Related papers: Aspects of multiscale modelling in a process algeb…
This thesis presents a new methodology to analyze one-dimensional signals trough a new approach called Multi Layer Analysis, for short MLA. It also provides some new insights on the relationship between one-dimensional signals processed by…
Complex systems are often characterized by the interplay of multiple interconnected dynamical processes operating across a range of temporal scales. This phenomenon is widespread in both biological and artificial scenarios, making it…
Timed transition systems are behavioural models that include an explicit treatment of time flow and are used to formalise the semantics of several foundational process calculi and automata. Despite their relevance, a general mathematical…
Biological systems are generally complicated and/or complex. In the former approach, one sets up a model with a large number of parameters to describe the system in detail. The latter approach focuses on understanding the universal aspects…
Complex processes in science and engineering are often formulated as multistage decision-making problems. In this paper, we consider a type of multistage decision-making process called a cascade process. A cascade process is a multistage…
Compensating CSP (cCSP) is a language defined to model long running business transactions within the framework of standard CSP process algebra. In earlier work, we have defined both traces and operational semantics of the language. We have…
The modelling, specification and study of the semantics of concurrent reactive systems have been interesting research topics for many years now. The aim of this thesis is to exploit the strengths of the (co)algebraic framework in modelling…
Large contingency tables summarizing categorical variables arise in many areas. For example in biology when a large number of biomarkers are cross-tabulated according to their discrete expression level. Interactions of the variables are…
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
Scientists often use observational time series data to study complex natural processes, but regression analyses often assume simplistic dynamics. Recent advances in deep learning have yielded startling improvements to the performance of…
This paper concerns the modeling and numerical simulation of the process of speciation. In particular, given conditions for which one or more speciation events within an ecosystem occur, our aim is to develop the necessary modeling and…
It is well known that we can use structural proof theory to refine, or generalize, existing paradigmatic computational primitives, or to discover new ones. Under such a point of view we keep developing a programme whose goal is establishing…
Multi-output Gaussian processes (MOGPs) have been introduced to deal with multiple tasks by exploiting the correlations between different outputs. Generally, MOGPs models assume a flat correlation structure between the outputs. However,…
Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory. One advantage of symbolic computation is its potential for qualitative answers to…
Systems biology focuses on the study of entire biological systems rather than on their individual components. With the emergence of high-throughput data generation technologies for molecular biology and the development of advanced…
We discuss the parallelization of algorithms for solving polynomial systems symbolically by way of triangular decomposition. Algorithms for solving polynomial systems combine low-level routines for performing arithmetic operations on…
Multilevel modeling and simulation (M&S) is becoming increasingly relevant due to the benefits that this methodology offers. Multilevel models allow users to describe a system at multiple levels of detail. From one side, this can make…
Research in cell biology is steadily contributing new knowledge about many different aspects of physiological processes like polymerization, both with respect to the involved molecular structures as well as their related function.…
The need for high-throughput, precise, and meaningful methods for measuring behavior has been amplified by our recent successes in measuring and manipulating neural circuitry. The largest challenges associated with moving in this direction,…
Process equivalences are formal methods that relate programs and system which, informally, behave in the same way. Since there is no unique notion of what it means for two dynamic systems to display the same behaviour there are a multitude…