Fig. 2

Validation of inference method on simulated data. This figure presents results of our parameter inference method when simulated data are used as input instead of experimental data. a–j Inferred posterior probability densities for chromatin compaction C and persistence length P for data generated by a model with parameters Π₀ = (P ₀, C ₀, W ₀, L ₀) = (41 nm, 50 bp/nm, 45 nm, 300 nm). The blue and red contour lines enclose regions corresponding to 68% and 95% of the probability mass, respectively. The red diamond indicates the true parameter values: (P ₀, C ₀) = (41 nm, 50 bp/nm). The green dot indicates the maximum a posteriori (MAP) estimate, i.e. the parameter values \( \left(\widehat{P},\widehat{C}\right) \) for which the estimated posterior probability density is maximum. Panels a–e were obtained from simulations with low levels of added noise, panels f–j from simulations with high noise (Additional file 1: Supplementary Methods). Panel pairs (a, f), (b, g), (c, h), (d, i), and (e, j) each correspond to a different subset of simulated observables. Panels a, f: probability densities obtained from distances between the pairs of loci corresponding to the experimental dataset O6 (see Table 2 and Additional file 3). Panels b, g: the same, for distances between pairs of telomeres (observable O1). Panels c, h: the same, for all locus positioning data, corresponding to observables O1–O7 combined. Panels d, i: the same, for contact frequencies between chromosomes (observables O8 or O9). Panels e, j: the same, for all distance and contact data combined (all observables, O1–O9). k, l: Errors of MAP estimates relative to the simulated ground truth for chromatin persistence length P (k) and compaction C (l). The root mean square (RMS) error is plotted for three different levels of noise and for five distinct simulated models (corresponding to five different values of the parameters), as indicated in the legend