Increasing certainty in systems biology models using Bayesian multimodel inference

Nathaniel Linden-Santangeli, Jin Zhang, Boris Kramer () and Padmini Rangamani ()
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Nathaniel Linden-Santangeli: University of California San Diego
Jin Zhang: University of California San Diego
Boris Kramer: University of California San Diego
Padmini Rangamani: University of California San Diego

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: Abstract Mathematical models are indispensable for studying the architecture and behavior of intracellular signaling networks. It is common to develop models using phenomenological approximations due to the difficulty of fully observing the intermediate steps in intracellular signaling pathways. Thus, multiple models can be built to represent the same pathway. This opens up challenges for model selection and decreases certainty in predictions. Here, we investigate Bayesian multimodel inference (MMI) as an approach to increase certainty in systems biology predictions, which becomes relevant when one wants to leverage a set of potentially incomplete models. Using existing models of the extracellular-regulated kinase (ERK) pathway, we show that MMI successfully combines models and yields predictors robust to model set changes and data uncertainties. We then use MMI to identify possible mechanisms of experimentally measured subcellular location-specific ERK activity. This work highlights MMI as a disciplined approach to increasing the certainty of intracellular signaling activity predictions.

Date: 2025
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DOI: 10.1038/s41467-025-62415-4

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