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allow organism specification for enformer pretrained model #174

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allow organism specification for enformer pretrained model #174

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13 changes: 9 additions & 4 deletions src/grelu/model/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -772,15 +772,21 @@ def __init__(
self,
n_tasks: int,
n_transformers: int = 11,
organism="human",
# head
crop_len=0,
final_pool_func="avg",
dtype=None,
device=None,
):
if organism == "human":
n_tasks_default = 5313
elif organism == "mouse":
n_tasks_default = 1643

model = EnformerModel(
crop_len=crop_len,
n_tasks=5313,
n_tasks=n_tasks_default,
channels=1536,
n_transformers=11,
n_heads=8,
Expand All @@ -797,10 +803,10 @@ def __init__(
# Load state dict
from grelu.resources import get_artifact

art = get_artifact("human_state_dict", project="enformer", alias="latest")
art = get_artifact(f"{organism}_state_dict", project="enformer", alias="latest")
with TemporaryDirectory() as d:
art.download(d)
state_dict = torch.load(Path(d) / "human.h5")
state_dict = torch.load(Path(d) / f"{organism}.h5")

model.load_state_dict(state_dict)

Expand All @@ -809,7 +815,6 @@ def __init__(
model.embedding.transformer_tower.blocks[:n_transformers]
)

# Change head
head = ConvHead(
n_tasks=n_tasks,
in_channels=3072,
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