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[python] Update scvi pipeline for the June LTS training #1173

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Jun 28, 2024
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[python] Update scvi pipeline for the June LTS training #1173

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5f19a27
Update scvi pipeline for the June LTS training
ebezzi May 31, 2024
48670ff
parametrize census config
ebezzi Jun 3, 2024
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4 changes: 3 additions & 1 deletion tools/models/scvi/scvi-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@ census:
null
obs_query_model: # Required when loading data for model training. Do not change.
'is_primary_data == True and nnz >= 300'
version:
"2024-05-20"
hvg:
top_n_hvg:
8000
Expand All @@ -19,7 +21,7 @@ model:
filename: "scvi.model"
n_hidden: 512
n_latent: 50
n_layers: 1
n_layers: 2
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What is the reason for incrementing n_layers? Apologies if you have already addressed this in our synchronous meeting and I missed the point.

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This was determined during the training phase last year, but I forgot to update it in the configuration file.

train:
max_epochs: 100
batch_size: 1024
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7 changes: 4 additions & 3 deletions tools/models/scvi/scvi-create-latent-update.py
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Expand Up @@ -14,12 +14,13 @@
with open(file) as f:
config = yaml.safe_load(f)

census = cellxgene_census.open_soma(census_version="2023-12-15")

census_config = config.get("census")
experiment_name = census_config.get("organism")
obs_value_filter = census_config.get("obs_query")

version = census_config.get("version")
census = cellxgene_census.open_soma(census_version=version)

hv = pd.read_pickle("hv_genes.pkl")
hv_idx = hv[hv].index

Expand All @@ -44,7 +45,7 @@

adata.var.set_index("feature_id", inplace=True)

idx = query.obs(column_names=["soma_joinid"]).concat().to_pandas().index.to_numpy()
idx = query.obs(column_names=["soma_joinid"]).concat().to_pandas().to_numpy()

del census, query, hv, hv_idx
gc.collect()
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5 changes: 3 additions & 2 deletions tools/models/scvi/scvi-prepare.py
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Expand Up @@ -11,13 +11,14 @@
with open(file) as f:
config = yaml.safe_load(f)

census = cellxgene_census.open_soma(census_version="2023-12-15")

census_config = config.get("census")
experiment_name = census_config.get("organism")
obs_query = census_config.get("obs_query")
obs_query_model = census_config.get("obs_query_model")

version = census_config.get("version")
census = cellxgene_census.open_soma(census_version=version)

if obs_query is None:
obs_value_filter = obs_query_model
else:
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