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Adding model with cycle consistency and VampPrior #2421

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a582251
add model and tests
Hrovatin Jan 14, 2024
bb359ac
update documentation
Hrovatin Jan 14, 2024
14e41f1
move embedding to device
Hrovatin Jan 14, 2024
5863b1f
Merge branch 'main' into main
martinkim0 Jan 19, 2024
3f49266
pr comments
Hrovatin Jan 21, 2024
6605682
Merge branch 'main' of https://github.com/Hrovatin/scvi-tools
Hrovatin Jan 21, 2024
3319fc8
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martinkim0 Jan 22, 2024
3a67d1c
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martinkim0 Feb 5, 2024
5edad83
updates
Hrovatin Feb 7, 2024
a4b080e
Merge branch 'main' of https://github.com/Hrovatin/scvi-tools
Hrovatin Feb 7, 2024
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Merge branch 'main' into main
martinkim0 Feb 20, 2024
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pre-commit-ci[bot] Feb 20, 2024
8c25dba
Merge branch 'main' into main
martinkim0 Mar 11, 2024
c5f5c37
Update scvi/external/sysvi/_base_components.py
martinkim0 Mar 15, 2024
5b4838c
Update scvi/external/sysvi/_base_components.py
martinkim0 Mar 15, 2024
c885e20
Update scvi/external/sysvi/_base_components.py
martinkim0 Mar 15, 2024
661bbc6
Update scvi/external/sysvi/_model.py
martinkim0 Mar 15, 2024
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Update scvi/external/sysvi/_model.py
martinkim0 Mar 15, 2024
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Update scvi/external/sysvi/_model.py
martinkim0 Mar 15, 2024
e4c1ef9
Update scvi/external/sysvi/_model.py
martinkim0 Mar 15, 2024
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Update scvi/external/sysvi/_model.py
martinkim0 Mar 15, 2024
9e0cba9
Update scvi/external/sysvi/_model.py
martinkim0 Mar 15, 2024
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Update scvi/external/sysvi/_model.py
martinkim0 Mar 15, 2024
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merge
Hrovatin Sep 14, 2024
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Hrovatin Sep 14, 2024
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Merge branch 'main' of https://github.com/Hrovatin/scvi-tools
Hrovatin Sep 14, 2024
3c93e7f
merge
Hrovatin Sep 14, 2024
3e8ffd0
extend var documentation and remove unused "linear" mode
Hrovatin Sep 14, 2024
4ce4614
update var documentation
Hrovatin Sep 14, 2024
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[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 14, 2024
bdd2c7a
var activation to softplus
Hrovatin Sep 14, 2024
4507602
clarify pseudoinputs_data_indices description and assert it matches s…
Hrovatin Sep 14, 2024
cc19d91
also check ndim for pseudoinputs_data_indices
Hrovatin Sep 14, 2024
c15b8a2
remove obtainng cycle latent representations in user interface
Hrovatin Sep 14, 2024
aacdafe
latent always returns np and add option to return_dist
Hrovatin Sep 14, 2024
de6db13
bugfix
Hrovatin Sep 14, 2024
235767c
rm unused cycle latent retrieval
Hrovatin Sep 14, 2024
5f04d65
bugfix
Hrovatin Sep 14, 2024
69759ec
rm adata validation parts repeated in super
Hrovatin Sep 14, 2024
2e447c8
bugfix
Hrovatin Sep 14, 2024
9e8cc35
put back original _validate_anndata
Hrovatin Sep 14, 2024
b0829c0
remove too many custom checks from adata validation
Hrovatin Sep 14, 2024
bf2e850
covariate type explanation
Hrovatin Sep 14, 2024
bd5a882
revert var exp
Hrovatin Sep 14, 2024
7f50353
bugfix
Hrovatin Sep 14, 2024
01db60a
rm reconstr loss f that not reused
Hrovatin Sep 14, 2024
6cdd3d6
explain why cycle loss computed on standardized values
Hrovatin Sep 14, 2024
62eb924
add return statement
Hrovatin Sep 14, 2024
b9a9047
Merge branch 'main' of https://github.com/Hrovatin/scvi-tools
Hrovatin Sep 14, 2024
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Merge branch 'main' of https://github.com/scverse/scvi-tools
Hrovatin Oct 19, 2024
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[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 19, 2024
041c6a4
unify SysVI with scvi-tools code
Hrovatin Oct 20, 2024
7743c19
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 20, 2024
1641654
use adatamanager to access filed statistics
Hrovatin Oct 26, 2024
7c3bddc
documentation
Hrovatin Oct 26, 2024
eb872bc
Merge branch 'main' of https://github.com/Hrovatin/scvi-tools
Hrovatin Oct 26, 2024
5015e82
optionally change var activation function
Hrovatin Oct 27, 2024
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pre-commit-ci[bot] Oct 27, 2024
9b78ba3
documentation improvements
Hrovatin Oct 27, 2024
2aab4b4
Use real instead of mock covariates in cycle
Hrovatin Oct 27, 2024
1b50be1
improve documentation
Hrovatin Oct 27, 2024
1abf15d
Merge branch 'main' of https://github.com/Hrovatin/scvi-tools
Hrovatin Oct 27, 2024
6d32d89
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 27, 2024
2e59be7
improve documentation
Hrovatin Oct 27, 2024
4e0988e
fix bug introduced when renaming parameters in generative function
Hrovatin Oct 27, 2024
f0eb2b0
Merge branch 'main' of https://github.com/Hrovatin/scvi-tools
Hrovatin Oct 27, 2024
3f8be47
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 27, 2024
776a8e2
rename tests to prevent automatic test failure
Hrovatin Oct 27, 2024
ebbe1ca
Merge branch 'main' of https://github.com/Hrovatin/scvi-tools
Hrovatin Oct 27, 2024
35e3385
fix typo in docstring and formatting
Hrovatin Oct 27, 2024
4601808
ruff fixes
Hrovatin Oct 27, 2024
87a367e
bugfix in embedding of covariates
Hrovatin Nov 1, 2024
df4b335
bugfix in test for checking cov embeding
Hrovatin Nov 1, 2024
6a2e3eb
Change var activation to softplus
Hrovatin Nov 19, 2024
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2 changes: 1 addition & 1 deletion docs/tutorials/notebooks
Empty file added src/__init__.py
Empty file.
2 changes: 2 additions & 0 deletions src/scvi/external/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
from .scbasset import SCBASSET
from .solo import SOLO
from .stereoscope import RNAStereoscope, SpatialStereoscope
from .sysvi import SysVI
from .tangram import Tangram
from .velovi import VELOVI

Expand All @@ -22,6 +23,7 @@
"SCBASSET",
"POISSONVI",
"ContrastiveVI",
"SysVI",
"VELOVI",
"MRVI",
"METHYLVI",
Expand Down
4 changes: 4 additions & 0 deletions src/scvi/external/sysvi/__init__.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
from ._model import SysVI
from ._module import SysVAE

__all__ = ["SysVI", "SysVAE"]
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