviák, J. Coutinho, and A. Stivala 2020 A man’s world? Comparing the structural positions of men and women in an organized criminal network. Crime, Law and Social Change 74(5):547-569. doi:10.1007/s10611-020-09910-5 [Full Text (CC BY 4.0 license )]

• A. Stivala, G. Robins, and A. Lomi 2020 Exponential random graph model parameter estimation for very large directed networks PloS One, 15(1), e0227804. arXiv preprint arXiv:1904.08063 [Preprint]

• 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] 

• 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.94.032303 [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 [Preprint]

• 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

Book chapter

• 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. [Accepted version at University of Melbourne research repository] 

Conferences

Slides from my conference presentations.

Unpublished manuscripts

• Stivala, A. (2023). Geodesic cycle length distributions in fictional character networks. arXiv preprint arXiv:2303.11597

• Stivala, A., Gallagher, H. C., Rolls, D., Wang, P., & Robins, G. (2020). Using sampled network data with the autologistic actor attribute model. arXiv preprint arXiv:2002.00849

• Stivala, A. & Keeler, P. (2016). Another phase transition in the Axelrod model. arXiv preprint arXiv:1612.02537

• Stivala, A., Stuckey, P., & Wallace, M. (2011). Selecting and scheduling an optimal subset of road network upgrades. arXiv preprint arXiv:2204.10175

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/.

• Testing biological network motif significance with exponential random graph models

• Geodesic cycle length distributions in delusional and other social networks 

• Equilibrium Expectation (EE) to estimate exponential random graph model (ERGM) parameters for large directed networks

• 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

Grants

• Swiss National Science Foundation (SNSF) research grant: Advancing the applicability of exponential random graph models (ERGMs) for the analysis of social and other networks: Algorithms, implementation, and applications (grant number 200778 ). As named employee (PI Alessandro Lomi). 2021 - 2024. [Project details] 

• Swiss National Science Foundation (SNSF) Swiss National Research Programme 75 Big Data research grant:  The Global Structure of Knowledge Networks: Data, Models and Empirical Results (grant number 167326 ). 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) [Final report]

• PASC  "Snowball sampling" 1 April 2015 - 31 March 2017 (with Alessandro Lomi, Rolf Krause, Garry Robins, Alberto Caimo)

• XSEDE TG-SES140024 "Exponential random graph models for large networks: Snowball sampling and conditional estimation using parallel high performance computing" 1 October 2014 - 30 September 2015 (PI: Noshir Contractor [Northwestern]; with Yun Huang, Cindy Weng, Garry Robins, and others).

• 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)

Note regarding Pro-origami

Update (9 November 2022): The Pro-origami server is currently not working: retrieving a cartoon does nothing or returns an error (for SVG or PDF - you can still retrieve a a PNG version), and generating a cartoon shows an error screen regarding  OS error "No space left on device" (probably it has run out of disk space).  The server is currently undergoing maintenance and so hopefully this problem will soon be resolved.

More information on installing Pro-origami locally. 

UPDATE (1 March 2020): The Pro-origami server seems to be working properly again! But longer term, apparently it has to be moved to a new (virtual) server, this is being worked on now.

Update (18 January 2020): The Pro-origami server is currently (and for at least the last 5 days) not working: retrieving a cartoon does nothing or returns an error (for SVG or PDF - you can still retrieve a a PNG version), and generating a cartoon shows an error screen regarding  OS error "No space left on device" (probably it has run out of disk space). Unfortunately I no longer have any access to the server, but I have asked a collaborator at Uni. Melb. to ask IT to look into it (but I have no idea how long this will take). 

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).

Other research

• 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

Teaching

• Designed and taught USI  Faculty of Informatics  Masters level unit INF 524 Analysis of Social Networks, Fall semester 2020 and 2021.

Teaching materials are available here

Other

• 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.

Contact

Please use my gmail address below.

Please note that I can no longer access my old University of Melbourne address stivalaa@unimelb.edu.au. Email sent there will be silently lost forever.