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train larry mono and neu
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jiachen committed Apr 27, 2023
1 parent 9ee355a commit 16669e3
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Showing 11 changed files with 512 additions and 1 deletion.
42 changes: 42 additions & 0 deletions pyrovelocity/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -180,6 +180,24 @@ def create_reports_config(model_name: str, model_number: int):
process_method="load_data",
process_args=dict(),
),
larry_mono=create_dataset_config(
"larry_mono",
dl_root="${data_external.root_path}",
data_file="larry_mono.h5ad",
rel_path="${data_external.root_path}/larry_mono.h5ad",
url="${data_external.pyrovelocity.sources.figshare_root_url}/37028572",
process_method="load_data",
process_args=dict(),
),
larry_neu=create_dataset_config(
"larry_neu",
dl_root="${data_external.root_path}",
data_file="larry_neu.h5ad",
rel_path="${data_external.root_path}/larry_neu.h5ad",
url="${data_external.pyrovelocity.sources.figshare_root_url}/37028575",
process_method="load_data",
process_args=dict(),
),
),
),
model_training=dict(
Expand All @@ -193,6 +211,8 @@ def create_reports_config(model_name: str, model_number: int):
"pons_model1",
"pons_model2",
"larry_model2",
"larry_mono_model2",
"larry_neu_model2",
],
simulate_model1=create_model_config(
"simulate",
Expand Down Expand Up @@ -275,6 +295,28 @@ def create_reports_config(model_name: str, model_number: int):
offset=True,
max_epochs=1000,
),
larry_mono_model2=create_model_config(
"pyrovelocity",
"larry_mono",
2,
"emb",
svi_train=True,
batch_size=4000,
cell_state="state_info",
offset=True,
max_epochs=1000,
),
larry_neu_model2=create_model_config(
"pyrovelocity",
"larry_neu",
2,
"emb",
svi_train=True,
batch_size=4000,
cell_state="state_info",
offset=True,
max_epochs=1000,
),
),
reports=dict(
model_summary=dict(
Expand Down
5 changes: 4 additions & 1 deletion pyrovelocity/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -90,6 +90,9 @@ def load_data(
adata = scv.datasets.dentategyrus()
elif data == "larry":
adata = load_larry()
elif data in ['larry_mono', 'larry_neu']:
adata = load_unipotent_larry(data.split('-')[1])
adata = adata[adata.obs.state_info != "Centroid", :]
else:
adata = sc.read(data)

Expand Down Expand Up @@ -118,7 +121,7 @@ def load_data(
scv.tl.velocity(adata, mode="dynamical", use_raw=False)
scv.tl.velocity_graph(adata, n_jobs=-1)

if data == "larry":
if "larry" in data:
scv.tl.velocity_embedding(adata, basis="emb")
else:
scv.tl.velocity_embedding(adata)
Expand Down
92 changes: 92 additions & 0 deletions reproducibility/figures/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -93,6 +93,26 @@ data_external:
process_method: load_data
process_args: {}
rel_path: data/processed/larry_processed.h5ad
larry_mono:
data_file: larry_mono.h5ad
dl_root: data/external
dl_path: data/external/larry_mono.h5ad
rel_path: data/external/larry_mono.h5ad
url: https://ndownloader.figshare.com/files/37028572
derived:
process_method: load_data
process_args: {}
rel_path: data/processed/larry_mono_processed.h5ad
larry_neu:
data_file: larry_neu.h5ad
dl_root: data/external
dl_path: data/external/larry_neu.h5ad
rel_path: data/external/larry_neu.h5ad
url: https://ndownloader.figshare.com/files/37028575
derived:
process_method: load_data
process_args: {}
rel_path: data/processed/larry_neu_processed.h5ad
model_training:
train:
- simulate_model1
Expand All @@ -104,6 +124,8 @@ model_training:
- pons_model1
- pons_model2
- larry_model2
- larry_mono_model2
- larry_neu_model2
simulate_model1:
path: models/medium_model1
model_path: models/medium_model1/model
Expand Down Expand Up @@ -419,6 +441,76 @@ model_training:
cell_specific_kinetics: null
kinetics_num: 2
loss_plot_path: models/larry_model2/loss_plot.png
larry_mono_model2:
path: models/larry_mono_model2
model_path: models/larry_mono_model2/model
input_data_path: data/processed/larry_mono_processed.h5ad
trained_data_path: models/larry_mono_model2/trained.h5ad
pyrovelocity_data_path: models/larry_mono_model2/pyrovelocity.pkl
metrics_path: models/larry_mono_model2/metrics.json
run_info_path: models/larry_mono_model2/run_info.json
vector_field_parameters:
basis: emb
training_parameters:
_target_: pyrovelocity.api.train_model
_partial_: true
guide_type: auto
model_type: auto
svi_train: true
batch_size: 4000
train_size: 1.0
use_gpu: 0
likelihood: Poisson
num_samples: 30
log_every: 100
cell_state: state_info
patient_improve: 0.0001
patient_init: 45
seed: 99
lr: 0.01
max_epochs: 1000
include_prior: true
library_size: true
offset: true
input_type: raw
cell_specific_kinetics: null
kinetics_num: 2
loss_plot_path: models/larry_mono_model2/loss_plot.png
larry_neu_model2:
path: models/larry_neu_model2
model_path: models/larry_neu_model2/model
input_data_path: data/processed/larry_neu_processed.h5ad
trained_data_path: models/larry_neu_model2/trained.h5ad
pyrovelocity_data_path: models/larry_neu_model2/pyrovelocity.pkl
metrics_path: models/larry_neu_model2/metrics.json
run_info_path: models/larry_neu_model2/run_info.json
vector_field_parameters:
basis: emb
training_parameters:
_target_: pyrovelocity.api.train_model
_partial_: true
guide_type: auto
model_type: auto
svi_train: true
batch_size: 4000
train_size: 1.0
use_gpu: 0
likelihood: Poisson
num_samples: 30
log_every: 100
cell_state: state_info
patient_improve: 0.0001
patient_init: 45
seed: 99
lr: 0.01
max_epochs: 1000
include_prior: true
library_size: true
offset: true
input_type: raw
cell_specific_kinetics: null
kinetics_num: 2
loss_plot_path: models/larry_neu_model2/loss_plot.png
reports:
model_summary:
summarize:
Expand Down
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