A Tutorial on Sobol’ Global Sensitivity Analysis Applied to Biological Models

Michel Tosin (1) , Adriano M A Côrtes (2) , Americo Cunha Jr (1)

1 UERJ - Universidade do Estado do Rio de Janeiro [Brasil] = Rio de Janeiro State University [Brazil] = Université d'État de Rio de Janeiro [Brésil]
2 UFRJ - Universidade Federal do Rio de Janeiro [Brasil] = Federal University of Rio de Janeiro [Brazil] = Université fédérale de Rio de Janeiro [Brésil]

Nowadays, in addition to traditional qualitative methods, quantitative techniques are also a standard tool to describe biological systems behavior. An example is the broad class of mathematical models, based on differential equations, used in ecology, biochemical kinetics, epidemiology, gene regulatory networks, etc. Independent of their simplicity or complexity, all these models have in common (generally unknown a priori) parameters that need to be identified from observations (data) of the real system, usually available on the literature, obtained by specific assays or surveyed by public health offices. Before using this data to calibrate the models, a good practice is to judge the most influential parameters. That can be done with aid of the Sobol’ indices, a variance-based statistical technique for global sensitivity analysis, which measures the individual importance of each parameter, as well as their joint-effect, on the model output (a.k.a. quantity of interest). These variance-based indexes may be computed using Monte Carlo simulation but, depending on the model, this task can be very costly. An alternative approach for this scenario is the use of surrogate models to speed-up the calculations. Using simple biological models, from different areas, we develop a tutorial that illustrates how practitioners can use Sobol’ indices to quantify, in a probabilistic manner, the relevance of the parameters of their models. This tutorial describes a very robust framework to compute Sobol’ indices employing a polynomial chaos surrogate model constructed with the UQLab package.

Domaines: Bio-informatique [q-bio.QM]; Systèmes dynamiques [math.DS]; Science non linéaire [physics]

Michel Tosin, Adriano M A Côrtes, Americo Cunha Jr. A Tutorial on Sobol’ Global Sensitivity Analysis Applied to Biological Models. da Silva F.A.B., Carels N., Trindade dos Santos M., Lopes F.J.P. Networks in Systems Biology: Applications for Disease Modeling, Springer, Cham, 2020, Mechanisms and Machine Science, ⟨10.1007/978-3-030-51862-2_6⟩. ⟨hal-02967410⟩