Learning Hybrid Process Models From Events: Process Discovery Without Faking Confidence

Process discovery techniques return process models that are either formal (precisely describing the possible behaviors) or informal (merely a "picture" not allowing for any form of formal reasoning). Formal models are able to classify traces (i.e., sequences of events) as fitting or non-fitting. Most process mining approaches described in the literature produce such models. This is in stark contrast with the over 25 available commercial process mining tools that only discover informal process models that remain deliberately vague on the precise set of possible traces. There are two main reasons why vendors resort to such models: scalability and simplicity. In this paper, we propose to combine the best of both worlds: discovering hybrid process models that have formal and informal elements. As a proof of concept we present a discovery technique based on hybrid Petri nets. These models allow for formal reasoning, but also reveal information that cannot be captured in mainstream formal models. A novel discovery algorithm returning hybrid Petri nets has been implemented in ProM and has been applied to several real-life event logs. The results clearly demonstrate the advantages of remaining "vague" when there is not enough "evidence" in the data or standard modeling constructs do not "fit". Moreover, the approach is scalable enough to be incorporated in industrial-strength process mining tools.Comment: 25 pages, 12 figure

A Posterior Probability Approach for Gene Regulatory Network Inference in Genetic Perturbation Data

Inferring gene regulatory networks is an important problem in systems biology. However, these networks can be hard to infer from experimental data because of the inherent variability in biological data as well as the large number of genes involved. We propose a fast, simple method for inferring regulatory relationships between genes from knockdown experiments in the NIH LINCS dataset by calculating posterior probabilities, incorporating prior information. We show that the method is able to find previously identified edges from TRANSFAC and JASPAR and discuss the merits and limitations of this approach

Saving the mutual manipulability account of constitutive relevance

Constitutive mechanistic explanations are said to refer to mechanisms that constitute the phenomenon-to-be-explained. The most prominent approach of how to understand this constitution relation is Carl Craver’s mutual manipulability approach to constitutive relevance. Recently, the mutual manipulability approach has come under attack (Leuridan 2012; Baumgartner and Gebharter 2015; Romero 2015; Harinen 2014; Casini and Baumgartner 2016). Roughly, it is argued that this approach is inconsistent because it is spelled out in terms of interventionism (which is an approach to causation), whereas constitutive relevance is said to be a non-causal relation. In this paper, I will discuss a strategy of how to resolve this inconsistency, so-called fat-handedness approaches (Baumgartner and Gebharter 2015; Casini and Baumgartner 2016; Romero 2015). I will argue that these approaches are problematic. I will present a novel suggestion of how to consistently define constitutive relevance in terms of interventionism. My approach is based on a causal interpretation of mutual manipulability, where manipulability is interpreted as a causal relation between the mechanism’s components and temporal parts of the phenomenon