A reaction network scheme for hidden Markov model parameter learning

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With a view towards artificial cells, molecular communication systems, molecular multiagent systems and federated learning, we propose a novel reaction network scheme (termed the Baum-Welch (BW) reaction network) that learns parameters for hidden Markov models (HMMs). All variables including inputs and outputs are encoded by separate species. Each reaction in the scheme changes only one molecule of one species to one molecule of another. The reverse change is also accessible but via a different set of enzymes, in a design reminiscent of futile cycles in biochemical pathways. We show that every positive fixed point of the BW algorithm for HMMs is a fixed point of the reaction network scheme, and vice versa. Furthermore, we prove that the 'expectation' step and the 'maximization' step of the reaction network separately converge exponentially fast and compute the same values as the E-step and the M-step of the BW algorithm. We simulate example sequences, and show that our reaction network learns the same parameters for the HMM as the BW algorithm, and that the log-likelihood increases continuously along the trajectory of the reaction network.

Original languageEnglish
Article number20220877
JournalJournal of the Royal Society Interface
Volume20
Issue number203
ISSN1742-5689
DOIs
Publication statusPublished - 2023

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© 2023 The Authors.

    Research areas

  • Baum-Welch algorithm, hidden Markov model, molecular programming, statistical learning, synthetic biology

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