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 my now defunct University of Melbourne website http://munk.cis.unimelb.edu.au/~stivalaa/ (via Wayback Machine).

Unpublished manuscripts

• Stivala, A., Wang, P., & Lomi, A. (2024). ALAAMEE: Open-source software for fitting autologistic actor attribute models. arXiv preprint arXiv:2404.03116 

• Stivala, A. (2023). New network models facilitate analysis of biological networks. arXiv preprint arXiv:2312.06047 

• Stivala, A. (2023). Overcoming near-degeneracy in the autologistic actor attribute model. arXiv preprint arXiv:2309.07338 

• 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 [Supplementary Material]

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

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 [Full text (CC BY-NC 4.0 license)]

• 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 [Full text (CC BY 4.0 license)] [Supplementary Information] [arXiv preprint arXiv:2001.11125]

• 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 [Full text (CC BY-NC 4.0 license) ]

• 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  (CC BY 4.0 license] [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 [Published paper (CC BY-NC-ND 3.0 license)] [Supplementary Information]

• 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 [Published paper (CC BY 2.0 license)]

• A. Stivala, A. Wirth and P. Stuckey 2009 Tableau-based protein substructure search using quadratic programming BMC Bioinformatics, 10:153 [Published paper (CC BY 2.0 license)]

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.

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/ (via Wayback Machine).

• 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 [archived copy on Internet Archive (Wayback Machine)]

• Lock-free parallel dynamic programming

• Fast and accurate protein substructure searching with simulated annealing and GPUs

• Tableau-based protein substructure search using quadratic programming

• Geodesic cycle length distributions in fictional character networks 

• Using sampled network data with the autologistic actor attribute model 

• Another phase transition in the Axelrod model 

• Selecting and scheduling an optimal subset of road network upgrades 

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 (22 May 2024): Now that there is no longer anyone associated with Pro-origami with an account at the University of Melbourne, it seems that the Pro-origami server [Pro-origami website on Internet Archive (Wayback Machine)] is no longer operating. The only option now is to download and run it locally on your own Linux PC, server,  or laptop. More information on installing Pro-origami locally. 

Other research

• Stivala, A. D. (2010). Algorithms for the study of RNA and protein structure. PhD thesis, Engineering - Computer Science and Software Engineering, The University of Melbourne. 

• PhD completion seminar slides: "Algorithms for the Study of RNA and Protein Structure" (2010)

• Stivala, A. D. (2009). Assessment of graphics processing units for acceleration of sequence database search programs. Technical report, Victorian Partnership for Advanced Computing (VPAC).

• Stivala, A. D. (2006) Computational gene finding in the human malaria parasite Plasmodium vivax. Honours thesis, Department of Computer Science and Software Engineering, The University of Melbourne.

• Useful Links for Bioinformatics Research (via Wayback Machine) (2016)

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 Postgraduate 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.