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Atte Aalto

Atte Aalto

Postdoctoral researcher / Research associate

Academic Area(s) Mathematics
Research Topics Parameter estimation, Control theory, System identification
Faculty or Centre Luxembourg Centre for Systems Biomedicine
Department Systems Control
Postal Address Université du Luxembourg
6, avenue du Swing
L-4367 Belvaux
Campus Office BioTech II, 0.06
Speaks English, Finnish
Research Stays 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

Since December 2019, I have been the principal investigator in an FNR CORE junior project on modelling gene expression dynamics from single-cell data, that consist of gene expression measurements at single-cell resolution. One cell can be measured only once, and so the data consist of snapshots of cell ensembles at different times. Although single-cell experiments produce data that is far richer compared to traditional bulk experiments, it is not evident how such data can be used for modelling cell dynamics. Before focusing on single-cell data, I developed a method for gene regulatory network inference from short time series data with low sampling frequency, combining techniques from machine learning, systems theory, and statistics. In the method, 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.

Method development

BINGO: a method for gene regulatory network inference from time series data

Last updated on: Thursday, 23 April 2020

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See detailStages of COVID-19 pandemic and paths to herd immunity by vaccination: dynamical model comparing Austria, Luxembourg and Sweden
Kemp, Francoise; Proverbio, Daniele; Aalto, Atte; Mombaerts, Laurent; Fouquier d'herouël, Aymeric; Husch, Andreas; Ley, Christophe; Goncalves, Jorge; Skupin, Alexander; Magni, Stefano

E-print/Working paper (2021)

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See detailDynamical SPQEIR model assesses the effectiveness of non-pharmaceutical interventions against COVID-19 epidemic outbreaks.
Proverbio, Daniele; Kemp, Francoise; Magni, Stefano; Husch, Andreas; Aalto, Atte; Mombaerts, Laurent; Skupin, Alexander; Goncalves, Jorge; Ameijeiras-Alonso, Jose; Ley, Christophe

in PloS one (2021), 16(5), 0252019

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See detailGene regulatory network inference from sparsely sampled noisy data
Aalto, Atte; Viitasaari, Lauri; Ilmonen, Pauliina; Mombaerts, Laurent; Goncalves, Jorge

in Nature Communications (2020), 11

See detailCOVID-19 Crisis Management in Luxembourg: Insights from an Epidemionomic Approach
burzynski, Michal; Machado, Joel; Aalto, Atte; Beine, Michel; Haas, Tom; Kemp, Francoise; Magni, Stefano; Mombaerts, Laurent; Picard, Pierre M; Proverbio, Daniele; Skupin, Alexander; Docquier, Frédéric

E-print/Working paper (2020)

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See detailAssessing suppression strategies against epidemicoutbreaks like COVID-19: the SPQEIR model
Proverbio, Daniele; Kemp, Francoise; Magni, Stefano; Husch, Andreas; Aalto, Atte; Mombaerts, Laurent; Goncalves, Jorge; Skupin, Alexander; Ameijeiras-Alonso, Jose; Ley, Christophe

E-print/Working paper (2020)

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

in Proceedings of the IEEE Conference on Decision and Control (2019, December)

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See detailA multifactorial evaluation framework for gene regulatory network reconstruction
Mombaerts, Laurent; Aalto, Atte; Markdahl, Johan; Goncalves, Jorge

in Foundations of Systems Biology in Engineering (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)

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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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