Research projects
This page aggregates results from some of my research projects:
- 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 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 (179).
Publications:
- Andrey Akinshin “Weighted quantile estimators” (2023) // arXiv. DOI: 10.48550/arXiv.2304.07265
- Andrey Akinshin “Finite-sample Rousseeuw-Croux scale estimators” (2022) // arXiv. DOI: 10.48550/arXiv.2209.12268
- Andrey Akinshin “Quantile absolute deviation” (2022) // arXiv. DOI: 10.48550/ARXIV.2208.13459
- 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
- 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
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 (8K+ GitHub stars, 15K+ dependent GitHub projects, 18M+ 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:
- Andrey Akinshin “Pro .NET Benchmarking” (2019) // Publisher: Apress. ISBN: 978-1-4842-4940-6. Pp. 662. DOI: 10.1007/978-1-4842-4941-3
- Andrey Akinshin “The hard world of microbenchmarking” (2017) // Logeek Magazine. Vol. 3. Pp. 10–15.
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:
- 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
- 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
- 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
- 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
- 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
- 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
- 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.
- 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
- 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.
- 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
- 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.
- 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.
- 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
- 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
- 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
- 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.
- 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.
- 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
- 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.
- 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.
- 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.
- 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
- 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.
- 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.
- 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.
Digital signal processing
I was working on this project during my postdoctoral research fellowship at the Weizmann Institute of Science.
Publications:
- 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
- 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
- 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