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.

This paper studies how to verify the conformity of a program with its specification and proposes a novel constraint-programming framework for bounded program verification (CPBPV). The CPBPV framework uses constraint stores to represent the specification and the program and explores execution paths nondeterministically. The input program is partially correct if each constraint store so produced implies the post-condition. CPBPV does not explore spurious execution paths as it incrementally prunes execution paths early by detecting that the constraint store is not consistent. CPBPV uses the rich language of constraint programming to express the constraint store. Finally, CPBPV is parametrized with a list of solvers which are tried in sequence, starting with the least expensive and less general. Experimental results often produce orders of magnitude improvements over earlier approaches, running times being often independent of the variable domains. Moreover, CPBPV was able to detect subtle errors in some programs while other frameworks based on model checking have failed.