Process mining meets abstract interpretation

The discovery of process models out of system traces is an interesting problem that has received significant attention in the last years. In this work, a theory for the derivation of a Petri net from a set of traces is presented. The method is based on the theory of abstract interpretation, which has been applied successfully in other areas. The principal application of the theory presented is Process Mining, an area that tries to incorporate the use of formal models both in the design and use of information systems.Postprint (published version

Model Checking Linear Logic Specifications

The overall goal of this paper is to investigate the theoretical foundations of algorithmic verification techniques for first order linear logic specifications. The fragment of linear logic we consider in this paper is based on the linear logic programming language called LO enriched with universally quantified goal formulas. Although LO was originally introduced as a theoretical foundation for extensions of logic programming languages, it can also be viewed as a very general language to specify a wide range of infinite-state concurrent systems. Our approach is based on the relation between backward reachability and provability highlighted in our previous work on propositional LO programs. Following this line of research, we define here a general framework for the bottom-up evaluation of first order linear logic specifications. The evaluation procedure is based on an effective fixpoint operator working on a symbolic representation of infinite collections of first order linear logic formulas. The theory of well quasi-orderings can be used to provide sufficient conditions for the termination of the evaluation of non trivial fragments of first order linear logic.Comment: 53 pages, 12 figures "Under consideration for publication in Theory and Practice of Logic Programming

Independence and concurrent separation logic

A compositional Petri net-based semantics is given to a simple language allowing pointer manipulation and parallelism. The model is then applied to give a notion of validity to the judgements made by concurrent separation logic that emphasizes the process-environment duality inherent in such rely-guarantee reasoning. Soundness of the rules of concurrent separation logic with respect to this definition of validity is shown. The independence information retained by the Petri net model is then exploited to characterize the independence of parallel processes enforced by the logic. This is shown to permit a refinement operation capable of changing the granularity of atomic actions

Process discovery algorithms using numerical abstract domains

The discovery of process models from event logs has emerged as one of the crucial problems for enabling the continuous support in the life-cycle of an information system. However, in a decade of process discovery research, the algorithms and tools that have appeared are known to have strong limitations in several dimensions. The size of the logs and the formal properties of the model discovered are the two main challenges nowadays. In this paper we propose the use of numerical abstract domains for tackling these two problems, for the particular case of the discovery of Petri nets. First, numerical abstract domains enable the discovery of general process models, requiring no knowledge (e.g., the bound of the Petri net to derive) for the discovery algorithm. Second, by using divide and conquer techniques we are able to control the size of the process discovery problems. The methods proposed in this paper have been implemented in a prototype tool and experiments are reported illustrating the significance of this fresh view of the process discovery problem.Peer ReviewedPostprint (author’s final draft

COSMICAH 2005: workshop on verification of COncurrent Systems with dynaMIC Allocated Heaps (a Satellite event of ICALP 2005) - Informal Proceedings

Lisboa Portugal, 10 July 200

Supporting user-oriented analysis for multi-view domain-specific visual languages

This is the post-print version of the final paper published in Information and Software Technology. The published article is available from the link below. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. Copyright @ 2008 Elsevier B.V.The integration of usable and flexible analysis support in modelling environments is a key success factor in Model-Driven Development. In this paradigm, models are the core asset from which code is automatically generated, and thus ensuring model correctness is a fundamental quality control activity. For this purpose, a common approach is to transform the system models into formal semantic domains for verification. However, if the analysis results are not shown in a proper way to the end-user (e.g. in terms of the original language) they may become useless. In this paper we present a novel DSVL called BaVeL that facilitates the flexible annotation of verification results obtained in semantic domains to different formats, including the context of the original language. BaVeL is used in combination with a consistency framework, providing support for all steps in a verification process: acquisition of additional input data, transformation of the system models into semantic domains, verification, and flexible annotation of analysis results. The approach has been validated analytically by the cognitive dimensions framework, and empirically by its implementation and application to several DSVLs. Here we present a case study of a notation in the area of Digital Libraries, where the analysis is performed by transformations into Petri nets and a process algebra.Spanish Ministry of Education and Science and MODUWEB

A structured approach for the engineering of biochemical network models, illustrated for signalling pathways

http://dx.doi.org/10.1093/bib/bbn026Quantitative models of biochemical networks (signal transduction cascades, metabolic pathways, gene regulatory circuits) are a central component of modern systems biology. Building and managing these complex models is a major challenge that can benefit from the application of formal methods adopted from theoretical computing science. Here we provide a general introduction to the field of formal modelling, which emphasizes the intuitive biochemical basis of the modelling process, but is also accessible for an audience with a background in computing science and/or model engineering. We show how signal transduction cascades can be modelled in a modular fashion, using both a qualitative approach { Qualitative Petri nets, and quantitative approaches { Continuous Petri Nets and Ordinary Differential Equations. We review the major elementary building blocks of a cellular signalling model, discuss which critical design decisions have to be made during model building, and present ..

Application of Petri net based analysis techniques to signal transduction pathways

BACKGROUND: Signal transduction pathways are usually modelled using classical quantitative methods, which are based on ordinary differential equations (ODEs). However, some difficulties are inherent in this approach. On the one hand, the kinetic parameters involved are often unknown and have to be estimated. With increasing size and complexity of signal transduction pathways, the estimation of missing kinetic data is not possible. On the other hand, ODEs based models do not support any explicit insights into possible (signal-) flows within the network. Moreover, a huge amount of qualitative data is available due to high-throughput techniques. In order to get information on the systems behaviour, qualitative analysis techniques have been developed. Applications of the known qualitative analysis methods concern mainly metabolic networks. Petri net theory provides a variety of established analysis techniques, which are also applicable to signal transduction models. In this context special properties have to be considered and new dedicated techniques have to be designed. METHODS: We apply Petri net theory to model and analyse signal transduction pathways first qualitatively before continuing with quantitative analyses. This paper demonstrates how to build systematically a discrete model, which reflects provably the qualitative biological behaviour without any knowledge of kinetic parameters. The mating pheromone response pathway in Saccharomyces cerevisiae serves as case study. RESULTS: We propose an approach for model validation of signal transduction pathways based on the network structure only. For this purpose, we introduce the new notion of feasible t-invariants, which represent minimal self-contained subnets being active under a given input situation. Each of these subnets stands for a signal flow in the system. We define maximal common transition sets (MCT-sets), which can be used for t-invariant examination and net decomposition into smallest biologically meaningful functional units. CONCLUSION: The paper demonstrates how Petri net analysis techniques can promote a deeper understanding of signal transduction pathways. The new concepts of feasible t-invariants and MCT-sets have been proven to be useful for model validation and the interpretation of the biological system behaviour. Whereas MCT-sets provide a decomposition of the net into disjunctive subnets, feasible t-invariants describe subnets, which generally overlap. This work contributes to qualitative modelling and to the analysis of large biological networks by their fully automatic decomposition into biologically meaningful modules

Quality of process modeling using BPMN: a model-driven approach

Dissertação para obtenção do Grau de Doutor em Engenharia InformáticaContext: The BPMN 2.0 specification contains the rules regarding the correct usage of the language’s constructs. Practitioners have also proposed best-practices for producing better BPMN models. However, those rules are expressed in natural language, yielding sometimes ambiguous interpretation, and therefore, flaws in produced BPMN models. Objective: Ensuring the correctness of BPMN models is critical for the automation of processes. Hence, errors in the BPMN models specification should be detected and corrected at design time, since faults detected at latter stages of processes’ development can be more costly and hard to correct. So, we need to assess the quality of BPMN models in a rigorous and systematic way. Method: We follow a model-driven approach for formalization and empirical validation of BPMN well-formedness rules and BPMN measures for enhancing the quality of BPMN models. Results: The rule mining of BPMN specification, as well as recently published BPMN works, allowed the gathering of more than a hundred of BPMN well-formedness and best-practices rules. Furthermore, we derived a set of BPMN measures aiming to provide information to process modelers regarding the correctness of BPMN models. Both BPMN rules, as well as BPMN measures were empirically validated through samples of BPMN models. Limitations: This work does not cover control-flow formal properties in BPMN models, since they were extensively discussed in other process modeling research works. Conclusion: We intend to contribute for improving BPMN modeling tools, through the formalization of well-formedness rules and BPMN measures to be incorporated in those tools, in order to enhance the quality of process modeling outcomes