Batched inference CEBRA & padding at the `Solver` level#168

Merged

MMathisLab merged 107 commits intoAdaptiveMotorControlLab:mainfrom

CeliaBenquet:batched-inference-and-padding

May 23, 2025

Commits on Aug 23, 2024

first proposal for batching in tranform method

gonlairo
authored and
stes
committed
first running version of padding with batched inference

gonlairo
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stes
committed
start tests

gonlairo
authored and
stes
committed
add pad_before_transform to fit function and add support for convolutional models in _transform

gonlairo
authored and
stes
committed
remove print statements

gonlairo
authored and
stes
committed
first passing test

gonlairo
authored and
stes
committed
add support for hybrid models

gonlairo
authored and
stes
committed
rewrite transform in sklearn API

gonlairo
authored and
stes
committed
baseline version of a torch.Datset

gonlairo
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stes
committed
move batching logic outside solver

gonlairo
authored and
stes
committed
move functionality to base file in solver and separate in functions

gonlairo
authored and
stes
committed
add test_select_model for single session

gonlairo
authored and
stes
committed
add checks and test for _process_batch

gonlairo
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stes
committed
add test_select_model for multisession

gonlairo
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stes
committed
make self.num_sessions compatible with single session training

gonlairo
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stes
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improve test_batched_transform_singlesession

gonlairo
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stes
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make it work with small batches

gonlairo
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stes
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make test with multisession work

gonlairo
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stes
committed
change to torch padding

gonlairo
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stes
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add argument to sklearn api

gonlairo
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stes
committed
add torch padding to _transform

gonlairo
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stes
committed
convert to torch if numpy array as inputs

gonlairo
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stes
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add distinction between pad with data and pad with zeros and modify test accordingly

gonlairo
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stes
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differentiate between data padding and zero padding

gonlairo
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stes
committed
remove float16

gonlairo
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stes
committed
change argument position

gonlairo
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stes
committed
clean test

gonlairo
authored and
stes
committed
clean test

gonlairo
authored and
stes
committed
Fix warning

CeliaBenquet
authored and
stes
committed
Improve modularity remove duplicate code and todos

CeliaBenquet
authored and
stes
committed
Add tests to solver

CeliaBenquet
authored and
stes
committed
Remove unused import in solver/utils

CeliaBenquet
authored and
stes
committed
Fix test plot

CeliaBenquet
authored and
stes
committed
Add some coverage

CeliaBenquet
authored and
stes
committed
Fix save/load

CeliaBenquet
authored and
stes
committed
Remove duplicate configure_for in multi dataset

CeliaBenquet
authored and
stes
committed
Make save/load cleaner

CeliaBenquet
authored and
stes
committed

Commits on Sep 19, 2024

Add review updates
CeliaBenquet
committed

Commits on Oct 20, 2024

Commits on Oct 27, 2024

Commits on Jan 21, 2025

Concatenate last batches for batched inference (#200)
CeliaBenquet
authored

Commits on Apr 23, 2025

Fix linting errors in tests (#188)

stes
authored and
CeliaBenquet
committed
Fix `scikit-learn` reference in conda environment files (#195)

stes
authored and
CeliaBenquet
committed
Add support for new __sklearn_tags__ (#205)

stes
authored and
CeliaBenquet
committed
Update workflows to actions/setup-python@v5, actions/cache@v4 (#212)

stes
authored and
CeliaBenquet
committed
Fix deprecation warning force_all_finite -> ensure_all_finite for sklearn>=1.6 (#206)

icarosadero
authored and
CeliaBenquet
committed
Add tests to check legacy model loading (#214)

stes
authored and
CeliaBenquet
committed
Add improved goodness of fit implementation (#190)

stes
and
CeliaBenquet
committed
Support numpy 2, upgrade tests to support torch 2.6 (#221)

stes
authored and
CeliaBenquet
committed
Release 0.5.0rc1 (#189)

authored and
CeliaBenquet
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Fix pypi action (#222)

stes
authored and
CeliaBenquet
committed
Update base.py (#224)

icarosadero
authored and
CeliaBenquet
committed
Change max consistency value to 100 instead of 99 (#227)

committed
Update assets.py --> force check for parent dir (#230)

MMathisLab
authored and
CeliaBenquet
committed
User docs minor edit (#229)

authored and
CeliaBenquet
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General Doc refresher (#232)

authored and
CeliaBenquet
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render plotly in our docs, show code/doc version (#231)

MMathisLab
authored and
CeliaBenquet
committed
Update layout.html (#233)

MMathisLab
authored and
CeliaBenquet
committed
Update conf.py (#234)

MMathisLab
authored and
CeliaBenquet
committed
Refactoring setup.cfg (#228)

MMathisLab
authored and
CeliaBenquet
committed
Home page landing update (#235)

MMathisLab
authored and
CeliaBenquet
committed
v0.5.0 (#238)

MMathisLab
authored and
CeliaBenquet
committed
Upgrade docs build (#241)

stes
authored and
CeliaBenquet
committed
Allow indexing of the cebra docs (#242)

stes
authored and
CeliaBenquet
committed
Fix broken docs coverage workflows (#246)

stes
authored and
CeliaBenquet
committed
Add xCEBRA implementation (AISTATS 2025) (#225)

authored and
CeliaBenquet
committed
start tests

gonlairo
authored and
CeliaBenquet
committed
remove print statements

gonlairo
authored and
CeliaBenquet
committed
first passing test

gonlairo
authored and
CeliaBenquet
committed
move functionality to base file in solver and separate in functions

gonlairo
authored and
CeliaBenquet
committed
add test_select_model for multisession

gonlairo
authored and
CeliaBenquet
committed
remove float16

gonlairo
authored and
CeliaBenquet
committed
Improve modularity remove duplicate code and todos
CeliaBenquet
committed
Add tests to solver
CeliaBenquet
committed
Fix save/load
CeliaBenquet
committed
Fix extra docs errors
CeliaBenquet
committed
Add review updates
CeliaBenquet
committed
apply ruff auto-fixes

stes
authored and
CeliaBenquet
committed
fix linting errors

stes
authored and
CeliaBenquet
committed
Run isort, ruff, yapf
CeliaBenquet
committed
Merge remote-tracking branch 'upstream/main' into batched-inference-and-padding
CeliaBenquet
committed
Merge branch 'main' into batched-inference-and-padding
MMathisLab
authored

Commits on Apr 25, 2025

Commits on Apr 28, 2025

Commits on Apr 30, 2025

Fix docs error
CeliaBenquet
committed

Commits on May 2, 2025

Add tests on the private functions in base solver
CeliaBenquet
committed

Commits on May 5, 2025