Message Passing and Metabolism
Active inference is an increasingly prominent paradigm in theoretical biology. It frames the dynamics of living systems as if they were solving an inference problem. This rests upon their flow towards some (non-equilibrium) steady state—or equivalently, their maximisation of the Bayesian model evide...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-05-01
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| Series: | Entropy |
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| Online Access: | https://www.mdpi.com/1099-4300/23/5/606 |
| _version_ | 1797534171850080256 |
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| author | Thomas Parr |
| author_facet | Thomas Parr |
| author_sort | Thomas Parr |
| collection | DOAJ |
| description | Active inference is an increasingly prominent paradigm in theoretical biology. It frames the dynamics of living systems as if they were solving an inference problem. This rests upon their flow towards some (non-equilibrium) steady state—or equivalently, their maximisation of the Bayesian model evidence for an implicit probabilistic model. For many models, these self-evidencing dynamics manifest as messages passed among elements of a system. Such messages resemble synaptic communication at a neuronal network level but could also apply to other network structures. This paper attempts to apply the same formulation to biochemical networks. The chemical computation that occurs in regulation of metabolism relies upon sparse interactions between coupled reactions, where enzymes induce conditional dependencies between reactants. We will see that these reactions may be viewed as the movement of probability mass between alternative categorical states. When framed in this way, the master equations describing such systems can be reformulated in terms of their steady-state distribution. This distribution plays the role of a generative model, affording an inferential interpretation of the underlying biochemistry. Finally, we see that—in analogy with computational neurology and psychiatry—metabolic disorders may be characterized as false inference under aberrant prior beliefs. |
| first_indexed | 2024-03-10T11:25:49Z |
| format | Article |
| id | doaj.art-60dc120f670b491fa9209c8c8f5cbfa1 |
| institution | Directory Open Access Journal |
| issn | 1099-4300 |
| language | English |
| last_indexed | 2024-03-10T11:25:49Z |
| publishDate | 2021-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Entropy |
| spelling | doaj.art-60dc120f670b491fa9209c8c8f5cbfa12023-11-21T19:41:38ZengMDPI AGEntropy1099-43002021-05-0123560610.3390/e23050606Message Passing and MetabolismThomas Parr0Wellcome Centre for Human Neuroimaging, Queen Square Institute of Neurology, University College London, London WC1N 3AR, UKActive inference is an increasingly prominent paradigm in theoretical biology. It frames the dynamics of living systems as if they were solving an inference problem. This rests upon their flow towards some (non-equilibrium) steady state—or equivalently, their maximisation of the Bayesian model evidence for an implicit probabilistic model. For many models, these self-evidencing dynamics manifest as messages passed among elements of a system. Such messages resemble synaptic communication at a neuronal network level but could also apply to other network structures. This paper attempts to apply the same formulation to biochemical networks. The chemical computation that occurs in regulation of metabolism relies upon sparse interactions between coupled reactions, where enzymes induce conditional dependencies between reactants. We will see that these reactions may be viewed as the movement of probability mass between alternative categorical states. When framed in this way, the master equations describing such systems can be reformulated in terms of their steady-state distribution. This distribution plays the role of a generative model, affording an inferential interpretation of the underlying biochemistry. Finally, we see that—in analogy with computational neurology and psychiatry—metabolic disorders may be characterized as false inference under aberrant prior beliefs.https://www.mdpi.com/1099-4300/23/5/606message passingmetabolismBayesianstochasticnon-equilibriummaster equations |
| spellingShingle | Thomas Parr Message Passing and Metabolism Entropy message passing metabolism Bayesian stochastic non-equilibrium master equations |
| title | Message Passing and Metabolism |
| title_full | Message Passing and Metabolism |
| title_fullStr | Message Passing and Metabolism |
| title_full_unstemmed | Message Passing and Metabolism |
| title_short | Message Passing and Metabolism |
| title_sort | message passing and metabolism |
| topic | message passing metabolism Bayesian stochastic non-equilibrium master equations |
| url | https://www.mdpi.com/1099-4300/23/5/606 |
| work_keys_str_mv | AT thomasparr messagepassingandmetabolism |