1

Modeling Biological Systems in Stochastic Concurrent Constraint Programming

Reconstruction with Interval Constraints Propagation

In this paper we demonstrate how Interval Analysis and Constraint Logic Programming can be used to obtain an accurate geometric model of a scene that rigorously takes into account the propagation of data errors and roundoff. Image points are …

Stem-loop structure search for helitron discovery

Views on Time in Systems Biology

A comparison of CLP(FD) and ASP solutions to NP-complete problems

This paper presents experimental comparisons between declarative encodings of various computationally hard problems in both Answer Set Programming (ASP) and Constraint Logic Programming (CLP) over finite domains. The objective is to identify how the …

A New Constraint Solver for 3D Lattices and Its Application to the Protein Folding Problem

The paper describes the formalization and implementation of an efficient constraint programming framework operating on 3D crystal lattices. The framework is motivated and applied to address the problem of solving the abinitio protein structure …

A unifying model of variables and names

We investigate a category theoretic model where both “variables” and “names”, usually viewed as separate notions, are particular cases of the more general notion of distinction. The key aspect of this model is to consider functors over the category …

Algebraic Model Checking II: Decidability of Semi-Algebraic Model Checking and its Applications to Systems Biology

Motivated by applications to systems biology, and the emergence of semi-algebraic hybrid systems as a natural framework for modeling biochemical networks, we continue exploring the decidability problem for model-checking with TCTL (Timed Computation …

Algorithmic Algebraic Model Checking I: Challenges from Systems Biology⋆

In this paper, we suggest a possible confluence of the theory of hybrid automata and the techniques of algorithmic algebra to create a computational basis for systems biology. We describe a method to compute bounded reachability by combining Taylor …

An algorithmic account of winning strategies in Ehrenfeucht games on labelled successor structures

Ehrenfeucht-Fraïssé games are commonly used as a method to measure the expressive power of a logic, but they are also a flexible tool to compare structures. To exploit such a comparison power, explicit conditions characterizing the winning strategies …