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Reaction–diffusion equations are commonly used to model a diverse array of complex systems, including biological, chemical, and physical processes. Typically, these models are phenomenological, requiring the fitting of parameters to experimental data. In the present work, we introduce a novel formalism to construct reaction–diffusion models that is grounded in the principle of maximum entropy. This new formalism aims to incorporate various types of experimental data, including ensemble currents, distributions at different points in time, or moments of such. To this end, we expand the framework of Schrödinger bridges and maximum caliber problems to nonlinear interacting systems. We illustrate the usefulness of the proposed approach by modeling the evolution of (i) a morphogen across the fin of a zebrafish and (ii) the population of two varieties of toads in Poland, so as to match the experimental data.
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Inferring phenomenological models of first passage processes
Biochemical processes in cells are governed by complex networks of many chemical species interacting stochastically in diverse ways and on different time scales. Constructing microscopically accurate models of such networks is often infeasible. Instead, here we propose a systematic framework for building phenomenological models of such networks from experimental data, focusing on accurately approximating the time it takes to complete the process, the First Passage (FP) time. Our phenomenological models are mixtures of Gamma distributions, which have a natural biophysical interpretation. The complexity of the models is adapted automatically to account for the amount of available data and its temporal resolution. The framework can be used for predicting behavior of FP systems under varying external conditions. To demonstrate the utility of the approach, we build models for the distribution of inter-spike intervals of a morphologically complex neuron, a Purkinje cell, from experimental and simulated data. We demonstrate that the developed models can not only fit the data, but also make nontrivial predictions. We demonstrate that our coarse-grained models provide constraints on more mechanistically accurate models of the involved phenomena.
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- PAR ID:
- 10282951
- Editor(s):
- Faeder, James R.
- Date Published:
- Journal Name:
- PLOS Computational Biology
- Volume:
- 17
- Issue:
- 3
- ISSN:
- 1553-7358
- Page Range / eLocation ID:
- e1008740
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1371/journal.pcbi.1008740
