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feat: TotalANVI model updated #3259

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e4130ed
Add totalANVI
canergen Mar 23, 2024
e12f5b7
Remove feed_labels codeblock
canergen Mar 23, 2024
185d610
Changed totalVI
canergen Apr 3, 2024
25d4d8b
Fixes totalANVI
canergen Oct 11, 2024
9e39617
update totalanvi branch with recent de maximum bayes branch
ori-kron-wis Jan 14, 2025
e70c56f
fix bug in merged new DE
ori-kron-wis Jan 15, 2025
b68d9ef
fix
ori-kron-wis Jan 15, 2025
b96e19a
merge with main
ori-kron-wis Mar 18, 2025
fed3b4a
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 18, 2025
4e31f12
merge with main
ori-kron-wis Mar 18, 2025
29fc913
updated to up to date changes
ori-kron-wis Mar 18, 2025
aab301a
adding new mixins to totalanvi, multi modality to IG
ori-kron-wis Mar 18, 2025
aeac61e
Merge remote-tracking branch 'origin/main' into Ori-totalanvi-updated
ori-kron-wis Mar 19, 2025
f805c54
fix IG to totalanvi
ori-kron-wis Mar 20, 2025
981f421
changlog
ori-kron-wis Mar 20, 2025
9103b49
Merge remote-tracking branch 'origin/main' into Ori-totalanvi-updated
ori-kron-wis Mar 25, 2025
adb6aaa
added scib support for totalvi/anvi and the corresponding training plans
ori-kron-wis Mar 25, 2025
d1699e8
added the extra_payload_autotune flag for the totalvae and totalanvi …
ori-kron-wis Mar 26, 2025
925461b
fix
ori-kron-wis Mar 26, 2025
bd7c15e
added extra payload flag
ori-kron-wis Mar 26, 2025
26504aa
fixed a link to adverserial training plan in the new semisupervised m…
ori-kron-wis Mar 26, 2025
1746c75
expose pseudocounts in DE for totalvi and totalanvi
ori-kron-wis Apr 1, 2025
53d1696
fix progress bar in get norm by parameter
ori-kron-wis Apr 1, 2025
c3a4b0d
Merge branch 'main' into Ori-totalanvi-updated
ori-kron-wis Apr 1, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@ to [Semantic Versioning]. Full commit history is available in the
- Add supervised module class {class}`scvi.module.base.SupervisedModuleClass`. {pr}`3237`.
- Add get normalized function model property for any generative model {pr}`3238` and changed
get_accessibility_estimates to get_normalized_accessibility, where needed.
- Add {class}`scvi.external.TOTALANVI`. {pr}`3259`.
- Add Early stopping KL warmup steps. {pr}`3262`.

#### Fixed
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorials/notebooks
2 changes: 2 additions & 0 deletions src/scvi/external/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
from .stereoscope import RNAStereoscope, SpatialStereoscope
from .sysvi import SysVI
from .tangram import Tangram
from .totalanvi import TOTALANVI
from .velovi import VELOVI

__all__ = [
Expand All @@ -23,6 +24,7 @@
"SpatialStereoscope",
"CellAssign",
"Tangram",
"TOTALANVI",
"SCBASSET",
"POISSONVI",
"ContrastiveVI",
Expand Down
3 changes: 3 additions & 0 deletions src/scvi/external/totalanvi/__init__.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
from ._model import TOTALANVI

__all__ = ["TOTALANVI"]
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