Logic Integer Programming Models for Signaling Networks

We propose a static and a dynamic approach to model biological signaling networks, and show how each can be used to answer relevant biological questions. For this we use the two different mathematical tools of Propositional Logic and Integer Programming. The power of discrete mathematics for handling qualitative as well as quantitative data has so far not been exploited in Molecular Biology, which is mostly driven by experimental research, relying on first-order or statistical models. The arising logic statements and integer programs are analyzed and can be solved with standard software. For a restricted class of problems the logic models reduce to a polynomial-time solvable satisfiability algorithm. Additionally, a more dynamic model enables enumeration of possible time resolutions in poly-logarithmic time. Computational experiments are included

12th International Workshop on Termination (WST 2012) : WST 2012, February 19–23, 2012, Obergurgl, Austria / ed. by Georg Moser

This volume contains the proceedings of the 12th International Workshop on Termination (WST 2012), to be held February 19–23, 2012 in Obergurgl, Austria. The goal of the Workshop on Termination is to be a venue for presentation and discussion of all topics in and around termination. In this way, the workshop tries to bridge the gaps between different communities interested and active in research in and around termination. The 12th International Workshop on Termination in Obergurgl continues the successful workshops held in St. Andrews (1993), La Bresse (1995), Ede (1997), Dagstuhl (1999), Utrecht (2001), Valencia (2003), Aachen (2004), Seattle (2006), Paris (2007), Leipzig (2009), and Edinburgh (2010). The 12th International Workshop on Termination did welcome contributions on all aspects of termination and complexity analysis. Contributions from the imperative, constraint, functional, and logic programming communities, and papers investigating applications of complexity or termination (for example in program transformation or theorem proving) were particularly welcome. We did receive 18 submissions which all were accepted. Each paper was assigned two reviewers. In addition to these 18 contributed talks, WST 2012, hosts three invited talks by Alexander Krauss, Martin Hofmann, and Fausto Spoto

Certainty Closure: Reliable Constraint Reasoning with Incomplete or Erroneous Data

Constraint Programming (CP) has proved an effective paradigm to model and solve difficult combinatorial satisfaction and optimisation problems from disparate domains. Many such problems arising from the commercial world are permeated by data uncertainty. Existing CP approaches that accommodate uncertainty are less suited to uncertainty arising due to incomplete and erroneous data, because they do not build reliable models and solutions guaranteed to address the user's genuine problem as she perceives it. Other fields such as reliable computation offer combinations of models and associated methods to handle these types of uncertain data, but lack an expressive framework characterising the resolution methodology independently of the model. We present a unifying framework that extends the CP formalism in both model and solutions, to tackle ill-defined combinatorial problems with incomplete or erroneous data. The certainty closure framework brings together modelling and solving methodologies from different fields into the CP paradigm to provide reliable and efficient approches for uncertain constraint problems. We demonstrate the applicability of the framework on a case study in network diagnosis. We define resolution forms that give generic templates, and their associated operational semantics, to derive practical solution methods for reliable solutions.Comment: Revised versio

Invariant Generation through Strategy Iteration in Succinctly Represented Control Flow Graphs

We consider the problem of computing numerical invariants of programs, for instance bounds on the values of numerical program variables. More specifically, we study the problem of performing static analysis by abstract interpretation using template linear constraint domains. Such invariants can be obtained by Kleene iterations that are, in order to guarantee termination, accelerated by widening operators. In many cases, however, applying this form of extrapolation leads to invariants that are weaker than the strongest inductive invariant that can be expressed within the abstract domain in use. Another well-known source of imprecision of traditional abstract interpretation techniques stems from their use of join operators at merge nodes in the control flow graph. The mentioned weaknesses may prevent these methods from proving safety properties. The technique we develop in this article addresses both of these issues: contrary to Kleene iterations accelerated by widening operators, it is guaranteed to yield the strongest inductive invariant that can be expressed within the template linear constraint domain in use. It also eschews join operators by distinguishing all paths of loop-free code segments. Formally speaking, our technique computes the least fixpoint within a given template linear constraint domain of a transition relation that is succinctly expressed as an existentially quantified linear real arithmetic formula. In contrast to previously published techniques that rely on quantifier elimination, our algorithm is proved to have optimal complexity: we prove that the decision problem associated with our fixpoint problem is in the second level of the polynomial-time hierarchy.Comment: 35 pages, conference version published at ESOP 2011, this version is a CoRR version of our submission to Logical Methods in Computer Scienc

Complexity classifications for different equivalence and audit problems for Boolean circuits

We study Boolean circuits as a representation of Boolean functions and consider different equivalence, audit, and enumeration problems. For a number of restricted sets of gate types (bases) we obtain efficient algorithms, while for all other gate types we show these problems are at least NP-hard.Comment: 25 pages, 1 figur

Applications of Finite Model Theory: Optimisation Problems, Hybrid Modal Logics and Games.

There exists an interesting relationships between two seemingly distinct fields: logic from the field of Model Theory, which deals with the truth of statements about discrete structures; and Computational Complexity, which deals with the classification of problems by how much of a particular computer resource is required in order to compute a solution. This relationship is known as Descriptive Complexity and it is the primary application of the tools from Model Theory when they are restricted to the finite; this restriction is commonly called Finite Model Theory. In this thesis, we investigate the extension of the results of Descriptive Complexity from classes of decision problems to classes of optimisation problems. When dealing with decision problems the natural mapping from true and false in logic to yes and no instances of a problem is used but when dealing with optimisation problems, other features of a logic need to be used. We investigate what these features are and provide results in the form of logical frameworks that can be used for describing optimisation problems in particular classes, building on the existing research into this area. Another application of Finite Model Theory that this thesis investigates is the relative expressiveness of various fragments of an extension of modal logic called hybrid modal logic. This is achieved through taking the Ehrenfeucht-Fraïssé game from Model Theory and modifying it so that it can be applied to hybrid modal logic. Then, by developing winning strategies for the players in the game, results are obtained that show strict hierarchies of expressiveness for fragments of hybrid modal logic that are generated by varying the quantifier depth and the number of proposition and nominal symbols available

The Connectivity of Boolean Satisfiability: Dichotomies for Formulas and Circuits

For Boolean satisfiability problems, the structure of the solution space is characterized by the solution graph, where the vertices are the solutions, and two solutions are connected iff they differ in exactly one variable. In 2006, Gopalan et al. studied connectivity properties of the solution graph and related complexity issues for CSPs, motivated mainly by research on satisfiability algorithms and the satisfiability threshold. They proved dichotomies for the diameter of connected components and for the complexity of the st-connectivity question, and conjectured a trichotomy for the connectivity question. Recently, we were able to establish the trichotomy [arXiv:1312.4524]. Here, we consider connectivity issues of satisfiability problems defined by Boolean circuits and propositional formulas that use gates, resp. connectives, from a fixed set of Boolean functions. We obtain dichotomies for the diameter and the two connectivity problems: on one side, the diameter is linear in the number of variables, and both problems are in P, while on the other side, the diameter can be exponential, and the problems are PSPACE-complete. For partially quantified formulas, we show an analogous dichotomy.Comment: 20 pages, several improvement