Backport PR scverse#2611: feat(external): add velovi to external

meeseeksmachine · Mar 11, 2024 · 41e41f6 · 41e41f6
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diff --git a/docs/api/developer.md b/docs/api/developer.md
@@ -178,6 +178,7 @@ Module classes in the external API with respective generative and inference proc
    external.tangram.TangramMapper
    external.scbasset.ScBassetModule
    external.contrastivevi.ContrastiveVAE
+   external.velovi.VELOVAE
 
 ```
 

diff --git a/docs/api/user.md b/docs/api/user.md
@@ -59,6 +59,7 @@ import scvi
    external.SCBASSET
    external.ContrastiveVI
    external.POISSONVI
+   external.VELOVI
 
 ```
 
@@ -102,6 +103,8 @@ Here we maintain a few package specific utilities for feature selection, etc.
    data.organize_multiome_anndatas
    data.add_dna_sequence
    data.reads_to_fragments
+   external.velovi.get_permutation_scores
+   external.velovi.preprocess_data
 ```
 
 ```{eval-rst}

diff --git a/docs/references.bib b/docs/references.bib
@@ -112,6 +112,18 @@ @article{GayosoSteier21
   publisher = {Nature Publishing Group}
 }
 
+@article{GayosoWeiler23,
+  title = {Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells},
+  author = {Adam Gayoso and Philipp Weiler and Mohammad Lotfollahi and Dominik Klein and Justin Hong and Aaron Streets and Fabian J. Theis and Nir Yosef},
+  doi = {10.1038/s41592-023-01994-w},
+  year = {2023},
+  month = sep,
+  journal = {Nature Methods},
+  volume = {21},
+  pages = {50-59},
+  publisher = {Nature Publishing Group}
+}
+
 @article{Ionides2008,
   title={Truncated Importance Sampling},
   author={Edward L. Ionides},

diff --git a/docs/release_notes/index.md b/docs/release_notes/index.md
@@ -25,6 +25,8 @@ is available in the [commit logs](https://github.com/scverse/scvi-tools/commits/
     argument `generate_coordinates` {pr}`2603`.
 -   Add experimental support for using custom {class}`lightning.pytorch.core.LightningDataModule`s
     in {func}`scvi.autotune.run_autotune` {pr}`2605`.
+-   Add {class}`scvi.external.VELOVI` for RNA velocity estimation using variational inference
+    {pr}`2611`.
 
 #### Changed
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -99,8 +99,9 @@ pymde = ["pymde"]  # scvi.model.utils.mde dependencies
 regseq = ["biopython>=1.81", "genomepy"]  # scvi.data.add_dna_sequence
 loompy = ["loompy>=3.0.6"]  # read loom
 scanpy = ["scanpy>=1.6"]  # scvi.criticism and read 10x
+velovi = ["scvelo>=0.3.0"]  # scvi.external.velovi
 optional = [
-    "scvi-tools[autotune,aws,criticism,hub,loompy,pymde,regseq,scanpy]"
+    "scvi-tools[autotune,aws,criticism,hub,loompy,pymde,regseq,scanpy,velovi]"
 ]  # all optional user functionality
 
 tutorials = [

diff --git a/scvi/external/__init__.py b/scvi/external/__init__.py
@@ -7,6 +7,7 @@
 from .solo import SOLO
 from .stereoscope import RNAStereoscope, SpatialStereoscope
 from .tangram import Tangram
+from .velovi import VELOVI
 
 __all__ = [
     "SCAR",
@@ -19,4 +20,5 @@
     "SCBASSET",
     "POISSONVI",
     "ContrastiveVI",
+    "VELOVI",
 ]
diff --git a/scvi/external/velovi/__init__.py b/scvi/external/velovi/__init__.py
@@ -0,0 +1,5 @@
+from ._model import VELOVI
+from ._module import VELOVAE
+from ._utils import get_permutation_scores, preprocess_data
+
+__all__ = ["VELOVI", "VELOVAE", "get_permutation_scores", "preprocess_data"]
diff --git a/scvi/external/velovi/_constants.py b/scvi/external/velovi/_constants.py
@@ -0,0 +1,9 @@
+from typing import NamedTuple
+
+
+class _REGISTRY_KEYS_NT(NamedTuple):
+    X_KEY: str = "X"
+    U_KEY: str = "U"
+
+
+VELOVI_REGISTRY_KEYS = _REGISTRY_KEYS_NT()