title: Hierarchical cluster-based partial least squares regression (HC-PLSR) is an efficient tool for metamodelling of nonlinear dynamic models.
abstract: BACKGROUND
  Deterministic dynamic models of complex biological systems contain a large number of parameters and state variables, related through nonlinear differential equations with various types of feedback. A metamodel of such a dynamic model is a statistical approximation model that maps variation in parameters and initial conditions (inputs) to variation in features of the trajectories of the state variables (outputs) throughout the entire biologically relevant input space. A sufficiently accurate mapping can be exploited both instrumentally and epistemically. Multivariate regression methodology is a commonly used approach for emulating dynamic models. However, when the input-output relations are highly nonlinear or non-monotone, a standard linear regression approach is prone to give suboptimal results. We therefore hypothesised that a more accurate mapping can be obtained by locally linear or locally polynomial regression. We present here a new method for local regression modelling, Hierarchical Cluster-based PLS regression (HC-PLSR), where fuzzy C-means clustering is used to separate the data set into parts according to the structure of the response surface. We compare the metamodelling performance of HC-PLSR with polynomial partial least squares regression (PLSR) and ordinary least squares (OLS) regression on various systems: six different gene regulatory network models with various types of feedback, a deterministic mathematical model of the mammalian circadian clock and a model of the mouse ventricular myocyte function.
  
  
  RESULTS
  Our results indicate that multivariate regression is well suited for emulating dynamic models in systems biology. The hierarchical approach turned out to be superior to both polynomial PLSR and OLS regression in all three test cases. The advantage, in terms of explained variance and prediction accuracy, was largest in systems with highly nonlinear functional relationships and in systems with positive feedback loops.
  
  
  CONCLUSIONS
  HC-PLSR is a promising approach for metamodelling in systems biology, especially for highly nonlinear or non-monotone parameter to phenotype maps. The algorithm can be flexibly adjusted to suit the complexity of the dynamic model behaviour, inviting automation in the metamodelling of complex systems.
authors.affiliation: Centre for Integrative Genetics, Dept. of Mathematical Sciences and Technology, Norwegian University of Life Sciences, N-1432 Ås, Norway. kristin.tondel@umb.no
authors.forename: Kristin
authors.initials: K
authors.lastname: Tøndel
authors.forename: Ulf G
authors.initials: UG
authors.lastname: Indahl
authors.forename: Arne B
authors.initials: AB
authors.lastname: Gjuvsland
authors.forename: Jon Olav
authors.initials: JO
authors.lastname: Vik
authors.forename: Peter
authors.initials: P
authors.lastname: Hunter
authors.forename: Stig W
authors.initials: SW
authors.lastname: Omholt
authors.forename: Harald
authors.initials: H
authors.lastname: Martens
mesh_terms: D000465:Algorithms; D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D006352:Heart Ventricles / Q000378:metabolism; D006801:Humans; D016018:Least-Squares Analysis; D051379:Mice; D008962:Models, Theoretical; D015999:Multivariate Analysis; D032342:Muscle Cells / Q000166:cytology; D010641:Phenotype; D012044:Regression Analysis; D015203:Reproducibility of Results; D049490:Systems Biology / Q000379:methods