## Abstract

Hidden Markov Models (HMMs) are a commonly used tool for inference of transcription factor (TF) binding sites from DNA sequence data. We exploit the mathematical equivalence between HMMs for TF binding and the "inverse" statistical mechanics of hard rods in a one-dimensional disordered potential to investigate learning in HMMs. We derive analytic expressions for the Fisher information, a commonly employed measure of confidence in learned parameters, in the biologically relevant limit where the density of binding sites is low. We then use techniques from statistical mechanics to derive a scaling principle relating the specificity (binding energy) of a TF to the minimum amount of training data necessary to learn it.

Original language | English (US) |
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Pages (from-to) | 1187-1205 |

Number of pages | 19 |

Journal | Journal of Statistical Physics |

Volume | 142 |

Issue number | 6 |

DOIs | |

State | Published - Apr 2011 |

## Keywords

- Bioinformatics
- Fisher information
- Hidden Markov Models
- Machine learning
- One-dimensional statistical mechanics

## ASJC Scopus subject areas

- Statistical and Nonlinear Physics
- Mathematical Physics