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Home Members Sikorski, Alexander

Sikorski, Alexander

Contact

Room
4033
Phone
+49 30 84185-199
Email
Email
Division
Mathematics of Complex Systems
Department
Modeling and Simulation of Complex Processes
Group
Computational Molecular Design

Projects

Projects as Member

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Empirical Bayes methods in systems medicine

One of the main goals of mathematical modeling related to medical applications is to obtain patient-specific parametrizations and model predictions. In clinical practice...

Empirical Bayes methods in systems medicine
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Probing Scales in Equilibrated Systems by Optimal Nonequilibrium Forcing

The dynamics of biomolecules show an inherent multiscale behaviour with cascades of timescales and strong interaction between them. Molecular dynamics (MD) simulations...

Probing Scales in Equilibrated Systems by Optimal Nonequilibrium Forcing
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Uncertainty Quantification for Bayesian Inverse Problems with Applications to Systems Biology

This research is carried out in the framework of MATHEON supported by Einstein Foundation Berlin.

Uncertainty Quantification for Bayesian Inverse Problems with Applications to Systems Biology

Publications

2025
Capturing the Macroscopic Behaviour of Molecular Dynamics with Membership Functions Mathematical Optimization for Machine Learning: Proceedings of the MATH+ Thematic Einstein Semester 2023, 2025 Alexander Sikorski, Robert Julian Rabben, Surahit Chewle, Marcus Weber BibTeX
arXiv
DOI
Exploring Metastable Dynamics of Gene Regulatory Networks with ISOKANN 23rd International Conference on Computational Methods in Systems Biology, CMSB 2025, 2025 (accepted for publication) Maryam Yousefian, Luca Donati, Alexander Sikorski, Marcus Weber, Susanna Röblitz BibTeX
2024
ISOKANN.jl 2024 Alexander Sikorski BibTeX
DOI
Learning Koopman eigenfunctions of stochastic diffusions with optimal importance sampling and ISOKANN Journal of Mathematical Physics, Vol.65, p. 013502, 2024 Alexander Sikorski, Enric Ribera Borrell, Marcus Weber BibTeX
arXiv
DOI
Spectral clustering of Markov chain transition matrices with complex eigenvalues Journal of Computational and Applied Mathematics, Vol.444, p. 115791, 2024 Anna-Simone Frank, Alexander Sikorski, Susanna Röblitz BibTeX
arXiv
DOI
Tensor-SqRA: Modeling the transition rates of interacting molecular systems in terms of potential energies Journal of Chemical Physics, Vol.160, p. 104112, 2024 Alexander Sikorski, Amir Niknejad, Marcus Weber, Luca Donati BibTeX
arXiv
DOI
Voronoi Graph - Improved raycasting and integration schemes for high dimensional Voronoi diagrams 2024 Alexander Sikorski, Martin Heida BibTeX
arXiv
2023
VoronoiGraph.jl 2023 Alexander Sikorski BibTeX
DOI
2022
Consistency and order 1 convergence of cell-centered finite volume discretizations of degenerate elliptic problems in any space dimension SIAM Journal on Numerical Analysis, 2022 (under review) Martin Heida, Alexander Sikorski, Marcus Weber BibTeX
DOI
2021
Estimation of the Koopman Generator by Newton's Extrapolation Multiscale Modeling and Simulation, 19(2), pp. 758-774, 2021 Renata Sechi, Alexander Sikorski, Marcus Weber BibTeX
DOI
Objective priors in the empirical Bayes framework Scandinavian Journal of Statistics, 48(4), pp. 1212-1233, 2021 Ilja Klebanov, Alexander Sikorski, Christof Schütte, Susanna Röblitz BibTeX
DOI
The Augmented Jump Chain Advanced Theory and Simulations, 4(4), 2021 Alexander Sikorski, Marcus Weber, Christof Schütte BibTeX
arXiv
DOI
cmdtools 2021 Alexander Sikorski, Renata Sechi, Luzie Helfmann BibTeX
DOI
2018
Spectral Clustering for Non-Reversible Markov Chains Computational and Applied Mathematics, 37(5), pp. 6376-6391, 2018 (preprint available as ZIB-Report 18-48) Konstantin Fackeldey, Alexander Sikorski, Marcus Weber PDF (ZIB-Report)
BibTeX
DOI
2017
An Information-Theoretic Empirical Bayes Method and its Application to a Systems Biology Model Master's thesis, Freie Universität Berlin, Susanna Röblitz (Advisor), 2017 Alexander Sikorski PDF
BibTeX
URN
2016
Empirical Bayes Methods for Prior Estimation in Systems Medicine ZIB-Report 16-57 Ilja Klebanov, Alexander Sikorski, Christof Schütte, Susanna Röblitz PDF
BibTeX
URN
arXiv
Empirical Bayes Methods, Reference Priors, Cross Entropy and the EM Algorithm ZIB-Report 16-56 Ilja Klebanov, Alexander Sikorski, Christof Schütte, Susanna Röblitz PDF
BibTeX
URN
Prior estimation and Bayesian inference from large cohort data sets ZIB-Report 16-09 Ilja Klebanov, Alexander Sikorski, Christof Schütte, Susanna Röblitz PDF
PDF
BibTeX
URN
2015
PCCA+ and Its Application to Spatial Time Series Clustering Bachelor's thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2015 Alexander Sikorski PDF
BibTeX
URN