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We describe a modular modelling approach permitting curation, updating, and distributed development of modules through joined community effort overcoming the problem of keeping a combinatorially exploding number of monolithic models up to…
One of our long term research goals is to develop systems to answer realistic questions (e.g., some mentioned in textbooks) about biological pathways that a biologist may ask. To answer such questions we need formalisms that can model…
We identify and demonstrate a weakness of Petri Nets (PN) in specifying composite behavior of reactive systems. Specifically, we show how, when specifying multiple requirements in one PN model, modelers are obliged to specify mechanisms for…
It is well known that the complex system operation requires the use of new scientific tools and computer simulation. This paper presents a modular approach for modeling and analysis of the complex systems (in communication or transport…
Biological cells rely on precise spatiotemporal coordination of biochemical reactions to control their many functions. Such cell signaling networks have been a common focus for mathematical models, but they remain challenging to simulate,…
Recent advances in microscopy and 3D reconstruction methods have allowed for characterization of cellular morphology in unprecedented detail, including the irregular geometries of intracellular subcompartments such as membrane-bound…
A biological regulatory network can be modeled as a discrete function that contains all available information on network component interactions. From this function we can derive a graph representation of the network structure as well as of…
It is well known that the complex system operation requires the use of new scientific tools and computer simulation. This paper presents a modular approach for modeling and analysis of the complex systems (in communication or transport…
Smart speakers and robots become ever more prevalent in our daily lives. These agents are able to execute a wide range of tasks and actions and, therefore, need systems to control their execution. Current state-of-the-art such as (deep)…
Automated synthesis from behavioural specifications is an attractive and powerful way of constructing concurrent systems. Here we focus on the problem of synthesising a membrane system from a behavioural specification given in the form of a…
We present a method for logical specification of the behavior of a system based on the specification of its components and for representing and specifying the effect of a class of communication "signaling pathways" among them. Variations in…
The situation calculus logic model is convenient for modelling the actions that can occur in an information system application. The interplay of pre-conditions and post-conditions determines a semantically justified partial order of the…
In systems biology effective models are widely used due to the complexity of biological system. They result from a coarse-graining process which employs specific assumptions. Frequently one does not start with a model taking all details…
Signalling pathways are abstractions that help life scientists structure the coordination of cellular activity. Cross-talk between pathways accounts for many of the complex behaviours exhibited by signalling pathways and is often critical…
For a large Markovian model, a "product form" is an explicit description of the steady-state behaviour which is otherwise generally untractable. Being first introduced in queueing networks, it has been adapted to Markovian Petri nets. Here…
While trajectory prediction plays a critical role in enabling safe and effective path-planning in automated vehicles, standardized practices for evaluating such models remain underdeveloped. Recent efforts have aimed to unify dataset…
We present a concurrent operational Petri net semantics for the join-calculus, a process calculus for specifying concurrent and distributed systems. There often is a gap between system specifications and the actual implementations caused by…
Spiking Transformers have recently emerged as promising architectures for combining the efficiency of spiking neural networks with the representational power of self-attention. However, the lack of standardized implementations, evaluation…
Petri networks and network models are two frameworks for the compositional design of systems of interacting entities. Here we show how to combine them using the concept of a "catalyst": an entity that is neither destroyed nor created by any…
Conventional joint modeling approaches generally characterize the relationship between longitudinal biomarkers and discrete event occurrences within terminal, recurring or competing risk settings, thereby offering a limited representation…