A branch-and-bound methodology within algebraic modelling systems

Through the use of application-specific branch-and-bound directives it is possible to find solutions to combinatorial models that would otherwise be difficult or impossible to find by just using generic branch-and-bound techniques within the framework of mathematical programming. {\sc Minto} is an example of a system which offers the possibility to incorporate user-provided directives (written in {\sc C}) to guide the branch-and-bound search. Its main focus, however, remains on mathematical programming models. The aim of this paper is to present a branch-and-bound methodology for particular combinatorial structures to be embedded inside an algebraic modelling language. One advantage is the increased scope of application. Another advantage is that directives are more easily implemented at the modelling level than at the programming level

Processor Verification Using Efficient Reductions of the Logic of Uninterpreted Functions to Propositional Logic

The logic of equality with uninterpreted functions (EUF) provides a means of abstracting the manipulation of data by a processor when verifying the correctness of its control logic. By reducing formulas in this logic to propositional formulas, we can apply Boolean methods such as Ordered Binary Decision Diagrams (BDDs) and Boolean satisfiability checkers to perform the verification. We can exploit characteristics of the formulas describing the verification conditions to greatly simplify the propositional formulas generated. In particular, we exploit the property that many equations appear only in positive form. We can therefore reduce the set of interpretations of the function symbols that must be considered to prove that a formula is universally valid to those that are ``maximally diverse.'' We present experimental results demonstrating the efficiency of this approach when verifying pipelined processors using the method proposed by Burch and Dill.Comment: 46 page

The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks

We investigate how scale-free (SF) and Erdos-Renyi (ER) topologies affect the interplay between evolvability and robustness of model gene regulatory networks with Boolean threshold dynamics. In agreement with Oikonomou and Cluzel (2006) we find that networks with SFin topologies, that is SF topology for incoming nodes and ER topology for outgoing nodes, are significantly more evolvable towards specific oscillatory targets than networks with ER topology for both incoming and outgoing nodes. Similar results are found for networks with SFboth and SFout topologies. The functionality of the SFout topology, which most closely resembles the structure of biological gene networks (Babu et al., 2004), is compared to the ER topology in further detail through an extension to multiple target outputs, with either an oscillatory or a non-oscillatory nature. For multiple oscillatory targets of the same length, the differences between SFout and ER networks are enhanced, but for non-oscillatory targets both types of networks show fairly similar evolvability. We find that SF networks generate oscillations much more easily than ER networks do, and this may explain why SF networks are more evolvable than ER networks are for oscillatory phenotypes. In spite of their greater evolvability, we find that networks with SFout topologies are also more robust to mutations than ER networks. Furthermore, the SFout topologies are more robust to changes in initial conditions (environmental robustness). For both topologies, we find that once a population of networks has reached the target state, further neutral evolution can lead to an increase in both the mutational robustness and the environmental robustness to changes in initial conditions.Comment: 16 pages, 15 figure

Symbolic Implementation of Connectors in BIP

BIP is a component framework for constructing systems by superposing three layers of modeling: Behavior, Interaction, and Priority. Behavior is represented by labeled transition systems communicating through ports. Interactions are sets of ports. A synchronization between components is possible through the interactions specified by a set of connectors. When several interactions are possible, priorities allow to restrict the non-determinism by choosing an interaction, which is maximal according to some given strict partial order. The BIP component framework has been implemented in a language and a tool-set. The execution of a BIP program is driven by a dedicated engine, which has access to the set of connectors and priority model of the program. A key performance issue is the computation of the set of possible interactions of the BIP program from a given state. Currently, the choice of the interaction to be executed involves a costly exploration of enumerative representations for connectors. This leads to a considerable overhead in execution times. In this paper, we propose a symbolic implementation of the execution model of BIP, which drastically reduces this overhead. The symbolic implementation is based on computing boolean representation for components, connectors, and priorities with an existing BDD package

Efficient enumeration of solutions produced by closure operations

In this paper we address the problem of generating all elements obtained by the saturation of an initial set by some operations. More precisely, we prove that we can generate the closure of a boolean relation (a set of boolean vectors) by polymorphisms with a polynomial delay. Therefore we can compute with polynomial delay the closure of a family of sets by any set of "set operations": union, intersection, symmetric difference, subsets, supersets $\dots$). To do so, we study the $Membership_{\mathcal{F}}$ problem: for a set of operations $\mathcal{F}$, decide whether an element belongs to the closure by $\mathcal{F}$ of a family of elements. In the boolean case, we prove that $Membership_{\mathcal{F}}$ is in P for any set of boolean operations $\mathcal{F}$. When the input vectors are over a domain larger than two elements, we prove that the generic enumeration method fails, since $Membership_{\mathcal{F}}$ is NP-hard for some $\mathcal{F}$. We also study the problem of generating minimal or maximal elements of closures and prove that some of them are related to well known enumeration problems such as the enumeration of the circuits of a matroid or the enumeration of maximal independent sets of a hypergraph. This article improves on previous works of the same authors.Comment: 30 pages, 1 figure. Long version of the article arXiv:1509.05623 of the same name which appeared in STACS 2016. Final version for DMTCS journa

Finite Boolean Algebras for Solid Geometry using Julia's Sparse Arrays

The goal of this paper is to introduce a new method in computer-aided geometry of solid modeling. We put forth a novel algebraic technique to evaluate any variadic expression between polyhedral d-solids (d = 2, 3) with regularized operators of union, intersection, and difference, i.e., any CSG tree. The result is obtained in three steps: first, by computing an independent set of generators for the d-space partition induced by the input; then, by reducing the solid expression to an equivalent logical formula between Boolean terms made by zeros and ones; and, finally, by evaluating this expression using bitwise operators. This method is implemented in Julia using sparse arrays. The computational evaluation of every possible solid expression, usually denoted as CSG (Constructive Solid Geometry), is reduced to an equivalent logical expression of a finite set algebra over the cells of a space partition, and solved by native bitwise operators.Comment: revised version submitted to Computer-Aided Geometric Desig