Related papers: Modular model building
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new…
Mathematical modelling has a long history in the context of collective cell migration, with applications throughout development, disease and regenerative medicine. The aim of modelling in this context is to provide a framework in which to…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
We develop a framework for combining differentiable programming languages with neural networks. Using this framework we create end-to-end trainable systems that learn to write interpretable algorithms with perceptual components. We explore…
Like other types of computational research, modeling and simulation of biological processes (biomodels) is still largely communicated without sufficient detail to allow independent reproduction of results. But reproducibility in this area…
The growing complexity of modern practical problems puts high demands on the mathematical modelling. Given that various models can be used for modelling one physical phenomenon, the role of model comparison and model choice becomes…
Computer-based modelling and simulation have become useful tools to facilitate humans to understand systems in different domains, such as physics, astrophysics, chemistry, biology, economics, engineering and social science. A complex system…
In spite of machine learning's rapid growth, its engineering support is scattered in many forms, and tends to favor certain engineering stages, stakeholders, and evaluation preferences. We envision a capability-based framework, which uses…
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…
Scaling model capacity has been vital in the success of deep learning. For a typical network, necessary compute resources and training time grow dramatically with model size. Conditional computation is a promising way to increase the number…
A number of machine learning models have been proposed with the goal of achieving systematic generalization: the ability to reason about new situations by combining aspects of previous experiences. These models leverage compositional…
In a Systems Engineering setting, various models are produced using a variety of methods and tools. Focusing on a type of models -- called descriptive models -- which we shall describe, we argue that, while the clarity and precision of…
Training a Neural Network (NN) with lots of parameters or intricate architectures creates undesired phenomena that complicate the optimization process. To address this issue we propose a first modular approach to NN design, wherein the NN…
Integrating diverse formalisms into modular knowledge representation systems offers increased expressivity, modeling convenience and computational benefits. We introduce concepts of abstract modules and abstract modular systems to study…
Piecewise smooth hybrid systems, involving continuous and discrete variables, are suitable models for describing the multiscale regulatory machinery of the biological cells. In hybrid models, the discrete variables can switch on and off…
Cellular Agent-Based Models are commonly employed to describe a variety biological systems. Over the course of the past years, many modeling tools have emerged which solve particular research questions. In this short opinion piece, we argue…
Coordinating multi-articulated bodies to generate purposeful movement is a formidable computational challenge. Yet the human motor system performs this task robustly in dynamic, uncertain environments, despite noisy and delayed feedback,…
A simple model for the formation of a complex organism is introduced. Individuals can communicate and specialize, leading to an increase in productivity. If there are limits to the capacity of individuals to communicate with other…
Interconnected ensembles of biological entities are perhaps some of the most complex systems that modern science has encountered so far. In particular, scientists have concentrated on understanding how the complexity of the interacting…