A two-phase approach to re-calibrating expensive computer simulation for sex-specific colorectal neoplasia development modeling

BMC Med Inform Decis Mak. 2022 Sep 18;22(1):244. doi: 10.1186/s12911-022-01991-7.


Background: Medical evidence from more recent observational studies may significantly alter our understanding of disease incidence and progression, and would require recalibration of existing computational and predictive disease models. However, it is often challenging to perform recalibration when there are a large number of model parameters to be estimated. Moreover, comparing the fitting performances of candidate parameter designs can be difficult due to significant variation in simulated outcomes under limited computational budget and long runtime, even for one simulation replication.

Methods: We developed a two-phase recalibration procedure. As a proof-of-the-concept study, we verified the procedure in the context of sex-specific colorectal neoplasia development. We considered two individual-based state-transition stochastic simulation models, estimating model parameters that govern colorectal adenoma occurrence and its growth through three preclinical states: non-advanced precancerous polyp, advanced precancerous polyp, and cancerous polyp. For the calibration, we used a weighted-sum-squared error between three prevalence values reported in the literature and the corresponding simulation outcomes. In phase 1 of the calibration procedure, we first extracted the baseline parameter design from relevant studies on the same model. We then performed sampling-based searches within a proper range around the baseline design to identify the initial set of good candidate designs. In phase 2, we performed local search (e.g., the Nelder-Mead algorithm), starting from the candidate designs identified at the end of phase 1. Further, we investigated the efficiency of exploring dimensions of the parameter space sequentially based on our prior knowledge of the system dynamics.

Results: The efficiency of our two-phase re-calibration procedure was first investigated with CMOST, a relatively inexpensive computational model. It was then further verified with the V/NCS model, which is much more expensive. Overall, our two-phase procedure showed a better goodness-of-fit than the straightforward employment of the Nelder-Mead algorithm, when only a limited number of simulation replications were allowed. In addition, in phase 2, performing local search along parameter space dimensions sequentially was more efficient than performing the search over all dimensions concurrently.

Conclusion: The proposed two-phase re-calibration procedure is efficient at estimating parameters of computationally expensive stochastic dynamic disease models.

Keywords: Colorectal neoplasia; Computationally expensive simulator; Model recalibration; State-transition model.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Calibration
  • Colorectal Neoplasms*
  • Computer Simulation
  • Humans
  • Precancerous Conditions*