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[ENH] MI and CMI simulation module and relevant estimators from the forest #83

Merged
merged 19 commits into from
Jun 20, 2023
Merged

[ENH] MI and CMI simulation module and relevant estimators from the forest #83

merged 19 commits into from
Jun 20, 2023

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adam2392
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Fixes #49
Fixes #48
Supersedes: #58

Changes proposed in this pull request:

  • simulation for MI and CMI data

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  • I've updated or added any relevant docstrings following the syntax described in the
    Writing docstrings section of the CONTRIBUTING docs.
  • If this PR fixes a bug, I've added a test that will fail without my fix.
  • If this PR adds a new feature, I've added tests that sufficiently cover my new functionality.

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@adam2392
Merge other branch
15699ce 
Signed-off-by: Adam Li <adam2392@gmail.com>
@adam2392
Add experiemntal subdir
3e63af5 
Signed-off-by: Adam Li <adam2392@gmail.com>
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codecov bot commented Jun 12, 2023 •
edited
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Codecov Report

Patch coverage: 69.21% and project coverage change: -7.07 ⚠️

Comparison is base (2768558) 93.39% compared to head (7463904) 86.33%.

Additional details and impacted files 
@@            Coverage Diff             @@
##             main      #83      +/-   ##
==========================================
- Coverage   93.39%   86.33%   -7.07%     
==========================================
  Files          16       24       +8     
  Lines        1469     1924     +455     
==========================================
+ Hits         1372     1661     +289     
- Misses         97      263     +166
Impacted Files Coverage Δ
sktree/experimental/mutual_info.py 20.51% <20.51%> (ø)
sktree/experimental/tests/test_mutual_info.py 62.06% <62.06%> (ø)
sktree/tree/_marginalize.py 76.74% <76.74%> (ø)
sktree/neighbors.py 86.20% <86.20%> (ø)
sktree/experimental/simulate.py 88.13% <88.13%> (ø)
sktree/__init__.py 79.16% <100.00%> (+0.90%) ⬆️
sktree/ensemble/_supervised_forest.py 100.00% <100.00%> (ø)
sktree/ensemble/_unsupervised_forest.py 70.63% <100.00%> (+0.23%) ⬆️
sktree/experimental/__init__.py 100.00% <100.00%> (ø)
sktree/experimental/tests/test_simulate.py 100.00% <100.00%> (ø)
... and 6 more

☔ View full report in Codecov by Sentry.
📢 Do you have feedback about the report comment? Let us know in this issue.

@adam2392
WIP to add marginalization capabilities
b688edc 
Signed-off-by: Adam Li <adam2392@gmail.com>
@adam2392
Update to most recent changes in sklearn fork
6ed89c5 
Signed-off-by: Adam Li <adam2392@gmail.com>
@adam2392
Tighten up the marginalization implementation
30bf7e7 
Signed-off-by: Adam Li <adam2392@gmail.com>
adam2392
adam2392 commented Jun 15, 2023
View reviewed changes
sktree/tree/_marginalize.py
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@adam2392 adam2392 Jun 15, 2023 •
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@YuxinB @PSSF23 @jovo in case you're interested, this is the method for marginalizing a fitted tree using the ideas that have been discussed.

This file and _marginal.pyx are the core files.

Specifically, I implement some ideas for traversing the tree, while "marginalizing out features".

@adam2392
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Next, I need to add now a simulation using a fitted forest and computing a bunch of quantities for MI/CMI

@adam2392
Update fork
9ab9fa3 
Signed-off-by: Adam Li <adam2392@gmail.com>
@adam2392
Merge branch 'cmi' of https://github.com/neurodata/scikit-tree into cmi
cf02d54
@adam2392
Add force
318c0e8 
Signed-off-by: Adam Li <adam2392@gmail.com>
@adam2392
Working nn meta estimator
7360056 
Signed-off-by: Adam Li <adam2392@gmail.com>
@adam2392
Refactor neighbors API and introduce the meta neighbors estimators
5c6b795 
Signed-off-by: Adam Li <adam2392@gmail.com>
@adam2392
Update submodule
d341146 
Signed-off-by: Adam Li <adam2392@gmail.com>
@adam2392
Fix
b493b49 
Signed-off-by: Adam Li <adam2392@gmail.com>
@adam2392
Fix
d1b5aba 
Signed-off-by: Adam Li <adam2392@gmail.com>
@adam2392
Update submodule
8d57305 
Signed-off-by: Adam Li <adam2392@gmail.com>
@adam2392
Update fork version
e9838c5 
Signed-off-by: Adam Li <adam2392@gmail.com>
@adam2392
Update fork version
debffb1 
Signed-off-by: Adam Li <adam2392@gmail.com>
@adam2392
Fixed docs
8b06c45 
Signed-off-by: Adam Li <adam2392@gmail.com>
@adam2392
Fix circleci
7463904 
Signed-off-by: Adam Li <adam2392@gmail.com>
@adam2392 adam2392 merged commit 7eb96e6 into main Jun 20, 2023
@adam2392 adam2392 deleted the cmi branch June 20, 2023 17:53
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