Electronic Resource
Shaping and Dilating the Fitness Landscape for Parameter Estimation in Stochastic Biochemical Models
| العنوان: | Shaping and Dilating the Fitness Landscape for Parameter Estimation in Stochastic Biochemical Models |
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| المؤلفون: | Nobile, M, Papetti, D, Spolaor, S, Cazzaniga, P, Manzoni, L, Nobile M. S., Papetti D. M., Spolaor S., Cazzaniga P., Manzoni L. |
| بيانات النشر: | MDPI AG country:CH 2022 |
| نوع الوثيقة: | Electronic Resource |
| مستخلص: | The parameter estimation (PE) of biochemical reactions is one of the most challenging tasks in systems biology given the pivotal role of these kinetic constants in driving the behavior of biochemical systems. PE is a non-convex, multi-modal, and non-separable optimization problem with an unknown fitness landscape; moreover, the quantities of the biochemical species appearing in the system can be low, making biological noise a non-negligible phenomenon and mandating the use of stochastic simulation. Finally, the values of the kinetic parameters typically follow a log-uniform distribution; thus, the optimal solutions are situated in the lowest orders of magnitude of the search space. In this work, we further elaborate on a novel approach to address the PE problem based on a combination of adaptive swarm intelligence and dilation functions (DFs). DFs require prior knowledge of the characteristics of the fitness landscape; therefore, we leverage an alternative solution to evolve optimal DFs. On top of this approach, we introduce surrogate Fourier modeling to simplify the PE, by producing a smoother version of the fitness landscape that excludes the high frequency components of the fitness function. Our results show that the PE exploiting evolved DFs has a performance comparable with that of the PE run with a custom DF. Moreover, surrogate Fourier modeling allows for improving the convergence speed. Finally, we discuss some open problems related to the scalability of our methodology. |
| مصطلحات الفهرس: | biochemical model, dilation function, fitness landscape manipulation, Fourier surrogate modeling, parameter estimation, stochastic simulation, info:eu-repo/semantics/article |
| URL: | info:eu-repo/semantics/altIdentifier/wos/WOS:000823666700001 volume:12 issue:13 journal:APPLIED SCIENCES |
| الاتاحة: | Open access content. Open access content |
| ملاحظة: | ELETTRONICO English |
| Other Numbers: | ITBAO oai:boa.unimib.it:10281/391251 10.3390/app12136671 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85133698544 1343245218 |
| المصدر المساهم: | BICOCCA OPEN ARCH From OAIster®, provided by the OCLC Cooperative. |
| رقم الانضمام: | edsoai.on1343245218 |
| قاعدة البيانات: | OAIster |
| الوصف غير متاح. |