Related papers: RuleVis: Constructing Patterns and Rules for Rule-…
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…
We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing…
Cells process external and internal signals through chemical interactions. Cells that constitute the immune system (e.g., antigen presenting cell, T-cell, B-cell, mast cell) can have different functions (e.g., adaptive memory, inflammatory…
Detailed modeling and simulation of biochemical systems is complicated by the problem of combinatorial complexity, an explosion in the number of species and reactions due to myriad protein-protein interactions and post-translational…
With the growing adoption of machine learning techniques, there is a surge of research interest towards making machine learning systems more transparent and interpretable. Various visualizations have been developed to help model developers…
This paper gives an introduction to rule-based modelling applied to topics in infectious diseases. Rule-based models generalise reaction-based models with reagents that have internal state and may be bound together to form complexes, as in…
We provide a visualization model that targets the visualization of Protein-Protein Interactions(PPI) and combines it with a super view based on publications and methods to extract interactions. Although there are several existing tools, our…
Autonomous vehicles need to model the behavior of surrounding human driven vehicles to be safe and efficient traffic participants. Existing approaches to modeling human driving behavior have relied on both data-driven and rule-based…
Rule-based models are often used for data analysis as they combine interpretability with predictive power. We present RuleKit, a versatile tool for rule learning. Based on a sequential covering induction algorithm, it is suitable for…
We investigate the use of an extension of rule-based modelling for cellular signalling to create a structured space of model variants. This enables the incremental development of rule sets that start from simple mechanisms and which, by a…
In domains where transparency and trustworthiness are crucial, such as healthcare, rule-based systems are widely used and often preferred over black-box models for decision support systems due to their inherent interpretability. However, as…
We present a bigraphical framework suited for modeling biological systems both at protein level and at membrane level. We characterize formally bigraphs corresponding to biologically meaningful systems, and bigraphic rewriting rules…
Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent…
Model repair is an essential topic in model-driven engineering. Since models are suitably formalized as graph-like structures, we consider the problem of rule-based graph repair: Given a rule set and a graph constraint, try to construct a…
Graph rewrite formalisms are a powerful approach to modeling complex molecular systems. They capture the intrinsic concurrency of molecular interactions, thereby enabling a formal notion of mechanism (a partially ordered set of events) that…
Motivated by chemical reaction rules, we introduce a rule-based epidemiological framework for the systematic mathematical modelling of future pandemics. Here we stress that we do not have a specific model in mind, but a whole collection of…
Smart systems are characterised by their ability to analyse measured data in live and to react to changes according to expert rules. Therefore, such systems exploit appropriate data models together with actions, triggered by domain-related…
This paper highlights the rationale for the development of BioViz, a tool to help visualize the existence of collective user interactions in online life science communities. The first community studied has approximately 22,750 unique users…
Database schema elements such as tables, views, triggers and functions are typically defined with many interrelationships. In order to support database users in understanding a given schema, a rule-based approach for analyzing the…
In this short note we review deterministic simulation of biochemical pathways, i.e. networks of biochemical reactions obeying the law of mass action. It is meant as a basis for the MATLAB code, written by the author, which permits easy…