Conformance checking of processes based on monitoring real behavior

There is increasing awareness that epistasis or gene-gene interaction plays a role in susceptibility to common human diseases In this paper, we formulate a working hypothesis that epistasis is a ubiquitous component of the genetic architecture of common human diseases and that complex interactions are more important than the independent main effects of any one susceptibility gene This working hypothesis is based on several bodies of evidence First, the idea that epistasis is important is not new In fact, the recognition that deviations from Mendelian ratios are due to interactions between genes has been around for nearly 100 years Second, the ubiquity of biomolecular interactions in gene regulation and biochemical and metabolic systems suggest that relationship between DNA sequence variations and clinical endpoints is likely to involve gene-gene interactions Third, positive results from studies of single polymorphisms typically do not replicate across independent samples This is true for both linkage and association studies Fourth, gene-gene interactions are commonly found when properly investigated We review each of these points and then review an analytical strategy called multifactor dimensionality reduction for detecting epistasis We end with ideas of how hypotheses about biological epistasis can be generated from statistical evidence using biochemical systems models If this working hypothesis is true, it suggests that we need a research strategy for identifying common disease susceptibility genes that embraces, rather than ignores, the complexity of the genotype to phenotype relationship

http://www.cs.duke.edu/brd/Teaching/Previous/Bio/Readings/Moore/Epistasis-Human-Heredity-FINAL.pdf

The Ubiquitous Nature of Epistasis in Determining Susceptibility to Common Human Diseases

The Petri Net Markup Language (PNML) is an XML-based interchange format for Petri nets. In order to support different versions of Petri nets and, in particular, future versions of Petri nets, PNML allows the definition of Petri net types. Due to this flexibility, PNML is a starting point for a standard interchange format for Petri nets. This paper discusses the design principles, the basic concepts, and the underlying XML technology of PNML. The main purpose of this paper is to disseminate the ideas of PNML and to stimulate discussion on and contributions to a standard Petri net interchange format.

/pdf/the-petri-net-markup-language-concepts-technology-and-tools-2paqymche5.pdf

The Petri net markup language: concepts, technology, and tools

Process mining includes the automated discovery of processes from event logs. Based on observed events (e.g., activities being executed or messages being exchanged) a process model is constructed. One of the essential problems in process mining is that one cannot assume to have seen all possible behavior. At best, one has seen a representative subset. Therefore, classical synthesis techniques are not suitable as they aim at finding a model that is able to exactly reproduce the log. Existing process mining techniques try to avoid such “overfitting” by generalizing the model to allow for more behavior. This generalization is often driven by the representation language and very crude assumptions about completeness. As a result, parts of the model are “overfitting” (allow only for what has actually been observed) while other parts may be “underfitting” (allow for much more behavior without strong support for it). None of the existing techniques enables the user to control the balance between “overfitting” and “underfitting”. To address this, we propose a two-step approach. First, using a configurable approach, a transition system is constructed. Then, using the “theory of regions”, the model is synthesized. The approach has been implemented in the context of ProM and overcomes many of the limitations of traditional approaches.

/pdf/process-mining-a-two-step-approach-to-balance-between-1960nrfw21.pdf

Process mining : a two-step approach to balance between underfitting and overfitting

The research domain of process discovery aims at constructing a process model (e.g. a Petri net) which is an abstract representation of an execution log. Such a model should (1) be able to reproduce the log under consideration and (2) be independent of the number of cases in the log. In this paper, we present a process discovery algorithm where we use concepts taken from the language-based theory of regions, a well-known Petri net research area. We identify a number of shortcomings of this theory from the process discovery perspective, and we provide solutions based on integer linear programming.

/pdf/process-discovery-using-integer-linear-programming-1o0tjolvjs.pdf

Process Discovery using Integer Linear Programming

The increasing number of Petri net variants naturally leads to the question whether the term "Petri net" is more than a common name for very different concepts. This contribution tries to identify aspects common to all or at least to most Petri nets. It concentrates on those features where Petri nets significantly differ from other modeling languages, i.e. we ask where the use of Petri nets leads to advantages compared to other languages. Different techniques that are usually comprised under the header "analysis" are distinguished with respect to the analysis aim. Finally, the role of Petri nets in the development of distributed systems is discussed.

What Is a Petri Net

The increasing number of Petri net variants naturally leads to the question whether the term “Petri net” is more than a common name for very different concepts This contribution tries to identify aspects common to all or at least to most Petri nets It concentrates on those features where Petri nets significantly differ from other modeling languages, ie we ask where the use of Petri nets leads to advantages compared to other languages Different techniques that are usually comprised under the header “analysis” are distinguished with respect to the analysis aim Finally, the role of Petri nets in the development of distributed systems is discussed

/pdf/what-is-a-petri-net-informal-answers-for-the-informed-reader-4luompydvu.pdf

“What Is a Petri Net?” Informal Answers for the Informed Reader

The increasing number of Petri net variants naturally leads to the question whether the term “Petri net” is more than a common name for very different concepts. This contribution tries to identify aspects common to all or at least to most Petri nets. It concentrates on those features where Petri nets significantly differ from other modeling languages, i.e. we ask where the use of Petri nets leads to advantages compared to other languages. Different techniques that are usually comprised under the header “analysis” are distinguished with respect to the analysis aim. Finally, the role of Petri nets in the development of distributed systems is discussed.

Unifying Petri Nets

In this paper we present a survey on methods for the synthesis of Petri nets from behavioral descriptions given as languages. We consider place/transition Petri nets, elementary Petri nets and Petri nets with inhibitor arcs. For each net class we consider classical languages, step languages and partial languages as behavioral description. All methods are based on the notion of regions of languages. We identify two different types of regions and two different principles of computing from the set of regions of a language a finite Petri net generating this language. For finite or regular languages almost each combination of Petri net class, language type, region type and computation principle can be considered to compute such a net. Altogether, we present a framework for region-based synthesis of Petri nets from languages which integrates almost all known approaches and fills several remaining gaps in literature.

/pdf/how-to-synthesize-nets-from-languages-a-survey-jqrvorq16s.pdf

How to synthesize nets from languages: a survey

"What Is a Petri Net?" Informal Answers for the Informed Reader.- Application Oriented Approaches.- The ?Petri Net Baukasten?: An Overview.- Improving the Usability of Petri Nets with the ?Petri Net Baukasten?.- Implementation of Parameterized Net Classes with the Petri Net Kernel of the ?Petrinetz-Baukasten?.- Process Landscaping: Modelling Distributed Processes and Proving Properties of Distributed Process Models.- Unifying Frameworks.- Petri Nets over Partial Algebra.- Parameterized Net Classes: A Uniform Approach to Petri Net Classes.- Behavior and Realization Construction for Petri Nets Based on Free Monoid and Power Set Graphs.- Rewriting Logic as a Unifying Framework for Petri Nets.- Theoretical Approaches.- Generalized Automata and Their Net Representations.- On Concurrent Realization of Reactive Systems and Their Morphisms.- Transactions and Zero-Safe Nets.- Two Algebraic Process Semantics for Contextual Nets.- Continuous Petri Nets and Transition Systems.

Gabriel Juhás

Papers

What Is a Petri Net

“What Is a Petri Net?” Informal Answers for the Informed Reader

Unifying Petri Nets

How to synthesize nets from languages: a survey

Unifying Petri Nets: Advances in Petri Nets