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We use deep learning to model interactions across two or more sets of objects, such as user-movie ratings, protein-drug bindings, or ternary user-item-tag interactions. The canonical representation of such interactions is a matrix (or a…

We introduce the BioBeta Framework, a meta-model for both protein-level and membrane-level interactions of living cells. This formalism aims to provide a formal setting where to encode, compare and merge models at different abstraction…

Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…

Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…

Continuous adaptation allows survival in an ever-changing world. Adjustments in the synaptic coupling strength between neurons are essential for this capability, setting us apart from simpler, hard-wired organisms. How these changes can be…

Molecular relational learning, whose goal is to learn the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. Recently, graph neural networks have recently shown…

Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach tom odeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like…

We propose RecSim, a configurable platform for authoring simulation environments for recommender systems (RSs) that naturally supports sequential interaction with users. RecSim allows the creation of new environments that reflect particular…

Recent years have seen the rise of statistical program learning based on neural models as an alternative to traditional rule-based systems for programming by example. Rule-based approaches offer correctness guarantees in an unsupervised way…

Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…

The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…

Urban traffic regulation policies are increasingly used to address congestion, emissions, and accessibility in cities, yet their impacts are difficult to assess due to the socio-technical complexity of urban mobility systems. Recent…

Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…

Multiscale models provide a unique tool for studying complex processes that study events occurring at different scales across space and time. In the context of biological systems, such models can simulate mechanisms happening at the…

To study implementations and optimisations of interaction net systems we propose a calculus to allow us to reason about nets, a concrete data-structure that is in close correspondence with the calculus, and a low-level language to create…

This study explores the application of elongated particle interaction models, traditionally used in liquid crystal phase research, in the context of early bacterial biofilm development. Through computer simulations using an agent-based…

Multi-valued logical models can be used to describe biological networks on a high level of abstraction based on the network structure and logical parameters capturing regulatory effects. Interestingly, the dynamics of two distinct models…

Investigating the relation between the structure and behavior of complex biological networks often involves posing the following two questions: Is a hypothesized structure of a regulatory network consistent with the observed behavior? And…

In general, many dynamic processes are involved with interacting variables, from physical systems to sociological analysis. The interplay of components in the system can give rise to confounding dynamic behavior. Many approaches model…

Critical points separate distinct dynamical regimes of complex systems, often delimiting functional or macroscopic phases in which the system operates. However, the long-term prediction of critical regimes and behaviors is challenging given…