Publications
Preprints
- Singular Learning Theory for Factor Analysis, with Dimitra Kosta, Daniel Windisch, Mathias Drton, Anton Leykin, and Seth Sullivant.
- Identifiability of Phylogenetic Level-2 Networks under the Jukes-Cantor Model, with Aviva Englander, Martin Frohn, Niels Holtgrefe, Leo van Iersel, Mark Jones, and Seth Sullivant. bioRxiv (2025).
- Methodological considerations for semialgebraic hypothesis testing with incomplete U-statistics, with David Barnhill, Marina Garrote-López, Max Hill, Bryson Kagy, John Rhodes, and Joy Zhang.
- One-connection rule for structural equation models, with Bibhas Adhikari, Marc Härkönen, and Elias Tsigaridas.
- Goodness of fit for log-linear ERGMs, with Sonja Petrović and Despina Stasi.
- When do two networks have the same steady-state ideal?, with Maize Curiel and Carlos Munoz.
Research Articles
- Broken bracelets and Kostant’s partition function, with Maize Curiel and Pamela Harris. Journal of Combinatorics, to appear (2026+).
- The Pfaffian structure of CFN phylogenetic networks, with Joseph Cummings, Benjamin Hollering, Samuel Martin, and Ikenna Nometa. Journal of Mathematical Biology 92 no. 1 (2026) 21.
- Statistical learning with phylogenetic network invariants, with Travis Barton, Colby Long, and Joseph Rusinko. Bulletin of the Society of Systematic Biologists 4 no. 1 (2026).
- Routing Functions for Parameter Space Decomposition to Describe Stability Landscapes of Ecological Models, with Joseph Cummings, Kyle Dahlin, and Jonathan Hauenstein. Bulletin of Mathematical Biology 87 no. 12 (2025) 177.
- Group-based phylogenetic models on 3-sunlet networks, with Shelby Cox and Samuel Martin. Bulletin of Mathematical Biology 87 no. 9 (2025) 132.
- Maximum likelihood degree of the β-stochastic blockmodel, with Cashous Bortner, Jennifer Garbett, Naomi Krawzik, Christopher McClain, and Derek Young. Algebraic Statistics 16 no. 1 (2025) 77–94.
- Absolute concentration robustness: Algebra and geometry, with Luis David García Puente, Heather Harrington, Matthew Johnston, Nicolette Meshkat, Mercedes Pérez Millán, and Anne Shiu. Journal of Symbolic Computation 128 (2025): 102398.
- Mixed volumes of networks with binomial steady-states, with Jane Ivy Coons and Maize Curiel. Journal of Symbolic Computation 128 (2025): 102395.
- New directions in algebraic statistics: Three challenges from 2023, with Yulia Alexandr, Miles Bakenhus, Maize Curiel, Sameer K. Deshpande, Yuqi Gu, Max Hill, Joseph Johnson, Bryson Kagy, Vishesh Karwa, Jiayi Li, Hanbaek Lyu, Sonja Petrović, and Jose Israel Rodriguez. Algebraic Statistics 15 no. 2 (2024) 357–382.
- Dimensions of level-1 group-based phylogenetic networks, with Robert Krone and Samuel Martin. Bulletin of Mathematical Biology 86 no. 8 (2024) 90.
- Identifiability of linear compartmental tree models, with Cashous Bortner, Nicolette Meshkat, Anne Shiu, and Seth Sullivant. Advances in Applied Mathematics (2023) 102268.
- Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes, with Leo van Iersel, Remie Janssen, Mark Jones, Colby Long, and Yukihiro Murakami. Journal of Mathematical Biology 83 no. 3 (2021) 1–24.
- Identifiability of linear compartment models: the singular locus, with Nicolette Meshkat and Anne Shiu. Advances in Applied Mathematics (2021) 102490.
- Binomial ideals of domino tilings, with Nicole Yamzon. Discrete Mathematics 344 no. 11 (2021) 112530.
- Steady state degree and mixed volume of chemical reaction networks, with Cvetelina Hill. Advances in Applied Mathematics 131 (2021) 102254.
- Phylogenetic trees, with Hector Baños, Nathaniel Bushek, Ruth Davidson, Pamela Harris, Robert Krone, Colby Long, Allen Stewart, and Robert Walker. Journal of Software for Algebra and Geometry 11 no. 1 (2021) 1–7.
- Joining and decomposing reaction networks, with Heather Harrington, Nicolette Meshkat, and Anne Shiu. Journal of Mathematical Biology (2020).
- Identifying the number of components in Gaussian mixture models using numerical algebraic geometry, with Adel Alaeddini and Sara Shirinkam. Journal of Algebra and Its Applications (2020).
- Linear compartmental models: input-output equations and operations that preserve identifiability, with Heather Harrington, Nicolette Meshkat, and Anne Shiu. SIAM Journal on Applied Mathematics 79 no. 4 (2019) 1423–1447.
- Algebraic signatures of convex and non-convex codes, with Carina Curto, Jack Jeffries, Katherine Morrison, Zvi Rosen, Anne Shiu, and Nora Youngs. Journal of Pure and Applied Algebra 223 no. 9 (2019) 3919–3940.
- Dimensions of group-based mixtures, with Hector Baños, Nathaniel Bushek, Ruth Davidson, Pamela Harris, Robert Krone, Colby Long, Allen Stewart, and Robert Walker. Bulletin of Mathematical Biology 81 no. 2 (2019) 316–336.
- The multiple roots phenomenon in maximum likelihood estimation for factor analysis, with Sonja Petrovic, Donald Richards, and Despina Stasi. Advanced Studies in Pure Mathematics.
- Neural ideals and stimulus space visualization, with Nida Obatake and Nora Youngs. Advances in Applied Mathematics 95 (2018) 65–95.
- The maximum likelihood threshold of a graph, with Seth Sullivant. Bernoulli 24 no. 1 (2018) 386–407.
- Distinguishing phylogenetic networks, with Colby Long. SIAM Journal on Applied Algebra and Geometry 2 no. 1 (2018) 72–93.
- What makes a neural code convex?, with Carina Curto, Jack Jeffries, Katherine Morrison, Mohamed Omar, Zvi Rosen, Anne Shiu, and Nora Youngs. SIAM Journal on Applied Algebra and Geometry 1 (2017) 222–238.
- Goodness-of-fit for log-linear network models: Dynamic Markov bases using hypergraphs, with Sonja Petrović and Despina Stasi. Annals of the Institute of Statistical Mathematics 69 no. 3 (2017) 673–704.
- Numerical algebraic geometry for model selection and its applications to the life sciences, with Brent Davis, Kenneth L. Ho, Daniel J. Bates, and Heather A. Harrington. Journal of the Royal Society Interface 13 no. 123 (2016) 20160256.
- Algebraic systems biology: A case study for the Wnt Pathway, with Heather Harrington, Zvi Rosen, and Bernd Sturmfels. Bulletin of Mathematical Biology 78 (2016) 21–51.
- Maximum likelihood geometry in the presence of data zeros, with Jose Israel Rodriguez. ISSAC 2014 Conference Proceedings.
- Combinatorial degree bound for toric ideals of hypergraphs, with Sonja Petrović. International Journal of Algebra and Computation 23 (2013) 1503–1520.
- Interfacing with PHCpack, with Sonja Petrović and Jan Verschelde. Journal of Software for Algebra and Geometry 5 (2013) 20–25.
- Maximum likelihood degree of variance component models, with Mathias Drton and Sonja Petrović. Electronic Journal of Statistics 6 (2012) 993–1016.
- A proof of the set-theoretic version of the salmon conjecture, with Shmuel Friedland. Journal of Algebra 356 (2012) 374–379.
Book Chapters and Review Articles
- Phylogenetic Networks, with Colby Long and Joseph Rusinko. In Foundations for Undergraduate Research in Mathematics.
- Social Networks of Mobile Money in Kenya, with Sibel Kusimba and Gabriel Kunyu. In Money at the margins.
- What are higher-order networks?, with Christian Bick, Heather Harrington, and Michael Schaub. SIAM Review 65 no. 3 (2023) 686–731.
- Algebraic statistics, tables, and networks: The Fienberg advantage, with Vishesh Karwa and Sonja Petrović. Springer Series in the Data Sciences.