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arXiv · 2401.03571

{\alpha}-HMM: A Graphical Model for RNA Folding

Sixiang Zhang·Aaron J. Yang·Liming Cai
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Abstract

RNA secondary structure is modeled with the novel arbitrary-order hidden Markov model ({\alpha}-HMM). The {\alpha}-HMM extends over the traditional HMM with capability to model stochastic events that may be in influenced by historically distant ones, making it suitable to account for long-range canonical base pairings between nucleotides, which constitute the RNA secondary structure. Unlike previous heavy-weight extensions over HMM, the {\alpha}-HMM has the flexibility to apply restrictions on how one event may influence another in stochastic processes, enabling efficient prediction of RNA secondary structure including pseudoknots.

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Sixiang Zhang, Aaron J. Yang, Liming Cai. 2024-01-07. {\alpha}-HMM: A Graphical Model for RNA Folding. https://arxiv.org/abs/2401.03571

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