CGNM
Cluster Gauss-Newton Method
Find multiple solutions of a nonlinear least squares problem. Cluster Gauss-Newton method does not assume uniqueness of the solution of the nonlinear least squares problem and compute multiple minimizers. Please cite the following paper when this software is used in your research: Aoki et al. (2020)
CGNM: Cluster Gauss-Newton Method
An R package to find multiple approximate minimizers of a nonlinear least squares problem
argmin_x || f(x) - y* ||
without assuming the minimizer is unique. In the context of model fitting,
f is the model, x is the parameter to estimate, and y* is the observed
data. Because CGNM searches from a range of initial iterates rather than a
single starting point, and returns many approximate minimizers at once, it
can also reveal when a model's parameters are not practically identifiable
(the returned minimizers won't converge to a single point).
See the papers below for the algorithm and comparisons with conventional multi-start optimization:
- Aoki, Y., Hayami, K., Toshimoto, K., & Sugiyama, Y. (2020). Cluster Gauss–Newton method. Optimization and Engineering, 1-31. doi:10.1007/s11081-020-09571-2
- Aoki, Y. & Sugiyama, Y. (2024). Cluster Gauss-Newton method for a quick approximation of profile likelihood: With application to physiologically-based pharmacokinetic models. CPT Pharmacometrics Syst Pharmacol. 13(1):54-67. doi:10.1002/psp4.13055
If you use CGNM in your research, please cite the relevant paper(s) above.
When to use CGNM
- You want to fit a relatively complex parameterized model to data but are unsure of a good initial guess — CGNM takes an initial range instead of a point.
- You want to know whether the fit is practically identifiable (one best-fit parameter set, or many) — CGNM returns multiple approximate minimizers so non-identifiability shows up directly.
- Your model is a black box (not necessarily continuous or differentiable in its parameters) — CGNM makes no assumptions about the model's internal form.
When not to use CGNM
- You already know roughly where the best-fit parameter is and just need one
answer — plain
nls()will be faster. - The model is cheap to evaluate and computational cost isn't a concern —
CGNM's main advantage is reducing the number of model evaluations needed
compared to repeated multi-start
nls().
Installation
# from a local checkout of this repository
install.packages("path/to/CGNM", repos = NULL, type = "source")
# or, from within the checked-out directory
# R CMD INSTALL .
Quick example
library(CGNM)
# flip-flop kinetics: a model known to have two distinct best-fit solutions
model_function <- function(x) {
observation_time <- c(0.1, 0.2, 0.4, 0.6, 1, 2, 3, 6, 12)
Dose <- 1000; F <- 1
ka <- x[1]; V1 <- x[2]; CL_2 <- x[3]
t <- observation_time
Cp <- ka * F * Dose / (V1 * (ka - CL_2 / V1)) * (exp(-CL_2 / V1 * t) - exp(-ka * t))
log10(Cp)
}
observation <- log10(c(4.91, 8.65, 12.4, 18.7, 24.3, 24.5, 18.4, 4.66, 0.238))
CGNM_result <- Cluster_Gauss_Newton_method(
nonlinearFunction = model_function,
targetVector = observation,
initial_lowerRange = rep(0.01, 3),
initial_upperRange = rep(100, 3),
saveLog = FALSE
)
acceptedApproximateMinimizers(CGNM_result)
Then inspect the fit visually:
library(ggplot2)
plot_Rank_SSR(CGNM_result)
plot_goodnessOfFit(CGNM_result, plotType = 1,
independentVariableVector = c(0.1,0.2,0.4,0.6,1,2,3,6,12),
plotRank = seq(1, 50))
For the full workflow — fitting, residual-resampling bootstrap, accepted
minimizers, summary tables, and profile likelihood — see
vignette("CGNM-vignette", package = "CGNM") or
vignettes/CGNM-vignette.Rmd.
Documentation
?CGNM— package overview and workflow map.?Cluster_Gauss_Newton_method— the main fitting function.
By default, Cluster_Gauss_Newton_method() and the bootstrap/EBE variants
return a plain list. Pass outputS4 = TRUE to get a CGNM_result S4 object
instead (see ?"CGNM_result-class") — every field is still reachable via
$/[[ exactly as on the list, so this is a drop-in, fully backward-
compatible opt-in.
License
MIT. See LICENSE.