Related papers: Aspects of multiscale modelling in a process algeb…
Multiscale models allow for the treatment of complex phenomena involving different scales, such as remodeling and growth of tissues, muscular activation, and cardiac electrophysiology. Numerous numerical approaches have been developed to…
A trend across most areas where simulation-driven development is used is the ever increasing size and complexity of the systems under consideration, pushing established methods of modeling and simulation towards their limits. This paper…
Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and…
We address the problem of parameter estimation in models of systems biology from noisy observations. The models we consider are characterized by simultaneous deterministic nonlinear differential equations whose parameters are either taken…
Process algebra CSP only permits a process to engage in one event on a moment and records this single event into the traces of the process. CSP cannot process events simultaneously, it treat the events occurred simultaneously as one single…
A quantitative model of concurrent interaction is introduced. The basic objects are linear combinations of partial order relations, acted upon by a group of permutations that represents potential non-determinism in synchronisation. This…
Semantic equivalences are used in process algebra to capture the notion of similar behaviour, and this paper proposes a semi-quantitative equivalence for a stochastic process algebra developed for biological modelling. We consider…
A complete understanding of the brain requires an integrated description of the numerous scales of neural organization. It means studying the interplay of genes, synapses, and even whole brain regions which ultimately leads to different…
We learn multiple hypotheses for related tasks under a latent hierarchical relationship between tasks. We exploit the intuition that for domain adaptation, we wish to share classifier structure, but for multitask learning, we wish to share…
We learn multiple hypotheses for related tasks under a latent hierarchical relationship between tasks. We exploit the intuition that for domain adaptation, we wish to share classifier structure, but for multitask learning, we wish to share…
A computer simulation has to be fast to be helpful, if it is employed to study the behavior of a multicomponent dynamic system. This paper discusses modeling concepts and algorithmic techniques useful for creating such fast simulations.…
The modeling of bio-molecular system across molecular scales remains a central challenge in scientific research. Large language models (LLMs) are increasingly applied to bio-molecular discovery, yet systematic evaluation across multi-scale…
Effective utilization of Multiple-Instruction-Multiple-Data (MIMD) parallel computers requires the application of good load balancing techniques. In this paper we show that heuristics derived from observation of complex natural systems,…
Quantitative methods and mathematical modeling are playing an increasingly important role across disciplines. As a result, interdisciplinary mathematics courses are increasing in popularity. However, teaching such courses at an advanced…
As deep learning systems are scaled up to many billions of parameters, relating their internal structure to external behaviors becomes very challenging. Although daunting, this problem is not new: Neuroscientists and cognitive scientists…
We introduce a process algebra that concerns the timed behaviour of distributed systems with a known spatial distribution. This process algebra provides a communication mechanism that deals with the fact that a datum sent at one point in…
Complex system simulation has been playing an irreplaceable role in understanding, predicting, and controlling diverse complex systems. In the past few decades, the multi-scale simulation technique has drawn increasing attention for its…
In this paper, I outline several conceptual and methodological issues related to modeling individual and group processes embedded in clustered/hierarchical data structures. We position multilevel modeling techniques within a broader set of…
This topic review communicates working experiences regarding interaction of a multiplicity of processes. Our experiences come from climate change modelling, materials science, cell physiology and public health, and macroeconomic modelling.…
The BioAmbients calculus is a process algebra suitable for representing compartmentalization, molecular localization and movements between compartments. In this paper we enrich this calculus with a static type system classifying each…