Bayesian Annotation Networks for Complex Sequence Analysis

Probabilistic models that associate annotations to sequential data are widely used in computational biology and a range of other applications. Models integrating with logic programs provide, furthermore, for sophistication and generality, at the cost of potentially very high computational complexity. A methodology is proposed for modularization of such models into sub-models, each representing a particular interpretation of the input data to be analysed. Their composition forms, in a natural way, a Bayesian network, and we show how standard methods for prediction and training can be adapted for such composite models in an iterative way, obtaining reasonable complexity results. Our methodology can be implemented using the probabilistic-logic PRISM system, developed by Sato et al, in a way that allows for practical applications

Inference with Constrained Hidden Markov Models in PRISM

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

The Viterbi Algorithm expressed in Constraint Handling Rules

Abstract. The Viterbi algorithm is a classical example of a dynamic programming algorithm, in which pruning reduces the search space drastically, so that an otherwise exponential time complexity is reduced to linearity. The central steps of the algorithm, expansion and pruning, can be expressed in a concise and clear way in CHR, but additional control is needed in order to obtain the desired time complexity. It is shown how auxiliary constraints, called trigger constraints, can be applied to fine-tune the order of CHR rule applications in order to reach this goal. It is indicated how properties such as confluence can be useful for showing such optimized programs correct.