Alexander Andreychenko

Alexander Andreychenko

Former Member

PhD Student

Modeling and Simulation Group, Saarland University

Universität des Saarlandes

Room 326

66123 Saarbrücken

Germany

About Me

I am a PhD student at the MOSI group since September 2011.

Publications

  • A. Andreychenko, P. Crouzen, V. Wolf: On-the-fly Uniformization of Time-Inhomogeneous Infinite Markov Population Models QAPL'11. @arXiv, @rg
  • A. Andreychenko, L. Mikeev, D. Spieler, V. Wolf: Parameter Identification for Markov Models of Biochemical Reactions CAV'11
  • A. Andreychenko, L. Mikeev, D. Spieler, V. Wolf: Approximate Maximum Likelyhood Estimation for Stochastic Chemical Kinetics, WCSB_‘11_ (large file!)
  • A. Andreychenko, L. Mikeev, D. Spieler, V. Wolf: Approximate maximum likelihood estimation for stochastic chemical kinetics Journal on Bioinformatics and Systems Biology, Springer, 2012. Springer 2012
  • A. Andreychenko, T. Krüger, D. Spieler: Analyzing oscillatory behavior with formal methods ROCKS Autumn School Proceedings, LNCS, 2014.
  • A. Andreychenko, L. Mikeev, V. Wolf: Model Reconstruction for Moment-based Stochastic Chemical Kinetics ACM Transactions on Modeling and Computer Simulation (ACM) (TOMACS-2014-0026.R1), 2014.
  • A. Andreychenko, L. Mikeev, V. Wolf: Reconstruction of Multimodal Distributions for Hybrid Moment-based Chemical Kinetics Journal of Coupled Systems and Multiscale Dynamics (JCSMD) (arXiv), 2015
  • A. Andreychenko, M. Magnin, K. Inoue Modeling of Resilience Properties in Oscillatory Biological Systems using Parametric Time Petri Nets CMSB, 2015.
  • A. Andreychenko, L. Bortolussi, R. Grima, P. Thomas and V. Wolf: Distribution approximations for the chemical master equation: comparison of the method of moments and the system size expansion BIOMS Workshop Modeling Cellular Systems (arXiv), 2016
  • A. Andreychenko, M. Magnin, K. Inoue Analyzing resilience properties in oscillatory biological systems using parametric model checking Biosystems, 2016
  • A. Andreychenko, W. Sandmann, V. Wolf: Approximate adaptive uniformization of continuous-time Markov chains Applied Mathematical Modelling, 2018

Other

Reviews for: TACAS 2011, TACAS 2013, WSC 2012, YRCONCUR 2012, QEST 2012, MMB & DFT 2012, QEST 2010, CMSB 2011, CMSB 2012, TMS DEVS 2013, TOMCAS 2014, QEST 2015, FORMATS 2015, HSCC 2016, TACAS 2016

Interests

  • Efficient methods of solving Chemical Master Equation (CME)
  • Moment closure techniques (standard, conditional/hybrid)
  • Sensitivity analysis and parameter estimation of biochemical systems
  • Uniformization for Markov chains (time-homogeneous and inhomogeneous)
  • Maximum entropy method for reconstruction probability distributions

Publications (2)

2018

1 paper

Approximate adaptive uniformization of continuous-time Markov chains

Alexander Andreychenko, Werner Sandmann and Verena Wolf

2018 — Applied Mathematical Modelling

@article{andreychenkoApproximateAdaptiveUniformizationOf2018,
 author = {Alexander Andreychenko and Werner Sandmann and Verena Wolf},
 doi = {10.1016/j.apm.2018.05.009},
 journal = {Applied Mathematical Modelling},
 pages = {561-576},
 publisher = {ScienceDirect},
 title = {Approximate adaptive uniformization of continuous-time Markov chains},
 url = {https://www.sciencedirect.com/science/article/pii/S0307904X18302191},
 volume = {61},
 year = {2018}
}
DOI URL

2015

1 paper

Model Reconstruction for Moment-Based Stochastic Chemical Kinetics

Alexander Andreychenko, Linar Mikeev and Verena Wolf

2015 — ACM Transactions on Modeling and Computer Simulation (TOMACS)

@article{andreychenkoModelReconstructionForMomentBased2015,
 author = {Alexander Andreychenko and Linar Mikeev and Verena Wolf},
 doi = {10.1145/2699712},
 journal = {ACM Transactions on Modeling and Computer Simulation (TOMACS)},
 number = {2},
 pages = {1-19},
 publisher = {Association for Computing Machinery},
 title = {Model Reconstruction for Moment-Based Stochastic Chemical Kinetics},
 url = {https://dl.acm.org/doi/10.1145/2699712},
 volume = {25},
 year = {2015}
}
DOI URL

Teaching (9)

  • Probabilistic Methods and Data Analysis

    Assistant, in Winter 2015/16
    Lecture at Saarland University

  • Stochastic Dynamics in Systems Biology

    Assistant, in Winter 2013/14
    Lecture at Saarland University

  • Modeling and Simulation

    Assistant, in Winter 2012/13
    Lecture at Saarland University

  • Computational Systems Biology

    Assistant, in Summer 2012
    Lecture at Saarland University

  • Quantitative Model Checking (QMC)

    Assistant, in Summer 2012
    Lecture at Saarland University

  • Stochastic Simulation Techniques

    Assistant, in Winter 2011/12
    Seminar at Saarland University

  • Data Networks

    Assistant for a Small Part of the Course, in Summer 2011
    Lecture at Saarland University

  • Selected Stochastic Models

    Assistant, in Winter 2010/11
    Seminar at Saarland University

  • Modeling and Simulation

    Assistant, in Summer 2010
    Lecture at Saarland University

Supervised Students (2)

Assisting (as a second assistant) the Master thesis of Maxat Aipanov. Assisting the Master thesis of Miriam Bah (completed in September 2015).

  • Miriam Bah

    Master's Thesis, 2015

  • Maxat Aipanov

    Master's Thesis