Related papers: Towards modular verification of pathways: fairness…

Revealing possible long-living coherence in ultrafast processes allows detecting genuine quantum mechanical effects in molecules. To investigate such effects from a quantum chemistry perspective, we have developed a method for simulating…

Many practical problems can be understood as the search for a state of affairs that extends a fixed partial state of affairs, the \emph{environment}, while satisfying certain conditions that are formally specified. Such problems are found…

Under mass-action kinetics, biochemical reaction networks give rise to polynomial autonomous dynamical systems whose parameters are often difficult to estimate. We deal in this paper with the problem of identifying the kinetic parameters of…

Probabilistic graphical models are a fundamental tool in probabilistic modeling, machine learning and artificial intelligence. They allow us to integrate in a natural way expert knowledge, physical modeling, heterogeneous and correlated…

The evaluation of collective modes is fundamental in the analysis of molecular dynamics simulations. Several methods are available to extract that information, i.e normal mode analysis, principal component and spectral analysis of…

Reaction networks in the bulk and on surfaces are widespread in physical, chemical and biological systems. In macroscopic systems, which include large populations of reactive species, stochastic fluctuations are negligible and the reaction…

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These…

Bond graphs can be used to build thermodynamically-compliant hierarchical models of biomolecular systems. As bond graphs have been widely used to model, analyse and synthesise engineering systems, this paper suggests that they can play the…

Rule-based modeling is a powerful way to model kinetic interactions in biochemical systems. Rules enable a precise encoding of biochemical interactions at the resolution of sites within molecules, but obtaining an integrated global view…

In molecular communications, the direct detection of signaling molecules may be challenging due to a lack of suitable sensors and interference in the environment. Motivated by research in molecular biology, we investigate an indirect…

Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…

Compositionality supports the manipulation of large systems by working on their components. For model-based testing, this means that large systems can be tested by modelling and testing their components: passing tests for all components…

Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various…

Equations of motion that recognize biochemical patterns are described. The equations are partial differential equations in a continuous multiple component system in which adequate initial and boundary conditions are given. The biochemical…

Detecting and characterising vehicles is one of the purposes of embedded systems used in intelligent environments. An analysis of a vehicle characteristics can reveal inappropriate or dangerous behaviour. This detection makes it possible to…

Modelling complex real-world situations such as infectious diseases, geological phenomena, and biological processes can present a dilemma: the computer model (referred to as a simulator) needs to be complex enough to capture the dynamics of…

Verifying the truthfulness of claims usually requires joint multi-modal reasoning over both textual and visual evidence, such as analyzing both textual caption and chart image for claim verification. In addition, to make the reasoning…

Validation is often defined as the process of determining the degree to which a model is an accurate representation of the real world from the perspective of its intended uses. Validation is crucial as industries and governments depend…

Quantum computing will change the way we tackle certain problems. It promises to dramatically speed-up many chemical, financial, and machine-learning applications. However, to capitalize on those promises, complex design flows composed of…

Recent work has raised concerns on the risk of spurious correlations and unintended biases in statistical machine learning models that threaten model robustness and fairness. In this paper, we propose a simple and intuitive regularization…