Major changes and updates to AlgebraicStatistics #5228
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micjoswig merged 647 commits intooscar-system:masterfrom Nov 24, 2025
Merged
Major changes and updates to AlgebraicStatistics #5228micjoswig merged 647 commits intooscar-system:masterfrom
micjoswig merged 647 commits intooscar-system:masterfrom
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antonydellavecchia
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Data for small phylogenetic trees and loading them will appear in a separate pr. |
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…v/phylo-tree-in-model
Co-authored-by: Benjamin Lorenz <benlorenz@users.noreply.github.com>
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Co-authored-by: Benjamin Lorenz <benlorenz@users.noreply.github.com>
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@micjoswig @antonydellavecchia thank you for working on this and getting it in! One minor technical nitpick: when doing a squash merge, it is often a good idea to consider cleaning out the commit description generated by GitHub, esp. if there were a lot of commits involved -- in this case, it generated a 492 line commit message most of which is effectively garbage (titles of working commits etc.). |
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Currently there are still things to be done, but seeing as this pull request will be large I think it makes sense to get people's eyes on the changes earlier rather than later.
The main idea for the changes are that there are three (and a half) main types of graphical models and they are all subtypes of the abstract type
GraphicalModel.We introduce these types as being parametrized by their underlying graphs, but also the labels of the graph.
In this way functions can be overloaded when the graphs have certain labelings, this leads to less code duplication since users looking to extend functionality for their particular graph labelings need only overload the functions that require changes while still having access to the generic pipeline (eventually ended at taking the vanishing ideal).