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Updated: May 24, 2026
05:15
The (Spatial) Memory Game: Testing the Relationship Between Spatial Language, Object Knowledge, and Spatial Cognition
Published on: February 19, 2018
Description languages as modelling decisions: A comment on Wheeler and Varón (2025).
1Meise Botanic Garden, Meise, Belgium.
Summary
Phylogenetic Minimum Description Length (PMDL) uses algorithmic complexity for phylogenetic inference. However, its graph penalties are not solely determined by complexity but by chosen description languages, reflecting external modeling assumptions.
Area of Science:
- Evolutionary Biology
- Computational Biology
- Phylogenetics
Background:
- Phylogenetic Minimum Description Length (PMDL) is an optimality criterion for phylogenetic inference.
- PMDL is grounded in algorithmic (Kolmogorov) complexity and the Minimum Description Length (MDL) principle.
- The naturalness of PMDL's graph complexity penalties requires careful interpretation within the MDL framework.
Purpose of the Study:
- To critically evaluate the claim that PMDL's graph complexity penalties are 'natural' and 'not externally specified'.
- To clarify the role of description languages in encoding background assumptions within the MDL and PMDL frameworks.
- To highlight that external modeling decisions influence PMDL's penalties and interpretation.
Main Methods:
- Analysis of the MDL principle and its application to phylogenetic inference.
- Examination of description languages as implicit priors in model selection.
- Interpretation of graph complexity penalties in PMDL, particularly for phylogenetic networks.
Main Results:
- PMDL's graph complexity penalties are conditional on the chosen description language, not solely algorithmic complexity.
- The choice of description language represents a substantive external modeling decision.
- Both graph and model complexity in PMDL are influenced by these encoding choices.
Conclusions:
- PMDL's penalties are 'natural' only relative to a fixed description language.
- The selection of a description language for phylogenetic graphs is a crucial external modeling choice.
- Explicitly acknowledging these assumptions enhances the interpretability and evaluability of PMDL within the MDL framework.
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