# Publications

## Preprints (submitted)

### Learning a performance metric of Buchberger's algorithm,

Jelena Mojsilović, Dylan Peifer, and Sonja Petrović.

### Random graphs with node and block effects: models, goodness-of-fit tests, and applications to biological networks,

Elizabeth Gross, Sonja Petrović, and Despina Stasi.

### Threaded Gr\"obner Bases: a Macaulay2 package,

Sonja Petrović and Shahrzad Jamshidi Zelenberg.

### Exact tests for stochastic block models,

Vishesh Karwa, Debdeep Pati, Sonja Petrović, Liam Solus, Nikita Alexeev, Mateja Raič, Dane Wilburne, Robert Williams, Bowei Yan.

### DERGMs: Degeneracy-restricted exponential random graph models,

Vishesh Karwa, Sonja Petrović and Denis Bajić.

*Major* revision completed April 2021 (see arXiv v3).

Supplementary material: on GitHub.

## published / accepted / in press

Algebraic statistics, tables, and networks: The Fienberg advantage.

Elizabeth Gross, Vishesh Karwa, Sonja Petrovi\'c.

To appear in the Springer volume Statistics in the public interest - in memory of Stephen E. Fienberg.

arXiv:1910.01692.

Algebraic Statistics in Practice: Applications to Networks,

Marta Casanellas, Sonja Petrović and Caroline Uhler.

Annual Reviews of Statistics and its Applications 2020. 7:9.1–9.24.

arXiv:1906.09537.

Published version https://doi.org/10.1146/annurev-statistics-031017-100053

WHAT IS... a Markov basis?

Sonja Petrović. Notices of the American Mathematical Society 2019, 66 (7), 1088—1092.

Read the full article here or on arXiv:1907.07320.

“Old Wine in New Bottles,” and Some More New Wine – Stephen Fienberg’s Influence on Algebraic Statistics,

Sonja Petrović, Aleksandra Slavkovic, and Ruriko Yoshida.

Editorial piece for the Journal of Algebraic Statistics' Special Volume in honor of memory of S.E.Fienberg, 2019.

Read the article.

Random Monomial Ideals: a Macaulay2 package

Sonja Petrovic, Despina Stasi, Dane Wilburne.

Journal of Software for Algebra and Geometry, 9 (2019), 65–70.

arXiv:1711.10075.

Code available in Macaulay2 as of version 1.11.

Hypergraph encodings of arbitrary toric ideals,

Sonja Petrović, Apostolos Thoma and Marius Vladoiu.

Journal of Combinatorial Theory, Series A 166 (2019) pp. 11-41.

arXiv: 1711.04354.

Bouquet algebra of toric ideals,

Sonja Petrović, Apostolos Thoma and Marius Vladoiu.

Journal of Algebra 512 (2018) 493–525.

arXiv:1507.02740. (Revised 2017.)

Random Monomial Ideals,

Jesus A. De Loera, Sonja Petrovic, Lily Silverstein, Despina Stasi, Dane Wilburne

Journal of Algebra, 519(1): 440--473, 2019.

arXiv:1701.07130. (Revised April 2018.)

The multiple roots phenomenon in maximum likelihood estimation for factor analysis,

Elizabeth Gross, Sonja Petrovic, Donald Richards, Despina Stasi.

Adv. Stud. Pure Math. 75 (2017).

arXiv:1702.04477.

Statistical models for cores decomposition of an undirected random graph,

Vishesh Karwa, Michael J. Pelsmajer, Sonja Petrović, Despina Stasi, and Dane Wilburne.

Electronic Journal of Statistics 2017, Vol. 11, No. 1, 1949-1982.

arXiv:1410.7357 (v3, Nov 2016); http://dx.doi.org/10.1214/17-EJS1235.

Supplementary material: R code on GitHub.

Coauthorship and citation networks for statisticians: Comment,

Vishesh Karwa and Sonja Petrovic. Invited comment on the paper `Coauthorship and citation networks for statisticians' by Jin and Ji.

Annals of Applied Statistics, 10 (2016), no. 4, 1827--1834. doi:10.1214/16-AOAS978.

arXiv:1608.06667.

On the Geometry and Extremal Properties of the Edge-Degeneracy Model,

Nicolas Kim, Dane Wilburne, Sonja Petrovic, Alessandro Rinaldo.

MNG 2016: The Third SDM Workshop on Mining Networks and Graphs: A Big Data Analytic Challenge.

arXiv:1602.00180.

A survey of discrete methods in (algebraic) statistics for networks,

Sonja Petrović.

Contemporary Mathematics, vol. 685, 260-281, American Mathematical Society, 2017.

arXiv:1510.02838.

Blow-up algebras, determinantal ideals, and Dedekind-Mertens-like formulas,

Alberto Corso, Uwe Nagel, Sonja Petrovic, and Cornelia Yuen. (2016)

Forum Mathematicum, 29(4), pp. 799-830. DOI: 10.1515/forum-2016-0007.

arXiv:1502.03484.

Random Sampling in Computational Algebra: Helly Numbers and Violator Spaces,

Jesus A. De Loera, Sonja Petrovic, and Despina Stasi.

Journal of Symbolic Computation, 77 (2016) pp.1-15. 10.1016/j.jsc.2016.01.001.

Link to article.

arXiv:1503.08804.

Goodness of fit for log-linear network models: Dynamic Markov bases using hypergraphs,

Elizabeth Gross, Sonja Petrovic, and Despina Stasi.

Annals of the Institute of Statistical Mathematics (2017) 69: 673. DOI: 10.1007/s10463-016-0560-2

arXiv:1401.4896 .

Supplementary material.

Beta models for random hypergraphs with a given degree sequence,

Despina Stasi, Kayvan Sadeghi, Alessandro Rinaldo, Sonja Petrovic, and Stephen Fienberg.

Proceedings of 21st International Conference on Computational Statistics (2014). arXiv:1407.1004.

Fibers of multi-way contingency tables given conditionals: relation to marginals, cell bounds and Markov bases,

Aleksandra B. Slavkovic, Sonja Petrovic, and Xiaotian Zhu.

Annals of the Institute of Statistical Mathematics, August 2015, Volume 67, Issue 4, pp 621-648. DOI: 10.1007/s10463-014-0471-z.

arXiv:1401.1397. Published online: June 2014.

Toric algebra of hypergraphs,

Sonja Petrovic and Despina Stasi.

Journal of Algebraic Combinatorics, February 2014, Volume 39, Issue 1, pp 187-208.

arXiv:1206.1904. DOI link.

A combinatorial degree bound for toric ideals of hypergraphs,

Elizabeth Gross and Sonja Petrovic.

International Journal of Algebra and Computation, Volume 23, Issue 06, pp. 1503-1520, September 2013. DOI.

arXiv:1206.2512 (previous title: "Markov complexity of hypergraphs").

PHCpack in Macaulay2,

Elizabeth Gross, Sonja Petrovic, and Jan Verschelde,

Journal of Software for Algebra and Geometry, Volume 5, 2013; certified code also available with Macaulay2 release 1.6.

arXiv:1105.4881 (see the Software page for more information).

GraphicalModels in Macaulay2,

Luis Garcia-Puente, Sonja Petrovic, and Seth Sullivant.

Journal of Software for Algebra and Geometry, Volume 5, 2013; certified code also available with Macaulay2 release 1.5.

arXiv:1208.6550. (see the Software page for more information).

Maximum Likelihood Estimation in the Beta model,

Alessandro Rinaldo, Sonja Petrovic, and Stephen E. Fienberg.

Annals of Statistics 2013, Vol. 41, No. 3, 1085-1110.

arXiv:1105.6145. ( DOI)

Betti numbers of Stanley-Reisner rings determine hierarchical Markov degrees,

Sonja Petrovic and Erik Stokes.

Journal of Algebraic Combinatorics, Volume 37, Issue 4 (2013), Page 667-682.

arXiv:0910.1610 (DOI)

How Does Maximum Likelihood Estimation for the p1 Model Scale for Large Sparse Networks?,

Rinaldo, A., Petrovíc, S. and Fienberg, S.E. (2012).

NIPS 2012 workshop on Algorithmic and Statistical Approaches for Large Social Network Data Sets.

Equality of Graver and Universal Gröbner bases of colored partition identities,

Tristram Bogart, Raymond Hemmecke, and Sonja Petrovic.

Experimental Mathematics 2012, Vol. 21 (4), 395-401.

arXiv:1004.0840.

Maximum likelihood degree of variance component models,

Elizabeth Gross, Mathias Drton, and Sonja Petrovic.

Electronic Journal of Statistics 2012, Vol. 6, No. 0, 993-1016.

arXiv:1111.3308.

Algebraic Statistics,

Sonja Petrovic and Aleksandra Slavkovic.

In M. Lovric, editor, International Encyclopedia of Statistical Science, Part 1, 29-32, Springer. (2011) (DOI: 10.1007/978-3-642-04898-2_112)

Identifiability of two-tree mixtures under group-based models,

Elizabeth Allman, John Rhodes, Sonja Petrovic, and Seth Sullivant.

IEEE/ACM Transactions in Computational Biology and Bioinformatics, 8 no. 3 (2011) 710-722.

arXiv:0909.1854; Supplementary material.

Algebraic statistics for a directed random graph model with reciprocation,

Sonja Petrovic, Alessandro Rinaldo and Stephen E. Fienberg.

In: Algebraic Methods in Statistics and Probability II, M. Viana and H. Wynn (editors). CONM, vol 516. AMS.

arXiv:0909.0073

Algebraic statistics for p_1 random graph models: Markov bases and their uses,

Stephen E. Fienberg, Sonja Petrovic, and Alessandro Rinaldo.

Book chapter in S. Sinharay and N. J. Dorans, editors, Papers in Honor of Paul W. Holland. ETS. (2010) Springer

Properties of cut ideals of ring graphs,

Uwe Nagel and Sonja Petrovic.

J. Commut. Algebra 1 (2009), no. 3, 547--565.

arXiv:0806.0585

Universal Gröbner bases of varieties of minimal degree.

Math. Res. Lett. 15 (2008), no. 6, 1211--1221.

Toric ideals of phylogenetic invariants for the general group-based model on claw trees,

Julia Chifman and Sonja Petrovic.

In Proceedings of the Second international conference on Algebraic Biology, (eds. H.Anai, K. Horimoto and T. Kutsia),

Springer LNCS 454 (2007), 307--321.

arXiv:0702368

A nonlinear Sturm-Picone comparison theorem for dynamic equations on time scales,

Boris Belinskiy, John Graef, and Sonja Petrovic.

Int. J. Difference Equ. 2 (2007), no. 1, 25--35. (pdf)