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Reduce mem footprint of get_latent_representation #84

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Feb 14, 2024
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Reduce mem footprint of get_latent_representation #84

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17d8e82
Reduce mem footprint of latent representation
martinkim0 Feb 7, 2024
7f4984a
Undo renaming
martinkim0 Feb 7, 2024
31cd588
Merge branch 'main' into latent-repi
martinkim0 Feb 14, 2024
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13 changes: 8 additions & 5 deletions src/scvi_v2/_model.py
100755 → 100644
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Original file line number Diff line number Diff line change
Expand Up @@ -269,12 +269,15 @@ def get_latent_representation(
for array_dict in tqdm(scdl):
outputs = jit_inference_fn(self.module.rngs, array_dict)

us.append(outputs["u"])
zs.append(outputs["z"])
if give_z:
zs.append(jax.device_get(outputs["z"]))
else:
us.append(jax.device_get(outputs["u"]))

u = np.array(jax.device_get(jnp.concatenate(us, axis=0)))
z = np.array(jax.device_get(jnp.concatenate(zs, axis=0)))
return z if give_z else u
if give_z:
return np.array(jnp.concatenate(zs, axis=0))
else:
return np.array(jnp.concatenate(us, axis=0))

def compute_local_statistics(
self,
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