Publications

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.

Cite Code DOI ArXiv

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.

Cite Code arXiv

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.

Cite DOI

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

Cite Code DOI arXiv

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

Cite Code arXiv

Tobias Boege, Kaie Kubjas, Pratik Misra, Liam Solus (2024). Colored Gaussian DAG models.

Cite Code arXiv

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.

Cite Code DOI arXiv

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.

Cite Code DOI arXiv

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.

Cite DOI

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

Cite DOI arXiv

Kaie Kubjas, Olga Kuznetsova, Elina Robeva, Pardis Semnani, Luca Sodomaco (2022). Log-concave density estimation in undirected graphical models. Accepted to Bernoulli.

Cite Code arXiv

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

Cite Code DOI arXiv

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.

Cite Code DOI arXiv

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.

Cite Code DOI arXiv

Kaie Kubjas, Olga Kuznetsova, Luca Sodomaco (2021). Algebraic degree of optimization over a variety with an application to $p$-norm distance degree. Accepted to Acta Universitatis Sapientiae, Mathematica (Special Issue on Metric Algebraic Geometry).

Cite Code arXiv

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

Cite Code DOI arXiv

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

Cite DOI arXiv

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.

Cite DOI arXiv

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.

Cite Code DOI arXiv

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.

Cite DOI arXiv

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

Cite Code DOI arXiv

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).

Cite DOI arXiv

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.

Cite DOI arXiv

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

Cite DOI arXiv

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.

Cite DOI arXiv

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.

Cite DOI arXiv

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

Cite DOI arXiv

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.

Cite DOI arXiv

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

Cite DOI arXiv

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

PDF Cite Link

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

Cite DOI arXiv

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

Cite Code DOI arXiv