Tag: model

Genetic Algorithms for model refinement and rule discovery in a high-dimensional agent-based model of inflammation

Introduction: Agent-based modeling frequently used modeling method for multi-scale mechanistic modeling. However, the same properties that make agent-based models (ABMs) well suited to representing biological systems also present significant challenges with respect to their construction and calibration, particularly with respect to the large number of free parameters often present in these models. The challenge of…
Read more

Fully Interpretable Deep Learning Model of Transcriptional Control

The universal expressibility assumption of Deep Neural Networks (DNN) is the key motivation behind recent work in the system biology community to employ DNNs to solve important problems in functional genomics and molecular genetics. Because of the black-box nature of DNN, such assumptions, while useful in practice, are unsatisfactory for scientific analysis. In this paper,…
Read more

Nested Active Learning for Efficient Model Contextualization and Parameterization

The description of the environment in which a biomedical simulation operates (model context) and parameterization of internal model rules (model content) requires the optimization of a large number of free-parameters; given the wide range of variable combinations, along with the intractability of ab initio modeling techniques which could be used to constrain these combinations, an…
Read more