Related papers: Visualizing Regulation in Rule-based Models
Gene expression-based heterogeneity analysis has been extensively conducted. In recent studies, it has been shown that network-based analysis, which takes a system perspective and accommodates the interconnections among genes, can be more…
The ability of a cell to communicate with its environment is essential for key cellular functions like replication, metabolism, or cell fate decisions. The involved molecular mechanisms are highly dynamic and difficult to capture…
Biopharmaceutical manufacturing is a rapidly growing industry with impact in virtually all branches of medicines. Biomanufacturing processes require close monitoring and control, in the presence of complex bioprocess dynamics with many…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…
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…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
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…
Decision-making is a central yet under-defined goal in visualization research. While existing task models address decision processes, they often neglect the conditions framing a decision. To better support decision-making tasks, we propose…
Dynamical systems theory and complexity science provide powerful tools for analysing artificial agents and robots. Furthermore, they have been recently proposed also as a source of design principles and guidelines. Boolean networks are a…
Rule-based models, e.g., decision trees, are widely used in scenarios demanding high model interpretability for their transparent inner structures and good model expressivity. However, rule-based models are hard to optimize, especially on…
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…
Bioprocess mechanistic modeling is essential for advancing intelligent digital twin representation of biomanufacturing, yet challenges persist due to complex intracellular regulation, stochastic system behavior, and limited experimental…
Street-level visual appearances play an important role in studying social systems, such as understanding the built environment, driving routes, and associated social and economic factors. It has not been integrated into a typical…
Biologists are leading current research on genome characterization (sequencing, alignment, transcription), providing a huge quantity of raw data about many genome organisms. Extracting knowledge from this raw data is an important process…
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…
Simulations with an explicit description of intermolecular forces using electronic structure methods are still not feasible for many systems of interest. As a result, empirical methods such as force fields (FF) have become an established…
Humans have the ability to seamlessly combine low-level visual input with high-level symbolic reasoning often in the form of recognising objects, learning relations between them and applying rules. Neuro-symbolic systems aim to bring a…
Researchers got success in mining the Web usage data effectively and efficiently. But representation of the mined patterns is often not in a form suitable for direct human consumption. Hence mechanisms and tools that can represent mined…
Over the past decades, classification models have proven to be essential machine learning tools given their potential and applicability in various domains. In these years, the north of the majority of the researchers had been to improve…
In some entertainment and virtual reality applications, it is necessary to model and draw the real world realistically, so as to improve the fidelity of natural scenes and make users have a better sense of immersion. However, due to the…