Isomorphism Checking in GROOVE

In this paper we show how isomorphism checking can be used as an effective technique for symmetry reduction in graph-based state spaces, despite the inherent complexity of the isomorphism problem. In particular, we show how one can use element-based graph certificate mappings to help in recognising nonisomorphic graphs. These are mappings that assign to all elements (edges and nodes) of a given graph a number that is invariant under isomorphism, in the sense that any isomorphism between graphs is sure to preserve this number. The individual element certificates of a graph give rise to a certificate for the entire graph, which can be used as a hash key for the graph; hence, this yields a heuristic to decide whether a graph has an isomorphic representative in a previously computed set of graphs. We report some experiments that show the viability of this method. \u

Distributed graph-based state space generation

LTSMIN provides a framework in which state space generation can be distributed easily over many cores on a single compute node, as well as over multiple compute nodes. The tool works on the basis of a vector representation of the states; the individual cores are assigned the task of computing all successors of states that are sent to them. In this paper we show how this framework can be applied in the case where states are essentially graphs interpreted up to isomorphism, such as the ones we have been studying for GROOVE. This involves developing a suitable vector representation for a canonical form of those graphs. The canonical forms are computed using a third tool called BLISS. We combined the three tools to form a system for distributed state space generation based on graph grammars. We show that the time performance of the resulting system scales well (i.e., close to linear) with the number of cores. We also report surprising statistics on the memory\ud consumption, which imply that the vector representation used to store graphs in LTSMIN is more compact than the representation used in GROOVE

Inductive queries for a drug designing robot scientist

It is increasingly clear that machine learning algorithms need to be integrated in an iterative scientific discovery loop, in which data is queried repeatedly by means of inductive queries and where the computer provides guidance to the experiments that are being performed. In this chapter, we summarise several key challenges in achieving this integration of machine learning and data mining algorithms in methods for the discovery of Quantitative Structure Activity Relationships (QSARs). We introduce the concept of a robot scientist, in which all steps of the discovery process are automated; we discuss the representation of molecular data such that knowledge discovery tools can analyse it, and we discuss the adaptation of machine learning and data mining algorithms to guide QSAR experiments

A model-theoretic analysis of Fidel-structures for mbC

In this paper the class of Fidel-structures for the paraconsistent logic mbC is studied from the point of view of Model Theory and Category Theory. The basic point is that Fidel-structures for mbC (or mbC-structures) can be seen as first-order structures over the signature of Boolean algebras expanded by two binary predicate symbols N (for negation) and O (for the consistency connective) satisfying certain Horn sentences. This perspective allows us to consider notions and results from Model Theory in order to analyze the class of mbC-structures. Thus, substructures, union of chains, direct products, direct limits, congruences and quotient structures can be analyzed under this perspective. In particular, a Birkhoff-like representation theorem for mbC-structures as subdirect poducts in terms of subdirectly irreducible mbC-structures is obtained by adapting a general result for first-order structures due to Caicedo. Moreover, a characterization of all the subdirectly irreducible mbC-structures is also given. An alternative decomposition theorem is obtained by using the notions of weak substructure and weak isomorphism considered by Fidel for Cn-structures