Optimizing information flow in Gene Regulatory Networks: a geometric perspective
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| Main Authors: | , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866915487499157504 |
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| author | García-Ariza, Miguel Ángel Bravetti, Alessandro Padilla, Pablo Romero-Arias, J Roberto |
| author_facet | García-Ariza, Miguel Ángel Bravetti, Alessandro Padilla, Pablo Romero-Arias, J Roberto |
| contents | The dynamics of gene regulatory networks is governed by the interaction between deterministic biochemical reactions and molecular noise. To understand how gene regulatory networks process information during cell state transitions, we study stochastic dynamics derived from a Boolean network model via its representation on the parameter space of Gaussian distributions, equipped with the Fisher information metric. This reformulation reveals that the trajectories of optimal information transfer are gradient flows of the Kullback-Leibler divergence. We demonstrate that the most efficient dynamics require isotropic decay rates across all nodes and that the noise intensity quantitatively determines the potential differentiation between the initial and final states. Furthermore, we show that paths minimizing biological cost correspond to metric geodesics that require noise suppression, leading to biologically irrelevant deterministic dynamics. Our approach frames noise and decay rates as fundamental control parameters for cellular differentiation, providing a geometric principle for the analysis and design of synthetic networks. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2509_08167 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Optimizing information flow in Gene Regulatory Networks: a geometric perspective García-Ariza, Miguel Ángel Bravetti, Alessandro Padilla, Pablo Romero-Arias, J Roberto Molecular Networks Information Theory 37M25, 53Z10, 53B12, 92C42, The dynamics of gene regulatory networks is governed by the interaction between deterministic biochemical reactions and molecular noise. To understand how gene regulatory networks process information during cell state transitions, we study stochastic dynamics derived from a Boolean network model via its representation on the parameter space of Gaussian distributions, equipped with the Fisher information metric. This reformulation reveals that the trajectories of optimal information transfer are gradient flows of the Kullback-Leibler divergence. We demonstrate that the most efficient dynamics require isotropic decay rates across all nodes and that the noise intensity quantitatively determines the potential differentiation between the initial and final states. Furthermore, we show that paths minimizing biological cost correspond to metric geodesics that require noise suppression, leading to biologically irrelevant deterministic dynamics. Our approach frames noise and decay rates as fundamental control parameters for cellular differentiation, providing a geometric principle for the analysis and design of synthetic networks. |
| title | Optimizing information flow in Gene Regulatory Networks: a geometric perspective |
| topic | Molecular Networks Information Theory 37M25, 53Z10, 53B12, 92C42, |
| url | https://arxiv.org/abs/2509.08167 |