Related papers: Of (Biological) Models and Simulations
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
CONTEXT: There is growing interest in establishing software engineering as an evidence-based discipline. To that end, replication is often used to gain confidence in empirical findings, as opposed to reproduction where the goal is showing…
The nature of the scientific method is controversial with claims that a single scientific method does not even exist. However the scientific method does exist. It is the building of logical and self consistent models to describe nature. The…
We advocate the use of qualitative models in the analysis of large biological systems. We show how qualitative models are linked to theoretical differential models and practical graphical models of biological networks. A new technique for…
This thesis is about the study of complex systems through simple models. Our work evidences the relevance of this kind of modeling in science, which provides us with a better understanding of nature at minimum cost. The fundamentals tools…
As the world's democratic institutions are challenged by dissatisfied citizens, political scientists and also computer scientists have proposed and analyzed various (innovative) methods to select representative bodies, a crucial task in…
Researchers in physics education have advocated both for including modeling in science classrooms as well as promoting student engagement with sensemaking. These two processes facilitate the generation of new knowledge by connecting to…
Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript…
Quantitative social science is not only about regression analysis or, in general, data inference. Computer simulations of social mechanisms have a 60-year long history. They have been used for many different purposes -- to test scenarios,…
In recent years, human behavior simulation has drawn increasing attention from both academia and industry. The reasons fall into two aspects. First, simulation serves as a critical tool for understanding human behaviors, which has become…
We consider problems in which robots conspire to present a view of the world that differs from reality. The inquiry is motivated by the problem of validating robot behavior physically despite there being a discrepancy between the robots we…
It is essential to find new ways of enabling experts in different disciplines to collaborate more efficient in the development of ever more complex systems, under increasing market pressures. One possible solution for this challenge is to…
Experience in the physical sciences suggests that the only realistic means of understanding complex systems is through the use of mathematical models. Typically, this has come to mean the identification of quantitative models expressed as…
Model biomembrane systems play a crucial role in advancing biomedical research by providing simplified yet effective platforms for exploring complex biological mechanisms. These systems span a wide range of scales, from…
Conceptual modeling has been an important part of constructionist educational practices for many years, particularly in STEM (Science, Technology, Engineering and Mathematics) disciplines. What is not so common is using agent-based…
We develop a qualitative model of decision making with two aims: to describe how people make simple decisions and to enable computer programs to do the same. Current approaches based on Planning or Decisions Theory either ignore uncertainty…
Simulation is used extensively in autonomous systems, particularly in robotic manipulation. By far, the most common approach is to train a controller in simulation, and then use it as an initial starting point for the real system. We…
Advances in biology have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. Theoretical biology used to primarily provide a basis to rationally examine the frameworks…
Computer experiments refer to the study of real systems using complex simulation models. They have been widely used as alternatives to physical experiments. Design and analysis of computer experiments have attracted great attention in past…