My Research Projects

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Statistical performance analysis Software benchmarking Mathematical models of gene networks Digital signal processing

Statistical performance analysis

This project aims to develop advanced statistical procedures for the automatic analysis of software performance measurements. This included various location estimators, dispersion estimators, quantile estimators, effect size estimators, density estimators, change point detectors, outlier detectors, and multimodality detectors. The goal is to provide a set of non-parametric, robust, and efficient approaches that are applicable to software performance distributions.

I regularly share my preliminary research notes in the form of blog posts (178).

Publications:

  1. Andrey Akinshin “Quantile-respectful density estimation based on the Harrell-Davis quantile estimator” (2024) // arXiv. DOI: 10.48550/arXiv.2404.03835
    EN Article Preprint DOI arXiv PDF GitHub
  2. Andrey Akinshin “Weighted quantile estimators” (2023) // arXiv. DOI: 10.48550/arXiv.2304.07265
    EN Article Preprint DOI arXiv PDF GitHub
  3. Andrey Akinshin “Finite-sample Rousseeuw-Croux scale estimators” (2022) // arXiv. DOI: 10.48550/arXiv.2209.12268
    EN Article Preprint DOI arXiv PDF GitHub
  4. Andrey Akinshin “Quantile absolute deviation” (2022) // arXiv. DOI: 10.48550/ARXIV.2208.13459
    EN Article Preprint DOI arXiv PDF GitHub
  5. Andrey Akinshin “Finite-sample bias-correction factors for the median absolute deviation based on the Harrell-Davis quantile estimator and its trimmed modification” (2022) // arXiv. DOI: 10.48550/ARXIV.2207.12005
    EN Article Preprint DOI arXiv PDF GitHub
  6. Andrey Akinshin “Trimmed Harrell-Davis quantile estimator based on the highest density interval of the given width” (2022) // Communications in Statistics - Simulation and Computation. Publisher: Taylor & Francis. Pp. 1-11. DOI: 10.1080/03610918.2022.2050396
    EN Article Web of Science Scopus DOI Link arXiv PDF GitHub

Software benchmarking

This project aims to provide a set of reliable tools and approaches for software benchmarking.

Since 2013, I have been working on developing BenchmarkDotNet (≈10K GitHub stars, ≈20K dependent GitHub projects, 26M+ NuGet downloads). This .NET library helps to transform methods into benchmarks, track their performance, and share reproducible measurement experiments. In the context of the statistical performance analysis project, I’m working on the next-generation statistical engine for performance measurement analysis.

I also wrote a book Pro .NET Benchmarking about good practices of performance measurements. This book mostly covers general benchmarking practices, performance measurement analysis approaches, and environmental factors that can affect obtained measurements. It also contains dozens of case studies that demonstrate common benchmarking pitfalls and explain how to avoid them.

Publications:

  1. Andrey Akinshin “Pro .NET Benchmarking” (2019) // Publisher: Apress. ISBN: 978-1-4842-4940-6. Pp. 662. DOI: 10.1007/978-1-4842-4941-3
    EN Book Springer DOI Springer Apress
  2. Andrey Akinshin “The hard world of microbenchmarking” (2017) // Logeek Magazine. Vol. 3. Pp. 10–15.
    EN Article PDF

Mathematical models of gene networks

This project aims to describe the mathematical model of various gene networks: build systems of differential equations that simulate biological systems; analyze corresponding dynamical systems; find stationary points, limit cycles, and bifurcations; develop software for numerical simulations. The latest work is dedicated to the central regulatory circuit of the morphogenesis system of D. Melanogaster.

I was working on this project with fellows from Sobolev Institute of Mathematics SB RAS and Institute of Cytology and Genetics SB RAS. It was also the primary research topic of my PhD thesis “Mathematical and numerical modeling of gene network artificial regulatory circuits.”

Selected publications:

  1. V. P. Golubyatnikov, A. A. Akinshin, N. B. Ayupova, L. S. Minushkina “Stratifications and foliations in phase portraits of gene network models” (2023) // Vavilov Journal of Genetics and Breeding. Publisher: Institute of Cytology and Genetics, SB RAS. Vol. 26. No 8. Pp. 758–764. DOI: 10.18699/vjgb-22-91
    EN Article DOI
  2. A. A. Akinshin, N. B. Ayupova, V. P. Golubyatnikov, N. E. Kirillova, O. A. Podkolodnaya, N. L. Podkolodnyy “On a Numerical Model of a Circadian Oscillator” (2022) // Numerical Analysis and Applications. Vol. 15. No 3. Pp. 187-196. DOI: 10.1134/S1995423922030016
    EN Article Web of Science Springer Scopus DOI Link
  3. V Golubyatnikov, A Akinshin, N Ayupova, N Kirillova, N Podkolodnyy, O Podkolodnaya “Mathematical and numerical modelling of the circadian oscillator” (2022) // Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022). Pp. 1096–1096. DOI: 10.18699/SBB-2022-657
    EN Inproceedings DOI
  4. T.A. Bukharina, A.A. Akinshin, V.P. Golubyatnikov, D.P. Furman “A Model of one central regulatory circuit” (2020) // The Twelfth International Multiconference 'Bioinformatics of genome regulation and structure/systems biology (BGRS/SB-2020)'. Publisher: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk State University. Pp. 143–144. DOI: 10.18699/BGRS/SB-2020-090
    EN Inproceedings DOI PDF
  5. T. A. Bukharina, A. A. Akinshin, V. P. Golubyatnikov, D. P. Furman “Mathematical and Numerical Models of the Central Regulatory Circuit of the Morphogenesis System of Drosophila” (2020) // Journal of Applied and Industrial Mathematics. Vol. 14. No 2. Pp. 249-255. DOI: 10.1134/S1990478920020040
    EN Article Springer Scopus DOI Link Springer
  6. A.A. Akinshin, V P Golubyatnikov, M.V. Kazantsev “On discrete structures in phase portraits of some non-linear dynamical systems” (2016) // Siberian Electronic Mathematical Reports. Vol. 13. Pp. A.23–A.24. DOI: 10.17377/semi.2016.13.020
    EN Inproceedings DOI PDF
  7. A.A. Akinshin, M.V. Kazantsev “State transition diagrams in hypothetical models of cyclic gene networks functioning” (2015) // 5th International Young Scientists School “System Biology and Bioinformatics”. Novosibirsk. Pp. 1.
    EN Inproceedings Conference site
  8. A A Akinshin, T A Bukharina, D P Furman, V P Golubyatnikov “A model of one biological 2-cells complex” (2014) // Geometry days in Novosibirsk - 2014: Abstracts of the International Conference. Novosibirsk. ISBN: 978-5-86134-145-5. Pp. 85–86.
    EN Inproceedings
  9. A A Akinshin, T A Bukharina, D P Furman, V P Golubyatnikov “An Extended Model of D. Melanogaster Machrochaete Morphogenesis Gene Network” (2014) // International Conference «Mathematical Modeling and High Performance Computing in Bioinformatics, Biomedicine and Biotechnology». Pp. 10.
    EN Inproceedings Conference site
  10. A A Akinshin, T A Bukharina, D P Furman, V P Golubyatnikov “Modeling of Two-Cells Complex in Morphogenesis of D. Melanogaster Mechanoreceptors” (2014) // International Conference «Mathematical Modeling and High Performance Computing in Bioinformatics, Biomedicine and Biotechnology». Pp. 11.
    EN Inproceedings
  11. A A Akinshin, V P Golubyatnikov, V A Likhoshvai “Symmetry in gene network models” (2014) // The 12th Bioinformatics Research and Education Workshop. Bielefeld, Germany. Center for Biotechnology — CeBiTec. Pp. 1–5.
    EN Inproceedings Conference site
  12. A A Akinshin, T A Bukharina, D P Furman, V P Golubyatnikov “Mathematical modeling of interaction of two cells in proneural cluster of D.mealnogaster (In Russian)” (2014) // Vestnik NSU [NSU Herald]. Novosibirsk. Vol. 14. No 4. Pp. 3-10.
    RU Article MathNet
  13. A A Akinshin, V P Golubyatnikov “Oscillating trajectories in some nonlinear dynamical systems” (2013) // International Conference «Differential Equations. Function Spaces. Approximation Theory». Novosibirsk. IM SB RAS. Pp. 311.
    EN Inproceedings
  14. A A Akinshin “Analysis of phase portraits in some gene networks models” (2013) // 5th International Young Scientists School “System Biology and Bioinformatics”. Pp. 27.
    EN Inproceedings
  15. A A Akinshin “Numerical analysis of gene networks models” (2013) // 8th FEBS Congress, Saint Petersburg, Russia, July 6-11, 2013. Vol. 280. Pp. 547. DOI: 10.1111/febs.12396
    EN Inproceedings Web of Science DOI Web of Science Publons
  16. A A Akinshin, V P Golubyatnikov, V A Likhoshvai “Mathematical and computational models of gene networks functioning” (2013) // The 11th Bioinformatics Research and Education Workshop. Berlin, Germany. Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics and IMPRS-CBSC.
    EN Inproceedings Conference site
  17. A A Akinshin “Andronov-Hopf bifurcation for some nonlinear delay equations (In Russian)” (2013) // Sibirskii Zhurnal Industrial'noi Matematiki [Siberian Journal of Industrial Mathematics]. Novosibirsk. Vol. XVI. No 55. Pp. 3–15.
    RU Article RSCI MathNet
  18. A A Akinshin, V P Golubyatnikov, I V Golubyatnikov “On some multidimensional models of gene network functioning” (2013) // Journal of Applied and Industrial Mathematics. Publisher: Springer US. Vol. 7. No 3. Pp. 296–301. DOI: 10.1134/S1990478913030022
    EN Article Springer Scopus DOI RSCI Springer
  19. A A Akinshin, V P Golubyatnikov “Non-uniqueness of cycles in gene networks models” (2012) // The eighth international conference on bioinformatics of genome regulation and structure / systems biology. ISBN: 978-5-91291-011. Pp. 28.
    EN Inproceedings PDF
  20. A A Akinshin, V P Golubyatnikov, Yu A Gaidov, I V Golubyatnikov “Unstable cycles in gene networks models” (2012) // The eighth international conference on bioinformatics of genome regulation and structure / systems biology. ISBN: 978-5-91291-011. Pp. 29.
    EN Inproceedings PDF
  21. A A Akinshin, V P Golubyatnikov “On Nonuniqueness of Cycles in Dissipative Dynamical Systems of Chemical Kinetics” (2012) // VI-th international conference Solitons, Collapses and Turbulence: Achievements, Developments and Perspectives.. Pp. 71–72.
    EN Inproceedings PDF
  22. A A Akinshin “Computer analysis of phase portraits in gene networks models” (2012) // Abstracts of Young scientist's school “Bioinformatics ans systems biology”. Pp. 13.
    EN Inproceedings
  23. A A Akinshin “Research of discrete structures in some cyclic dynamical systems (In Russian)” (2012) // Polzunovskiy Vestnik [Polzunov Herald]. Barnaul. Vol. 4. Pp. 214–218.
    RU Article PDF RSCI
  24. A A Akinshin, V P Golubyatnikov “Geometric characteristics of cycles in some symmetric dynamical systems (In Russian)” (2012) // Vestnik NSU [NSU Herald]. Series “Mathematics, mechanics, and informatics'”. Novosibirsk. Vol. 12. No 2. Pp. 3–12.
    RU Article RSCI MathNet
  25. A A Akinshin, V P Golubyatnikov, I V Golubyatnikov “Mathematical and numerical modeling of gene network functioning” (2011) // International Conference “Modern Problems of Mathematics, Informatics and Bioinformatics”, devoted to the 100th anniversary of professor Alexei A. Lyapunov. Novosibirsk. ISBN: 978-5-905569-03-6. Pp. 81.
    EN Inproceedings Conference site PDF

Digital signal processing

I was working on this project during my postdoctoral research fellowship at the Weizmann Institute of Science.

Publications:

  1. Andrey Akinshin, Gil Goldman, Yosef Yomdin “Geometry of error amplification in solving the Prony system with near-colliding nodes” (2021) // Mathematics of Computation. Vol. 90. No 327. Pp. 267–302. DOI: 10.1090/mcom/3571
    EN Article Web of Science Scopus DOI Publons arXiv PDF
  2. Andrey Akinshin, Gil Goldman, Vladimir Golubyatnikov, Yosef Yomdin “Accuracy of reconstruction of spike-trains with two near-colliding nodes” (2017) // 7th International Conference on Complex Analysis and Dynamical Systems (CA&DS VII). Vol. 699. Pp. 1–17. DOI: 10.1090/conm/699/14078
    EN Inproceedings Web of Science Scopus DOI Publons arXiv PDF
  3. A Akinshin, D Batenkov, Y Yomdin “Accuracy of spike-train Fourier reconstruction for colliding nodes” (2015) // Sampling Theory and Applications (SampTA), 2015 International Conference on. Publisher: IEEE. Washington, DC. ISBN: 978-1-4673-7353-1. No 264. Pp. 617–621. DOI: 10.1109/SAMPTA.2015.7148965
    EN Inproceedings Web of Science Scopus DOI IEEE Publons arXiv PDF