Inhomogeneous Parsimonious Markov Models
- Cite this paper as:
- Eggeling R., Gohr A., Bourguignon PY., Wingender E., Grosse I. (2013) Inhomogeneous Parsimonious Markov Models. In: Blockeel H., Kersting K., Nijssen S., Železný F. (eds) Machine Learning and Knowledge Discovery in Databases. ECML PKDD 2013. Lecture Notes in Computer Science, vol 8188. Springer, Berlin, Heidelberg
We introduce inhomogeneous parsimonious Markov models for modeling statistical patterns in discrete sequences. These models are based on parsimonious context trees, which are a generalization of context trees, and thus generalize variable order Markov models. We follow a Bayesian approach, consisting of structure and parameter learning. Structure learning is a challenging problem due to an overexponential number of possible tree structures, so we describe an exact and efficient dynamic programming algorithm for finding the optimal tree structures.
We apply model and learning algorithm to the problem of modeling binding sites of the human transcription factor C/EBP, and find an increased prediction performance compared to fixed order and variable order Markov models. We investigate the reason for this improvement and find several instances of context-specific dependences that can be captured by parsimonious context trees but not by traditional context trees.
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