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 First-Order Theory of Sets with Cardinality Constraints is Decidable

We show that the decidability of the first-order theory of the language that combines Boolean algebras of sets of uninterpreted elements with Presburger arithmetic operations. We thereby disprove a recent conjecture that this theory is undecidable. Our language allows relating the cardinalities of sets to the values of integer variables, and can distinguish finite and infinite sets. We use quantifier elimination to show the decidability and obtain an elementary upper bound on the complexity. Precise program analyses can use our decidability result to verify representation invariants of data structures that use an integer field to represent the number of stored elements.Comment: 18 page