English

Rule-based Modelling and Tunable Resolution

Other Computer Science 2009-11-16 v1
Authors: Russ Harmer
View on arXiv ↗ PDF ↗ DOI ↗

Abstract

We investigate the use of an extension of rule-based modelling for cellular signalling to create a structured space of model variants. This enables the incremental development of rule sets that start from simple mechanisms and which, by a gradual increase in agent and rule resolution, evolve into more detailed descriptions.

Keywords

information modeling machine learning

Cite

@article{arxiv.0911.2508,
  title  = {Rule-based Modelling and Tunable Resolution},
  author = {Russ Harmer},
  journal= {arXiv preprint arXiv:0911.2508},
  year   = {2009}
}

Related papers

View all related →
Machine Learning · Computer Science
The Shape of Explanations: A Topological Account of Rule-Based Explanations in Machine Learning
Brett Mullins
2023-01-24
Artificial Intelligence · Computer Science
A knowledge representation meta-model for rule-based modelling of signalling networks
Adrien Basso-Blandin, Walter Fontana, Russ Harmer
2016-08-22
Machine Learning · Computer Science
Separating Rule Discovery and Global Solution Composition in a Learning Classifier System
Michael Heider, Helena Stegherr, Jonathan Wurth, Roman Sraj +1
2022-04-21
Quantitative Methods · Quantitative Biology
Mathematical modeling of variability in intracellular signaling
Carolin Loos, Jan Hasenauer
2019-04-18
Cell Behavior · Quantitative Biology
Agent-Based Modelling in Cellular Biology - Are we flexible yet?
Jonas Pleyer
2025-11-18
Quantitative Methods · Quantitative Biology
Simulating Organogenesis in COMSOL: Cell-based Signaling Models
Jannik Vollmer, Denis Menshykau, Dagmar Iber
2013-09-26
Molecular Networks · Quantitative Biology
An Introduction to Rule-based Modeling of Immune Receptor Signaling
John A. P. Sekar, James R. Faeder
2017-09-21
Cell Behavior · Quantitative Biology
Mapping, modeling, and reprogramming cell-fate decision making systems
Lucy Ham, Taylor E. Woodford, Megan A. Coomer, Michael P. H. Stumpf
2024-12-03
Cellular Automata and Lattice Gases · Physics
Self-referencing cellular automata: A model of the evolution of information control in biological systems
Theodore P. Pavlic, Alyssa M. Adams, Paul C. W. Davies, Sara Imari Walker
2014-07-11
Machine Learning · Computer Science
Generalized Linear Rule Models
Dennis Wei, Sanjeeb Dash, Tian Gao, Oktay Günlük
2019-06-06
Machine Learning · Statistics
Obtaining Explainable Classification Models using Distributionally Robust Optimization
Sanjeeb Dash, Soumyadip Ghosh, Joao Goncalves, Mark S. Squillante
2023-11-06
Biological Physics · Physics
Adjusting the range of cell-cell communication enables fine-tuning of cell fate patterns from checkerboard to engulfing
Simon Schardt, Sabine C. Fischer
2022-11-15
Machine Learning · Computer Science
Rule-Mining based classification: a benchmark study
Margaux Luck, Nicolas Pallet, Cecilia Damon
2017-07-03
Computational Complexity · Computer Science
Extension of cellular automata by introducing an algorithm of recursive estimation of neighbors
Yoshihiko Kayama
2015-12-22
Multiagent Systems · Computer Science
Models we Can Trust: Toward a Systematic Discipline of (Agent-Based) Model Interpretation and Validation
Gabriel Istrate
2021-02-24
Software Engineering · Computer Science
Rule-based Graph Repair
Christian Sandmann, Annegret Habel
2019-12-23
Quantitative Methods · Quantitative Biology
How high-resolution agent-based models can improve fundamental insights in tissue development and cell culturing methods
Paul Van Liedekerke, Jiří Pešek, Kevin Alessandri, Dirk Drasdo
2026-01-22
Programming Languages · Computer Science
Typing rule-based transformations over topological collections
Julien Cohen
2009-12-25
Other Computer Science · Computer Science
Rule based End-to-End Learning Framework for Urban Growth Prediction
Saptarshi Pal, Soumya K Ghosh
2018-05-30
Artificial Intelligence · Computer Science
Towards Exploratory Reformulation of Constraint Models
Ian Miguel, András Z. Salamon, Christopher Stone
2023-11-21
Molecular Networks · Quantitative Biology
The evolution of systems biology and systems medicine: From mechanistic models to uncertainty quantification
Lingxia Qiao, Ali Khalilimeybodi, Nathaniel J Linden-Santangeli, Padmini Rangamani
2024-08-13
Machine Learning · Computer Science
Learning Structured Declarative Rule Sets -- A Challenge for Deep Discrete Learning
Johannes Fürnkranz, Eyke Hüllermeier, Eneldo Loza Mencía, Michael Rapp
2020-12-09
Quantitative Methods · Quantitative Biology
A seven-step guide to spatial, agent-based modelling of tumour evolution
Blair Colyer, Maciej Bak, David Basanta, Robert Noble
2023-11-08
Artificial Intelligence · Computer Science
Rule-Based Semantic Sensing
Przemyslaw Woznowski, Alun Preece
2015-03-19
Quantitative Methods · Quantitative Biology
Emerging whole-cell modeling principles and methods
Arthur P. Goldberg, Balázs Szigeti, Yin Hoon Chew, John A. P. Sekar +2
2019-09-05
R2 v1 2026-06-21T14:11:00.749Z