Inference with constrained hidden Markov models in PRISM

DOI10.1017/S1471068410000219MaRDI QIDQ3585160zbMATH OpenOpenAlexWikidataFDO

Authors Henning Christiansen, Christian N. H. Theil Have, Ole Torp Lassen, Matthieu Petit

Publication date 19 August 2010

Published in Theory and Practice of Logic Programming (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1007.5421

zbMATH Keywords

hidden Markov model with side-constraintsinferenceprogramming in statistical modeling

Mathematics Subject Classification ID

Logic programming (68N17)

Abstract: A Hidden Markov Model (HMM) is a common statistical model which is widely used for analysis of biological sequence data and other sequential phenomena. In the present paper we show how HMMs can be extended with side-constraints and present constraint solving techniques for efficient inference. Defining HMMs with side-constraints in Constraint Logic Programming have advantages in terms of more compact expression and pruning opportunities during inference. We present a PRISM-based framework for extending HMMs with side-constraints and show how well-known constraints such as cardinality and all different are integrated. We experimentally validate our approach on the biologically motivated problem of global pairwise alignment.

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Cites work

• Biological Sequence Analysis
• Error bounds for convolutional codes and an asymptotically optimum decoding algorithm
• New Advances in Logic-Based Probabilistic Modeling by PRISM
• Non-discriminating arguments and their uses
• Solving weighted CSP by maintaining arc consistency

Cited in

(3)

• Duality between the local score of one sequence and constrained hidden Markov model
• Sequence annotation with HMMs: new problems and their complexity
• Logical hidden Markov models

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