Encoding conformance checking artefacts in SAT

Conformance checking strongly relies on the computation of artefacts, which enable reasoning on the relation between observed and modeled behavior. This paper shows how important conformance artefacts like alignments, anti-alignments or even multi-alignments, defined over the edit distance, can be computed by encoding the problem as a SAT instance. From a general perspective, the work advocates for a unified family of techniques that can compute conformance artefacts in the same way. The prototype implementation of the techniques presented in this paper show capabilities for dealing with some of the current benchmarks, and potential for the near future when optimizations similar to the ones in the literature are incorporated.Peer ReviewedPostprint (author's final draft

Encoding conformance checking artefacts in SAT

Conformance checking strongly relies on the computation of artefacts, which enable reasoning on the relation between observed and modeled behavior. This paper shows how important conformance artefacts like alignments, anti-alignments or even multi-alignments, defined over the edit distance, can be computed by encoding the problem as a SAT instance. From a general perspective, the work advocates for a unified family of techniques that can compute conformance artefacts in the same way. The prototype implementation of the techniques presented in this paper show capabilities for dealing with some of the current benchmarks, and potential for the near future when optimizations similar to the ones in the literature are incorporated.Peer ReviewedPostprint (author's final draft

An evolutionary technique to approximate multiple optimal alignments

The alignment of observed and modeled behavior is an essential aid for organizations, since it opens the door for root-cause analysis and enhancement of processes. The state-of-the-art technique for computing alignments has exponential time and space complexity, hindering its applicability for medium and large instances. Moreover, the fact that there may be multiple optimal alignments is perceived as a negative situation, while in reality it may provide a more comprehensive picture of the model’s explanation of observed behavior, from which other techniques may benefit. This paper presents a novel evolutionary technique for approximating multiple optimal alignments. Remarkably, the memory footprint of the proposed technique is bounded, representing an unprecedented guarantee with respect to the state-of-the-art methods for the same task. The technique is implemented into a tool, and experiments on several benchmarks are provided.Peer ReviewedPostprint (author's final draft

Interactions between metal ions and DNA

84 years elapsed between the announcements of the periodic table and that of the DNA double helix in 1953, and the two have been combined in many ways since then. In this chapter an outline of the fundamentals of DNA structure leads into a range of examples showing how the natural magnesium and potassium ions found in nature can be substituted in a diversity of applications. The dynamic structures found in nature have been studied in the more controlled but artificial environment of the DNA crystal using examples from sodium to platinum and also in a range of DNA-binding metal complexes. While NMR is an essential technique for studying nucleic acid structure and conformation, most of our knowledge of metal ion binding has come from X-ray crystallography. These days the structures studied, and therefore also the diversity of metal binding, go beyond the double helix to triplexes, hairpin loops, junctions and quadruplexes, and the chapter describes briefly how these pieces fit into the DNA jigsaw. In a final section, the roles of metal cations in the crystallisation of new DNA structures are discussed, along with an introduction to the versatility of the periodic table of absorption edges for nucleic acid structure determination