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

A Graph Grammar for Modelling RNA Folding

We propose a new approach for modelling the process of RNA folding as a graph transformation guided by the global value of free energy. Since the folding process evolves towards a configuration in which the free energy is minimal, the global behaviour resembles the one of a self-adaptive system. Each RNA configuration is a graph and the evolution of configurations is constrained by precise rules that can be described by a graph grammar.Comment: In Proceedings GaM 2016, arXiv:1612.0105

Test Case Generation for Object-Oriented Imperative Languages in CLP

Testing is a vital part of the software development process. Test Case Generation (TCG) is the process of automatically generating a collection of test cases which are applied to a system under test. White-box TCG is usually performed by means of symbolic execution, i.e., instead of executing the program on normal values (e.g., numbers), the program is executed on symbolic values representing arbitrary values. When dealing with an object-oriented (OO) imperative language, symbolic execution becomes challenging as, among other things, it must be able to backtrack, complex heap-allocated data structures should be created during the TCG process and features like inheritance, virtual invocations and exceptions have to be taken into account. Due to its inherent symbolic execution mechanism, we pursue in this paper that Constraint Logic Programming (CLP) has a promising unexploited application field in TCG. We will support our claim by developing a fully CLP-based framework to TCG of an OO imperative language, and by assessing it on a corresponding implementation on a set of challenging Java programs. A unique characteristic of our approach is that it handles all language features using only CLP and without the need of developing specific constraint operators (e.g., to model the heap)

On abstraction refinement for program analyses in Datalog

A central task for a program analysis concerns how to efficiently find a program abstraction that keeps only information relevant for proving properties of interest. We present a new approach for finding such abstractions for program analyses written in Datalog. Our approach is based on counterexample-guided abstraction refinement: when a Datalog analysis run fails using an abstraction, it seeks to generalize the cause of the failure to other abstractions, and pick a new abstraction that avoids a similar failure. Our solution uses a boolean satisfiability formulation that is general, complete, and optimal: it is independent of the Datalog solver, it generalizes the failure of an abstraction to as many other abstractions as possible, and it identifies the cheapest refined abstraction to try next. We show the performance of our approach on a pointer analysis and a typestate analysis, on eight real-world Java benchmark programs

TuLiPA : a syntax-semantics parsing environment for mildly context-sensitive formalisms

In this paper we present a parsing architecture that allows processing of different mildly context-sensitive formalisms, in particular Tree-Adjoining Grammar (TAG), Multi-Component Tree-Adjoining Grammar with Tree Tuples (TT-MCTAG) and simple Range Concatenation Grammar (RCG). Furthermore, for tree-based grammars, the parser computes not only syntactic analyses but also the corresponding semantic representations

A Duality-Based Approach for Distributed Optimization with Coupling Constraints

In this paper we consider a distributed optimization scenario in which a set of agents has to solve a convex optimization problem with separable cost function, local constraint sets and a coupling inequality constraint. We propose a novel distributed algorithm based on a relaxation of the primal problem and an elegant exploration of duality theory. Despite its complex derivation based on several duality steps, the distributed algorithm has a very simple and intuitive structure. That is, each node solves a local version of the original problem relaxation, and updates suitable dual variables. We prove the algorithm correctness and show its effectiveness via numerical computations