DOI
10.34229/KCA2522-9664.25.1.5
UDC 519.7
1 Educational and Research Institute for Applied System Analysis of the National Technical University of Ukraine
“Igor Sikorsky Kyiv Polytechnic Institute”, Kyiv, Ukraine
mzz@kpi.ua
|
2 Educational and Research Institute for Applied System Analysis of the National Technical University of Ukraine
“Igor Sikorsky Kyiv Polytechnic Institute”, Kyiv, Ukraine
kasyanov@i.ua
|
|
4 National Technical University of Ukraine “Igor Sikorsky Kyiv Polytechnic Institute”, Kyiv, Ukraine
vlad.novykov@gmail.com
|
AI METHODOLOGY FOR MODELING PROTEIN INTERACTIONS
IN BIOLOGICAL SYSTEMS
Abstract. This paper proposes a methodology for developing an artificial intelligence system for modeling protein interactions in biological systems based on reaction-diffusion equations with multivalued interaction functions. The primary goal of the research is to approximate the solutions of these equations using highly efficient computational methods, specifically physics-informed neural networks (PINN) and the deep learning Galerkin method (DLGM). The proposed system utilizes machine learning to model complex biological processes while accounting for real cellular conditions. The authors have developed and rigorously justified a computational algorithm that, on the current level of mathematical rigor, ensures the approximation of solutions to infinite-dimensional stochastic optimization problems and demonstrates superior efficiency compared to traditional methods. The high accuracy and speed of the obtained results enable extending this methodology to other types of partial differential equations, particularly for biological and medical applications.
Keywords: reaction-diffusion equation, multivariate interaction functions, machine learning, physical information neural network, approximation solution.
full text
REFERENCES
- 1. Singh A., Kundrotas P.J., Vakser I.A. Diffusion of proteins in crowded solutions studied by docking-based modeling. The Journal of Chemical Physics. 2024. Vol. 161. Article number 095101. https://doi.org/10.1063/5.0220545. .
- 2. Zgurovsky M.Z., Mel’nik V.S., Kasyanov P.O. Evolution inclusions and variation inequalities for Earth data processing I: Operator inclusions and variation inequalities for Earth data processing. AMMA. Vol. 24. Berlin; Heidelberg: Springer, 2010. XXX, 247 p. https://doi.org/ 10.1007/978-3-642-13837-9. .
- 3. Feinberg E.A., Kasyanov P.O., Royset J.O. Epi-convergence of expectation functions under varying measures and integrands. Journal of Convex Analysis. 2023. Vol. 30, N 3. P. 917–936. URL: https://www.heldermann.de/JCA/JCA30/JCA303/jca30043.htm. .
- 4. Zgurovsky M.Z., Kasyanov P.O. Qualitative and quantitative analysis of nonlinear systems. Sham: Springer, 2018. XXXIII, 240 p. https://doi.org/10.1007/978-3-319-59840-6. .
- 5. Zgurovsky M.Z., Kasyanov P.O., Kapustyan O.V., Valero J., Zadoianchuk N.V. Evolution inclusions and variation inequalities for Earth data processing III: Long-time behavior of evolution inclusions solutions in Earth data analysis. AMMA. Vol. 27. Berlin; Heidelberg: Springer, 2012. XLII, 330 p. https://doi.org/10.1007/978-3-642-28512-7. .
- 6. Jentzen A., Kuckuck B., von Wurstemberger P. Mathematical introduction to deep learning: Methods, implementations, and theory. arXiv:2310.20360v1 [cs.LG] 31 Oct. 2023. URL: https://doi. org/10.48550/arxiv.2310.20360. .
- 7. Sirignano J., Spiliopoulos K. DGM: A deep learning algorithm for solving partial differential equations. Journal of Computational Physics. 2018. Vol. 375. P. 1339–1364. https://doi.org/ 10.1016/j.jcp.2018.08.029. .
- 8. Sutton R.S., Barto A. Reinforcement learning: An introduction. Second edition. The MIT Press, 2018. 552 p. URL: https://mitpress.mit.edu/9780262039246/ .
- 9. Feinberg E.A., Kasyanov P.O., Zadoianchuk N.V. Average cost Markov decision processes with weakly continuous transition probabilities. Mathematics of Operations Research. 2012. Vol. 37, N 4. P. 559–674. URL: http://dx.doi.org/10.1287/moor.1120.0555. .
- 10. Feinberg E.A., Kasyanov P.O., Liang Y. Fatou’s lemma for weakly converging measures under the uniform integrability condition. Theory of Probability & Its Applications. 2020. Vol. 64, N 4. P. 615–630. https://doi.org/10.1137/S0040585X97T989738. .
- 11. Feinberg E.A., Kasyanov P.O., Zadoianchuk N.V. Berge’s theorem for noncompact image sets. Journal of Mathematical Analysis and Applications. 2013. Vol. 397, N 1. P. 255–259. https://doi.org/10.1016/j.jmaa.2012.07.051. .
- 12. Feinberg E.A., Kasyanov P.O. Continuity of minima: Local results. Set-Valued and Variational Analysis. 2015. Vol. 23, N 3. P. 485–499. URL: https://doi.org/10.1007/s11228-015-0318-7. .
- 13. Feinberg E.A., Kasyanov P.O., Zgurovsky M.Z. Uniform Fatou’s lemma. Journal of Mathematical Analysis and Applications. 2016. Vol. 444, Iss. 1. P. 550–567. https://doi.org/ 10.1016/j.jmaa.2016.06.044. .
- 14. Feinberg E.A., Kasyanov P.O., Zgurovsky M.Z. Continuity of equilibria for two-person zero-sum games with noncompact action sets and unbounded payoffs. Annals of Operations Research. 2022. Vol. 317, Iss. 2. P. 537–568. https://doi.org/10.1007/s10479-017-2677-y. .
- 15. Feinberg E.A., Ishizawa S., Kasyanov P.O., Kraemer D.N. Continuity of filters for discrete-time control problems defined by explicit equations. arXiv:2311.12184v1 [math.OC] 20 Nov 2023. https://doi.org/10.48550/arXiv.2311.12184. .
- 16. Kasyanov P.O., Kapustyan O.V., Levenchuk L.B., Novykov V.R. Machine learning method for approximate solutions for reaction-diffusion equations with multivalued interaction functions. Preprints, 2024. 2024072340. https://doi.org/10.20944/ preprints202407.2340.v1. .
- 17. Raissi M., Perdikaris P., Karniadakis G.E. Physics-informed neural networks: A deep learning framework for solving forward and inverse problems involving nonlinear partial differential equations. Journal of Computational physics. 2019. Vol. 378. P. 686–707. https://doi.org/ 10.1016/j.jcp.2018.10.045. .