Related papers: Analysis of parametric biological models with non-…
The theory of slow manifolds is an important tool in the study of deterministic dynamical systems, giving a practical method by which to reduce the number of relevant degrees of freedom in a model, thereby often resulting in a considerable…
This study presents the approach to analyzing the evolution of an arbitrary complex system whose behavior is characterized by a set of different time-dependent factors. The key requirement for these factors is only that they must contain an…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
Computational models provide crucial insights into complex biological processes such as cancer evolution, but their mechanistic nature often makes them nonlinear and parameter-rich, complicating calibration. We systematically evaluate…
We propose a novel approach to the estimation of multiple Graphical Models to analyse temporal patterns of association among a set of metabolites over different groups of patients. Our motivating application is the Southall And Brent…
Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…
The paper discusses a simple method of using the parametric continuation method to designate complex diagrams of steady states. The main advantage of the discussed approach is the fact that it does not require the installation of huge…
We study the problem of optimizing nonlinear objective functions over matroids presented by oracles or explicitly. Such functions can be interpreted as the balancing of multi-criteria optimization. We provide a combinatorial polynomial time…
A recent article by Weidner et al. [2021] presents a method to extract graph properties that are predictive of the dynamical behavior of multivariate, discrete models of biochemical regulation. In other words, a method that uses only…
We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental…
We prove the well posedness of a class of non linear and non local mixed hyperbolic-parabolic systems in bounded domains, with Dirichlet boundary conditions. In view of control problems, stability estimates on the dependence of solutions on…
Port-Hamiltonian neural networks (pHNNs) are emerging as a powerful modeling tool that integrates physical laws with deep learning techniques. While most research has focused on modeling the entire dynamics of interconnected systems, the…
We present a Bayesian hierarchical multi-view mixture model termed Symphony that simultaneously learns clusters of cells representing cell types and their underlying gene regulatory networks by integrating data from two views: single-cell…
This paper deals with the computation of polytopic invariant sets for polynomial dynamical systems. An invariant set of a dynamical system is a subset of the state space such that if the state of the system belongs to the set at a given…
A model of the heart tissue as a conductive system with two interacting pacemakers and a refractory time, is proposed. In the parametric space of the model the phase locking areas are investigated in detail. Obtained results allow us to…
When no arterial input function is available, quantification of dynamic PET images requires a previous step devoted to the extraction of a reference time-activity curve (TAC). Factor analysis is often applied for this purpose. This paper…
This paper proposes new parametric model adequacy tests for possibly nonlinear and nonstationary time series models with noncontinuous data distribution, which is often the case in applied work. In particular, we consider the correct…
Molecular dynamics simulations allow to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained…
Background: Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time…
In biomedical applications it is often necessary to estimate a physiological response to a treatment consisting of multiple components, and learn the separate effects of the components in addition to the joint effect. Here, we extend…