Atte Aalto

Atte Aalto

Postdoctoral researcher / Research associate

Fachgebiet(e) Mathematics
Forschungsthemen Parameter estimation, Control theory, System identification
Fakultät oder Zentrum Luxembourg Centre for Systems Biomedicine
Forschungseinheit LCSB
Postadresse Université du Luxembourg
6, avenue du Swing
L-4367 Belvaux
Büroadresse BioTech II, 0.06
Gesprochene Sprachen English, Finnish
Forschungsaufenthalte in France, Luxembourg, Finland

Postdoc in the Systems Control group (Gonçalves Lab)


  • December 2016-: Postdoc researcher at LCSB’s Systems Control group
  • 2015-2016: Postdoc researcher at INRIA Saclay Île-de-France research center
  • 2014: Doctor of Science, Department of Mathematics and Systems Analysis, Aalto University, Finland
  • 2009: Master of Science, Helsinki University of Technology, Finland

My background is in applied mathematics, and the area of my doctoral thesis was mathematical systems theory. In particular, I studied the effect of temporal discretization on Kalman filtering and the effect of spatial discretization on Kalman filtering for systems governed by partial differential equations (PDEs). During my first postdoctoral appointment, I studied state and parameter estimation problems for PDE systems.

Current research

At LCSB I have been working on method development for gene regulatory network inference from short time series data with low sampling frequency. Combining techniques from machine learning, systems theory, and statistics, I have developed a method where the gene expression is assumed to follow a nonlinear (stochastic) ordinary differential equation, where the dynamics function is modelled as a Gaussian process. This results in a stochastic process model of gene expression, whose properties depend on the underlying network. Network inference is then carried out by Markov chain Monte Carlo sampling. More recently, I have shifted focus on so-called single-cell data, which consists of gene expression measurements on single-cell level. One cell can only be measured once, and so the data consists of snapshots of cell ensembles at different times. Although single-cell experiments produce data that is far richer compared to traditional batch experiments, it is not evident how such data can be used for modelling the cell dynamics.

Last updated on: Dienstag, den 22. Januar 2019

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See detailLinear system identification from ensemble snapshot observations
Aalto, Atte; Goncalves, Jorge

E-print/Working paper (2019)

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See detailSpatial discretization error in Kalman filtering for discrete-time infinite dimensional systems
Aalto, Atte

in IMA Journal of Mathematical Control and Information (2018), 35(suppl_1), 51-72

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See detailIterative observer-based state and parameter estimation for linear systems
Aalto, Atte

in ESAIM: Control, Optimisation and Calculus of Variations (2018), 24(1), 265-288

See detailBayesian variable selection in linear dynamical systems
Aalto, Atte; Goncalves, Jorge

E-print/Working paper (2018)

See detailContinuous time Gaussian process dynamical models in gene regulatory network inference
Aalto, Atte; Viitasaari, Lauri; Ilmonen, Pauliina; Goncalves, Jorge

E-print/Working paper (2018)

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See detailModal Locking Between Vocal Fold Oscillations and Vocal Tract Acoustics
Murtola, Tiina; Aalto, Atte; Malinen, Jarmo; Aalto, Daniel; Vainio, Martti

in Acta Acustica United with Acustica (2018), 104(2), 323-337

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See detailConvergence of discrete time Kalman filter estimate to continuous time estimate
Aalto, Atte

in International Journal of Control (2016), 89(4), 668-679

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See detailAcoustic wave guides as infinite-dimensional dynamical systems
Aalto, Atte; Lukkari, Teemu; Malinen, Jarmo

in ESAIM: Control, Optimisation and Calculus of Variations (2015), 21(2), 324-347

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See detailComposition of passive boundary control systems
Aalto, Atte; Malinen, Jarmo

in Mathematical Control and Related Fields (2013), 3(1), 1-19

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See detailInteraction of vocal fold and vocal tract oscillations
Aalto, Atte; Aalto, Daniel; Malinen, Jarmo; Vainio, Martti

in Proceedings of the 24th Nordic Seminar on Computational Mechanics (2011)

See detailWave propagation in networks: a system theoretic approach
Aalto, Atte; Malinen, Jarmo

in Proceedings of the 18th World Congress of the IFAC (2011)

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See detailA LF-pulse from a simple glottal flow model
Aalto, Atte; Alku, Paavo; Malinen, Jarmo

in Proceedings of the 6th International Workshop on Models and Analysis of Vocal Emissions for Biomedical Applications (2009)

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