Universally sloppy parameter sensitivities in systems biology models

• Published in: PLoS computational biology 2007-10, Vol.3 (10), p.1871-1878
• Main Authors: Gutenkunst, Ryan N, Waterfall, Joshua J, Casey, Fergal P, Brown, Kevin S, Myers, Christopher R, Sethna, James P
• Format: Article
• Language: English
• Subjects: Algorithms; Analysis; Biological models; Biology; Computational Biology; Computer Simulation - trends; Confidence intervals; Experiments; Half-Life; Mathematics; Meta-Analysis as Topic; Metabolic Networks and Pathways; Models, Biological; Models, Statistical; Monte Carlo Method; None; Nonlinear Dynamics; Probability; Sensitivity and Specificity; Studies; Systems Biology - methods
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.0030189

Quantitative computational models play an increasingly important role in modern biology. Such models typically involve many free parameters, and assigning their values is often a substantial obstacle to model development. Directly measuring in vivo biochemical parameters is difficult, and collectively fitting them to other experimental data often yields large parameter uncertainties. Nevertheless, in earlier work we showed in a growth-factor-signaling model that collective fitting could yield well-constrained predictions, even when it left individual parameters very poorly constrained. We also showed that the model had a "sloppy" spectrum of parameter sensitivities, with eigenvalues roughly evenly distributed over many decades. Here we use a collection of models from the literature to test whether such sloppy spectra are common in systems biology. Strikingly, we find that every model we examine has a sloppy spectrum of sensitivities. We also test several consequences of this sloppiness for building predictive models. In particular, sloppiness suggests that collective fits to even large amounts of ideal time-series data will often leave many parameters poorly constrained. Tests over our model collection are consistent with this suggestion. This difficulty with collective fits may seem to argue for direct parameter measurements, but sloppiness also implies that such measurements must be formidably precise and complete to usefully constrain many model predictions. We confirm this implication in our growth-factor-signaling model. Our results suggest that sloppy sensitivity spectra are universal in systems biology models. The prevalence of sloppiness highlights the power of collective fits and suggests that modelers should focus on predictions rather than on parameters.