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Within the diverse interdisciplinary life sciences domains, semantic, workflow, and methodological ambiguities can prevent the appreciation of explanations of phenomena, handicap the use of computational models, and hamper communication…
In this paper, we deal with the problem of implementing an abstract machine for a stochastic version of the Brane Calculus. Instead of defining an ad hoc abstract machine, we consider the generic stochastic abstract machine introduced by…
Several complexity metrics are described which are related to logic structure, data structure and size of spreadsheet models. They primarily concentrate on the dispersion of cell references and cell paths. Most metrics are newly defined,…
We advocate here the use of computational logic for systems biology, as a \emph{unified and safe} framework well suited for both modeling the dynamic behaviour of biological systems, expressing properties of them, and verifying these…
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…
In [1] we present an extension of Prime Event Structures by a mechanism to express dynamicity in the causal relation. More precisely we add the possibility that the occurrence of an event can add or remove causal dependencies between events…
The living cell expends energetic and material resources to reliably process information from its environment. To do so, it utilises unreliable molecular circuitry that is subject to thermal and other fluctuations. Here, we argue that…
This manuscript contributes a general and practical framework for casting a Markov process model of a system at equilibrium as a structural causal model, and carrying out counterfactual inference. Markov processes mathematically describe…
A number of exciting advances have been made in automated fact-checking thanks to increasingly larger datasets and more powerful systems, leading to improvements in the complexity of claims which can be accurately fact-checked. However,…
In nonlinear dynamics, basins of attraction link a given set of initial conditions to its corresponding final states. This notion appears in a broad range of applications where several outcomes are possible, which is a common situation in…
One of the central aims of neuroscience is to reliably predict the behavioral response of an organism using its neural activity. If possible, this implies we can causally manipulate the neural response and design brain-computer-interface…
Gas transport across cell membrane is a very important process in biochemistry which is essential for many crucial tasks, including cell respiration pH regulation in the cell. In the late 1990's, the suggestion that gasses are transported…
We present an improvement of a recent funnel controller design for uncertain nonlinear multi-input, multi-output systems modeled by higher order functional differential equations in the presence of input constraints. The objective is to…
When a mathematical or computational model is used to analyse some system, it is usual that some parameters resp.\ functions or fields in the model are not known, and hence uncertain. These parametric quantities are then identified by…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
The goal of this paper is to define and analyze systems which exhibit brittle behavior. This behavior is characterized by a sudden and steep decline in performance as the system approaches the limits of tolerance. This can be due to input…
In this work we to develop a general statistical mechanic formalism to study systems restricted to surfaces of revolution, these are a very well model to study the termodinamical properties of microbiological systems and macromolecules lies…
The biological membrane, which compartmentalizes the cell and its organelles, exhibit wide variety of macroscopic shapes of varying morphology and topology. A systematic understanding of the relation of membrane shapes to composition,…
Approximate computing trades off accuracy of results for resources such as energy or computing time. There is a large and rapidly growing literature on approximate computing that has focused mostly on showing the benefits of approximation.…
Computational models are invaluable in capturing the complexities of real-world biological processes. Yet, the selection of appropriate algorithms for inference tasks, especially when dealing with real-world observational data, remains a…