Research and Teaching

My current research interests lie in the application of stochastic processes in modeling the evolution of species. In particular, I am interested in understanding the various factors that drive speciation and extinction events on species. Recently, I become deeply fascinated in how environmental and geographical changes affect species evolution. 

During my undergraduate years, I studied various subject in Mathematics and Statistics, ranging from mathematical analysis, applied mathematics, to statistical methods. My Bachelor's thesis was under the supervision of Ariyanto, M.Si. and (alm) Dr. Jafaruddin Hamid with a research in point-set topology. We studied various characteristics and relationships from the separation axioms of topological spaces. Both my studies and research were supported by the Academic Achievement scholarships from the Indonesian Ministry of Research, Technology, and Higher Education, and the Van Deventer-Maas scholarship from the Van-Deventer-Maas Indonesia. 

During my postgraduate studies as a Master's student at the Australian National University, I took several courses in Bioinformatics and Mathematical Population Genetics. I wrote a Master's thesis under the guidance of Assoc. Prof. Conrad Burden. For the thesis, we investigated the elapsed time since the most recent common ancestor of a finite random sample drawn from a present-day population which has evolved according to a Bienaymé-Galton-Watson branching process. Both research and studies for the degree were supported by the Indonesian Ministry of Finance under the LPDP scholarship. 

I began working with mathematical models for the evolution of species in 2019 as part of my PhD degree under Prof. Barbara Holland and Assoc. Prof. Małgorzata O'Reilly. I submitted a PhD thesis in developing various models for species evolution. Specifically, we developed a model where events on species trees depend on their species age. In another occasion, we developed a trait-dependent model where speciation and extinction events are driven by species' inherited traits. Last but not least, we developed an environmental-dependent model where geography and change in environments drive species evolution. In summary, my PhD research combine stochastic modeling to study evolutionary processes. 

Scientific Publications

Journal Article

1. Soewongsono, A. C., & Landis, M. J. (2024). A Diffusion-Based Approach for Simulating Forward-in-Time State-Dependent Speciation and Extinction Dynamics. arXiv preprint arXiv:2402.00246 (*accepted for publication in Bulletin of Mathematical Biology) https://doi.org/10.48550/arXiv.2402.00246  

2. Soewongsono, A. C., Diao, J., Stark, T., Wilson, A. E., Holland, D. A., & O'Reilly, M. M. (2023). Matrix-analytic methods for the evolution of species trees, gene trees, and their reconciliation. arXiv preprint arXiv:2309.06447 (Preprint) https://doi.org/10.48550/arXiv.2309.06447 

3. Soewongsono, A. C., Holland, B. R., & O'Reilly, M. M. (2022). Stochastic niche-based models for the evolution of species. In MAM11 2022 (pp. 1-4). (Conference Paper)

4. Soewongsono, A. C., Holland, B. R., & O’Reilly, M. M. (2022). The Shape of Phylogenies Under Phase-Type Distributed Times to Speciation and Extinction. Bulletin of Mathematical Biology, 84(10), 118. https://doi.org/10.1007/s11538-022-01072-w.

5. Burden, C. J., & Soewongsono, A. C. (2019). Coalescence in the diffusion limit of a Bienaymé–Galton–Watson branching process. Theoretical Population Biology, 130, 50-59. https://doi.org/10.1016/j.tpb.2019.09.009.

6. Soewongsono, A. C., & Ariyanto, J. (2015). Teorema Berbasis Aksioma Separasi dalam Ruang Topologi. Jurnal Matematika Integratif ISSN, 1412, 6184. https://doi.org/10.24198/jmi.v11.n2.9420.85-96.

Thesis

1. Soewongsono, A.C. (2023). Mathematical models for the evolution of species. PhD Thesis, University of Tasmania (Supervised by Prof. Barbara Holland and Assoc. Prof. Malgorzata O'Reilly)

2. Soewongsono, A.C. (2018). The most recent common ancestor of a randomly chosen sample in a Galton-Watson process. Masters Thesis, Australian National University (Supervised by Assoc. Prof. Conrad J. Burden) (e-access)

3. Soewongsono, A.C. (2015). Teorema berbasis aksioma separasi dalam ruang topologi. Honors Thesis, Nusa Cendana University (Supervised by Dr. Jafaruddin Hamid and Ariyanto)

In Preparations

1. Exploring relationships between rates and patterns generated under state-dependent speciation and extinction models . With Michael Landis

2. Inferring rates under density-dependent GeoSSE with geographic overlap using deep learning approach. With Ammon Thompson and Michael Landis

3. Stochastic environmentally-driven model for the evolution of species. With Barbara Holland and Małgorzata O'Reilly.
   
   

Tutoring Experience

1. MATH1013: Mathematics and Applications 1, Mathematical Sciences Institute, ANU (Semester 1 & 2, 2018).

2. KMA153: Data Handling and Statistics, Mathematics, UTas (Semester 1 & 2, 2020; Semester 1 & 2, 2021; Semester 1 & 2, 2022).

3. KMA155: Computational Science and Discrete Mathematics 1 (Semester 2, 2020).

4. KME272: Engineering Mathematics 2B (Semester 2, 2020; Semester 2, 2021; Semester 2, 2022).

5. KMA252: Calculus and Applications 2 (Semester 1, 2021; Semester 1, 2022).

6. KMA154: Mathematics 1B (Semester 2, 2021; Semester 2, 2022).

Teaching Experience

1. Mathematical Biology, Mathematics, Nusa Cendana University (Contract, Semester 1 2019).

2. English for Specific Purposes, Mathematics, Nusa Cendana University (Contract, Semester 1 2019).