Publications

Dario Gasbarra, Kaie Kubjas, Sangita Kulathinal, Nataliia Kushnerchuk, Fatemeh Mohammadi, Etienne Sebag (2026). Discrete-time, discrete-state multistate Markov models from the perspective of algebraic statistics.

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Kaie Kubjas, Lilja Metsalampi (2026). Geometry of low nonnegative rank matrix completion.

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Kaie Kubjas, Olga Kuznetsova, Elina Robeva, Pardis Semnani, Luca Sodomaco (2025). Log-concave density estimation in undirected graphical models. Bernoulli, 31(4): 2916-2939.

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Sean Dewar, Georg Grasegger, Kaie Kubjas, Fatemeh Mohammadi, Anthony Nixon (2025). On the uniqueness of collections of pennies and marbles. Examples and Counterexamples, 7, 100181.

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Kaie Kubjas, Olga Kuznetsova, Luca Sodomaco (2025). Algebraic degree of optimization over a variety with an application to $p$-norm distance degree. Acta Universitatis Sapientiae, Mathematica (Special Issue on Metric Algebraic Geometry), volume 17, article number 3.

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Sean Dewar, Georg Grasegger, Kaie Kubjas, Fatemeh Mohammadi, Anthony Nixon (2025). Single-cell 3D genome reconstruction in the haploid setting using rigidity theory. Journal of Mathematical Biology, 90, article number 45.

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Alexandros Grosdos, Alexander Heaton, Kaie Kubjas, Olga Kuznetsova, Georgy Scholten, Miruna-Stefana Sorea (2025). Corrigendum to “Exact solutions in log-concave maximum likelihood estimation” [Adv. Appl. Math. 143 (2023) 102448]. Advances in Applied Mathematics, 162: 102777.

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Kaie Kubjas, Jiayi Li, Maximilian Wiesmann (2024). Geometry of Polynomial Neural Networks. Algebraic Statistics, 15(2), 295-328.

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Kristen Dawson, Serkan Hoşten, Kaie Kubjas, Lilja Metsalampi (2024). Uniqueness of size-2 positive semidefinite matrix factorizations.

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Tobias Boege, Kaie Kubjas, Pratik Misra, Liam Solus (2024). Colored Gaussian DAG models. Accepted to Journal of the Royal Statistical Society: Series B.

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Diego Cifuentes, Jan Draisma, Oskar Henriksson, Annachiara Korchmaros, Kaie Kubjas (2024). 3D genome reconstruction from partially phased Hi-C data. Bulletin of Mathematical Biology, 86, 33.

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Alexandros Grosdos, Alexander Heaton, Kaie Kubjas, Olga Kuznetsova, Georgy Scholten, Miruna-Stefana Sorea (2023). Exact Solutions in Log-Concave Maximum Likelihood Estimation. Advances in Applied Mathematics, 143.

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Carlos D'Andrea, Kaie Kubjas, Fatemeh Mohammadi (2023). Foreword: Special issue of JSC on the occasion of MEGA 2021. Journal of Symbolic Computation, 114:99-101.

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Per Austrin, Petteri Kaski, Kaie Kubjas (2022). Tensor network complexity of multilinear maps. Theory of Computing, 18(16):1-54.

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Kaie Kubjas, Luca Sodomaco, Elias Tsigaridas (2022). Exact solutions in low-rank approximation with zeros. Linear Algebra and its Applications, 641:67–97.

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Anastasiya Belyaeva, Kaie Kubjas, Lawrence J. Sun, Caroline Uhler (2022). Identifying 3D Genome Organization in Diploid Organisms via Euclidean Distance Geometry. SIAM Journal on Mathematics of Data Science, 4(1):204–228.

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Muhammad Ardiyansyah, Dimitra Kosta, Kaie Kubjas (2021). The model-specific Markov embedding problem for symmetric group-based models. Journal of Mathematical Biology, 83, Article number: 33.

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Robert Krone, Kaie Kubjas (2021). Uniqueness of nonnegative matrix factorizations by rigidity theory. SIAM Journal on Matrix Analysis and Applications, 42(1), 134–164.

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Carlos Améndola, Dimitra Kosta, Kaie Kubjas (2020). Maximum Likelihood Estimation of Toric Fano Varieties. Algebraic Statistics, 11(1):5–30.

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Elizabeth S Allman, Hector Banos Cervantes, Robin Evans, Serkan Hoşten, Kaie Kubjas, Daniel Lemke, John A Rhodes, Piotr Zwiernik (2019). Maximum likelihood estimation of the latent class model through model boundary decomposition. Journal of Algebraic Statistics (Issue in honor of S. E. Fienberg), 10(1):51-84.

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Dimitra Kosta, Kaie Kubjas (2019). Maximum likelihood estimation of symmetric group-based models via numerical algebraic geometry. Bulletin of Mathematical Biology (Special Issue: Algebraic Methods in Phylogenetics), 81(2):337-360.

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Per Austrin, Petteri Kaski, Kaie Kubjas (2018). Tensor network complexity of multilinear maps. 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), 7:1-7:21.

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Kaie Kubjas, Elina Robeva, Richard Z Robinson (2018). Positive semidefinite rank and nested spectrahedra. Linear and Multilinear Algebra, 66(10):1952-1974.

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Luca Weihs, Bill Robinson, Emilie Dufresne, Jennifer Kenkel, Kaie Kubjas, Reginald McGee II, Nhan Nguyen, Elina Robeva, Mathias Drton (2018). Determinantal generalizations of instrumental variables. Journal of Causal Inference, 6(1).

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Thomas Kahle, Kaie Kubjas, Mario Kummer, Zvi Rosen (2017). The geometry of rank-one tensor completion. SIAM Journal on Applied Algebra and Geometry, 1(1):200-221.

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Kaie Kubjas, Zvi Rosen (2017). Matrix completion for the independence model. Journal of Algebraic Statistics, 8(1):1-21.

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Kaie Kubjas, Pablo A Parrilo, Bernd Sturmfels (2017). How to flatten a soccer ball. Homological and Computational Methods in Commutative Algebra, editors A. Conca, J. Gubeladze and T. Römer, Springer INdAM series, volume 20, pages 141-162.

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Rob H Eggermont, Emil Horobeţ, Kaie Kubjas (2016). Algebraic boundary of matrices of nonnegative rank at most three. Linear Algebra and its Applications, 508:62-80.

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Kaie Kubjas (2015). Low degree minimal generators of phylogenetic semigroups. European Journal of Mathematics, 1(1):2-24.

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Kaie Kubjas, Elina Robeva, Bernd Sturmfels (2015). Fixed points of the EM algorithm and nonnegative rank boundaries. The Annals of Statistics, 43(1):422-461.

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Kaie Kubjas, Christopher Manon (2014). Conformal blocks, Berenstein--Zelevinsky triangles, and group-based models. Journal of Algebraic Combinatorics, 40(3):861-886.

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Kaie Kubjas (2013). Algebraic and combinatorial aspects of group-based models.

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Weronika Buczyńska, Jarosław Buczyński, Kaie Kubjas, Mateusz Michałek (2013). On the graph labellings arising from phylogenetics. Open Mathematics, 11(9):1577-1592.

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Kaie Kubjas (2012). Hilbert polynomial of the Kimura 3-parameter model. Journal of Algebraic Statistics, 3(1):64-69.

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