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Context-dependent nature of biological phenomena are well documented in every branch of biology. While there have been few previous attempts to (implicitly) model various facets of biological context-dependence, a formal and general…

Other Quantitative Biology · Quantitative Biology 2011-11-28 Anirban Banerji

Dependency syntax represents the structure of a sentence as a tree composed of dependencies, i.e., directed relations between lexical units. While in its more general form any such tree is allowed, in practice many are not plausible or are…

Computation and Language · Computer Science 2026-04-07 Gómez-Rodríguez , Carlos , Alemany-Puig , Lluís

Events and entities are closely related; entities are often actors or participants in events and events without entities are uncommon. The interpretation of events and entities is highly contextually dependent. Existing work in information…

Computation and Language · Computer Science 2016-09-14 Bishan Yang , Tom Mitchell

We present an approach for flux analysis in process algebra models of biological systems. We perceive flux as the flow of resources in stochastic simulations. We resort to an established correspondence between event structures, a broadly…

Computational Engineering, Finance, and Science · Computer Science 2010-02-23 Ozan Kahramanoğullari

Taking an interaction network oriented perspective in informatics raises the challenge to describe deterministic finite systems which take part in networks of nondeterministic interactions. The traditional approach to describe processes as…

Distributed, Parallel, and Cluster Computing · Computer Science 2012-02-22 Johannes Reich

Our world is shaped by events of various complexity. This includes both small-scale local events like local farmer markets and large complex events like political and military conflicts. The latter are typically not observed directly but…

Computation and Language · Computer Science 2024-04-26 Florian Plötzky , Niklas Kiehne , Wolf-Tilo Balke

These lecture notes cover basic automata-theoretic concepts and logical formalisms for the modeling and verification of concurrent and distributed systems. Many of these concepts naturally extend the classical automata and logics over…

Logic in Computer Science · Computer Science 2021-10-19 Benedikt Bollig , Paul Gastin

The discipline of process mining aims to study processes in a data-driven manner by analyzing historical process executions, often employing Petri nets. Event data, extracted from information systems (e.g. SAP), serve as the starting point…

Artificial Intelligence · Computer Science 2022-04-11 Marco Pegoraro , Merih Seran Uysal , Wil M. P. van der Aalst

These lecture notes concern the basics of the theory of process behaviour. First the concept of a (labelled) transition system receives ample treatment and then the following issues concerning process behaviour are elaborated in the setting…

Logic in Computer Science · Computer Science 2016-10-06 C. A. Middelburg

For one-safe Petri nets or condition/event-systems, a process as defined by Carl Adam Petri provides a notion of a run of a system where causal dependencies are reflected in terms of a partial order. Goltz and Reisig have generalised this…

Logic in Computer Science · Computer Science 2021-03-03 Rob van Glabbeek , Ursula Goltz , Jens-Wolfhard Schicke-Uffmann

Dependency analysis is a technique to identify and determine data dependencies between service protocols. Protocols evolving concurrently in the service composition need to impose an order in their execution if there exist data…

Software Engineering · Computer Science 2010-07-30 Javier Cubo , Ernesto Pimentel , Gwen Salaün , Carlos Canal

Developing algorithms for distributed systems is an error-prone task. Formal models like Petri nets with transits and Petri games can prevent errors when developing such algorithms. Petri nets with transits allow us to follow the data flow…

Logic in Computer Science · Computer Science 2021-03-30 Manuel Gieseking , Jesko Hecking-Harbusch , Ann Yanich

The notion of events has occupied a central role in modeling and has an influence in computer science and philosophy. Recent developments in diagrammatic modeling have made it possible to examine conceptual representation of events. This…

Artificial Intelligence · Computer Science 2017-04-28 Sabah Al-Fedaghi

The mathematical formalisms used to model biological systems induce both latent and ambiguous assumptions that can limit or distort their representational capabilities. Developing formalisms that can represent systems more precisely is…

Quantitative Methods · Quantitative Biology 2026-05-25 Léo Diaz , Sean T. Vittadello , Michael P. H. Stumpf

In the era of intelligent computing, computational progress in text processing is an essential consideration. Many systems have been developed to process text over different languages. Though, there is considerable development, they still…

Artificial Intelligence · Computer Science 2020-02-26 Sumant Pushp , Pragya Kashmira , Shyamanta M Hazarika

Previous models of international conflict have suffered two shortfalls. They tended not to embody dynamic changes, focusing rather on static slices of behavior over time. These models have also been empirically evaluated in ways that…

Applications · Statistics 2015-05-01 Shahryar Minhas , Peter D. Hoff , Michael D. Ward

One of the well-known results in concurrency theory concerns the relationship between event structures and occurrence nets: an occurrence net can be associated with a prime event structure, and vice versa. More generally, the relationships…

Logic in Computer Science · Computer Science 2019-10-25 Hernán Melgratti , Claudio Antares Mezzina , Iain Phillips , G. Michele Pinna , Irek Ulidowski

Classical Petri nets provide a canonical model of concurrency, with unfolding semantics linking nets, occurrence nets, and event structures. No comparable framework exists for quantum concurrency: existing ''quantum Petri nets'' lack…

Logic in Computer Science · Computer Science 2025-09-18 Julien Saan Joachim , Marc de Visme , Stefan Haar , Glynn Winskel

In the late 1970s, C.A. Petri introduced partially ordered event occurrences (runs), then called \emph{processes}, as the appropriate model to describe the individual evolutions of distributed systems. Here, we present a unified framework…

Logic in Computer Science · Computer Science 2026-02-13 Peter Fettke , Wolfgang Reisig

Automated decision making is often complicated by the complexity of the knowledge involved. Much of this complexity arises from the context sensitive variations of the underlying phenomena. We propose a framework for representing…

Artificial Intelligence · Computer Science 2013-03-25 Tze-Yun Leong