Kaie Kubjas

Kaie Kubjas

Assistant Professor

Aalto University


Since 2017 I am a tenure-track assistant professor in the Department of Mathematics and Systems Analysis at Aalto University. I received my PhD in mathematics in 2013 from Freie Universität Berlin under supervision of Christian Haase and Klaus Altmann. As a postdoctoral researcher I visited Max Planck Institute for Mathematics, Aalto Science Institute, Simons Institute for the Theory of Computing, Institute of Data, Systems and Society at MIT and PolSys Team at Sorbonne University.

I work in the field of applied nonlinear algebra. I am particularly interested in algebraic statistics and applications in biology, for example in phylogenetics and 3D genome reconstruction. I am also interested in questions about matrix and tensor decompositions, e.g. nonnegative and positive semidefinite factorizations, and low-rank matrix/tensor completion. Besides nonlinear algebra, I like to use tools from combinatorics, polyhedral geometry and convex optimization.

Currently I am the Vice Chair of the SIAM Activity Group on Algebraic Geometry. In 2020-2022 I was the Deputy Convenor of European Women in Mathematics.

Academy of Finland is funding my research through project funding for early-career researchers.

  • Algebraic statistics
  • Nonlinear algebra in biology
  • Structured matrix and tensor decompositions
  • PhD in Mathematics, 2013

    Free University of Berlin

  • BSc in Mathematics, 2007

    University of Tartu

Editorial and organizatorial work


The model-specific Markov embedding problem for symmetric group-based models
Together with my PhD student Muhammad Ardiyansyah and Dimitra Kosta we study the model specific embedding problem for symmetric group-based models in phylogenetics. We provide a characterisation of model embeddable Markov matrices corresponding to symmetric group-based phylogenetic models. Our paper is published in the Journal of Mathematical Biology.
Olga Kuznetsova wins Second Place Poster Award at MEGA 2021
My PhD student Olga Kuznetsova won shared Second Place Poster Award at MEGA 2021 for her poster Algebraic Degree of Optimization Over a Variety. The poster is based on our recent preprint Algebraic degree of optimization over a variety with an application to p-norm distance degree together with Olga Kuznetsova and Luca Sodomaco. Congratulations, Olga!
Distinguishing Level-2 Phylogenetic Networks Using Phylogenetic Invariants
My PhD student Muhammad Ardiyansyah has just posted his first single-authored paper on arXiv. In the paper, he studies the distinguishibility of simple and semisimple level-2 phylogenetic networks extending the earlier work on large-cycle and level-1 networks. Congratulations, Ardi!


  • P.O. Box 11100
    FI-00076 Aalto
  • Visiting address: Room Y237, Otakaari 1, 02150 Espoo