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

Answer Sets for Logic Programs with Arbitrary Abstract Constraint Atoms

In this paper, we present two alternative approaches to defining answer sets for logic programs with arbitrary types of abstract constraint atoms (c-atoms). These approaches generalize the fixpoint-based and the level mapping based answer set semantics of normal logic programs to the case of logic programs with arbitrary types of c-atoms. The results are four different answer set definitions which are equivalent when applied to normal logic programs. The standard fixpoint-based semantics of logic programs is generalized in two directions, called answer set by reduct and answer set by complement. These definitions, which differ from each other in the treatment of negation-as-failure (naf) atoms, make use of an immediate consequence operator to perform answer set checking, whose definition relies on the notion of conditional satisfaction of c-atoms w.r.t. a pair of interpretations. The other two definitions, called strongly and weakly well-supported models, are generalizations of the notion of well-supported models of normal logic programs to the case of programs with c-atoms. As for the case of fixpoint-based semantics, the difference between these two definitions is rooted in the treatment of naf atoms. We prove that answer sets by reduct (resp. by complement) are equivalent to weakly (resp. strongly) well-supported models of a program, thus generalizing the theorem on the correspondence between stable models and well-supported models of a normal logic program to the class of programs with c-atoms. We show that the newly defined semantics coincide with previously introduced semantics for logic programs with monotone c-atoms, and they extend the original answer set semantics of normal logic programs. We also study some properties of answer sets of programs with c-atoms, and relate our definitions to several semantics for logic programs with aggregates presented in the literature

Compiling ER Specifications into Declarative Programs

This paper proposes an environment to support high-level database programming in a declarative programming language. In order to ensure safe database updates, all access and update operations related to the database are generated from high-level descriptions in the entity- relationship (ER) model. We propose a representation of ER diagrams in the declarative language Curry so that they can be constructed by various tools and then translated into this representation. Furthermore, we have implemented a compiler from this representation into a Curry program that provides access and update operations based on a high-level API for database programming.Comment: Paper presented at the 17th Workshop on Logic-based Methods in Programming Environments (WLPE2007

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