A comparison of methods for quantifying prediction uncertainty in systems biology

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Villaverde, Alejandro F., et al. "A comparison of methods for quantifying prediction uncertainty in systems biology." IFAC-PapersOnLine 52.26 (2019): 45-51.

Permanent link to the paper


Three methods for quantifying prediction uncertainty in ODE models are assessed. Here, prediction uncertainty does not refer to estimated parameters, but to the uncertatinty of state trajectories. The three methods are: Fisher Information Matrix (FIM), Prediction Posetrior (PP), Ensemble Consensus (ENS).

Study outcomes

Outcome O1

For a small, fully-observed ODE model (α-pinene), all three methods yield nearly same results consistent with the known true trajectories. For a larger, only-partially observed ODE model (JAK2/STAT5), PP and ENS yield better accuracy than FIM. However, even for PP and ENS, confidence levels do not cover the truth.

Outcome O2

The computational cost of the three models is differing, especially for large problems: FIM (small), ENS (intermediate), PP (high)

Study design and evidence level

General aspects

Synthetic data is generated for two examplary ODE models given a true parameter set. One model is smaller (5 parameter, 5 states, 5 observables) and used as sanity check, the other is larger (27 parameter, 25 states, 20 observables). The sample correlation coefficient is used to quantify agreement between predicted and true state trajectories. For FIM and ENS the MATLAB version of the MEIGO toolbox was used for parameter estimation, whereas for PP it was used MATLAB parameter estimation toolbox PESTO.

Design for Outcome O1

Sample correlation coefficient is compared for the three different methods for the two different models, respectively.

Design for Outcome O2

Computation time is compared for the different models.

Further comments and aspects


Egea et al.