Related papers: Prospects for Declarative Mathematical Modeling of…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
Declarative approaches to process modeling are regarded as well suited for highly volatile environments as they provide a high degree of flexibility. However, problems in understanding and maintaining declarative business process models…
Declarative machine learning (ML) aims at the high-level specification of ML tasks or algorithms, and automatic generation of optimized execution plans from these specifications. The fundamental goal is to simplify the usage and/or…
In this paper, we present an approach to define the semantics for object-oriented modeling languages. One important property of this semantics is to support underspecified and incomplete models. To this end, semantics is given as predicates…
Formalisms for specifying statistical models, such as probabilistic-programming languages, typically consist of two components: a specification of a stochastic process (the prior), and a specification of observations that restrict the…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
Computational models are quantitative representations of systems. By analyzing and comparing the outputs of such models, it is possible to gain a better understanding of the system itself. Though as the complexity of model outputs…
We introduce the Declaratron, a system which takes a declarative approach to specifying mathematically based scientific computation. This uses displayable mathematical notation (Content MathML) and is both executable and semantically well…
Agent-based models (ABMs) are ubiquitous in research and industry. Currently, simulating ABMs involves at least some imperative (step-by-step) computer instructions. An alternative approach is declarative programming, in which a set of…
Modern numerical models are increasingly complex, opaque, and computationally expensive, yet frequently fail to predict even qualitative features of observed phenomena. We propose a new paradigm, Declarative Bespoke Modelling, in which the…
Mathematical models are increasingly used in both academia and the pharmaceutical industry to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations…
High-dimensional distributed semantic spaces have proven useful and effective for aggregating and processing visual, auditory, and lexical information for many tasks related to human-generated data. Human language makes use of a large and…
We present a general theory and corresponding declarative model for the embodied grounding and natural language based analytical summarisation of dynamic visuo-spatial imagery. The declarative model ---ecompassing spatio-linguistic…
Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory. One advantage of symbolic computation is its potential for qualitative answers to…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
Modeling biological processes is a highly demanding task because not all processes are fully understood. Mathematical models allow us to test hypotheses about possible mechanisms of biological processes. The mathematical mechanisms…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
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…
Complex systems' modeling and simulation are powerful ways to investigate a multitude of natural phenomena providing extended knowledge on their structure and behavior. However, enhanced modeling and simulation require integration of…