# DestVI: how to load a DestVI model that was saved as a pickle

**URL:** <https://discourse.scverse.org/t/destvi-how-to-load-a-destvi-model-that-was-saved-as-a-pickle/3530>\
**Category:** scvi-tools\
**Tags:** destvi\
**Created:** [March 7, 2025, 8:34pm UTC](https://discourse.scverse.org/t/destvi-how-to-load-a-destvi-model-that-was-saved-as-a-pickle/3530 "2025-03-07T20:34:17Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![jliu678](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/jliu678/32/1328_2.png) [@jliu678](https://discourse.scverse.org/u/jliu678)\
**Post date:** [March 7, 2025, 8:34pm UTC](https://discourse.scverse.org/t/destvi-how-to-load-a-destvi-model-that-was-saved-as-a-pickle/3530/1 "2025-03-07T20:34:17Z")

</div>

Hi scvi team,

DestVI model was saved as a pickle as below:

```auto
DestVI.setup_anndata(st_adata, layer="counts")
st_model = DestVI.from_rna_model(st_adata, sc_model)
st_model.view_anndata_setup()
st_model.train(max_epochs=2500)

with open("st_model.pkl", "wb") as f:
    pickle.dump(st_model, f)

```

And below error occurs

```auto
Traceback (most recent call last):
 File "/data/wanglab_mgberis/UT_scRNAseq/./cuda_to_cpu.py", line 39, in <module>
   st_adata.obsm["proportions"] = st_model.get_proportions()
 File "/usr/local/lib/python3.10/dist-packages/scvi/model/_destvi.py", line 198, in get_proportions
   stdl = self._make_data_loader(adata=self.adata, indices=indices, batch_size=batch_size)
 File "/usr/local/lib/python3.10/dist-packages/scvi/model/base/_base_model.py", line 431, in _make_data_loader
   raise AssertionError(
AssertionError: AnnDataManager not found. Call `self._validate_anndata` prior to calling this function.

```

when i tried to load it to proceed downstream analysis as blow.

```auto
print('.1')
import pickle
with open("st_adata.pkl", "rb") as f:
    st_adata = pickle.load(f)

with open("sc_model.pkl", "rb") as f:
    sc_model = pickle.load(f)

print(sc_model)

DestVI.setup_anndata(st_adata, layer="counts")
st_model = DestVI.from_rna_model(st_adata, sc_model)
st_model.view_anndata_setup()

with open("st_model.pkl", "rb") as f:
    st_model = pickle.load(f) 
    
print('.2')
st_model._validate_anndata(st_adata)

print('.3')
st_adata.obsm["proportions"] = st_model.get_proportions()

```

Is it possible i can still use this pickle instead of retraining it ?

While awaiting the response, I re-train it and save using below codes:

```auto
import tempfile
import destvi_utils
import matplotlib.pyplot as plt
import numpy as np
import scanpy as sc
import scvi
import seaborn as sns
import torch
from scvi.model import CondSCVI, DestVI
torch.set_float32_matmul_precision("high")
import pickle
with open("st_adata.pkl", "rb") as f:
    st_adata = pickle.load(f)
with open("sc_model.pkl", "rb") as f:
    sc_model = pickle.load(f)
print(sc_model)
DestVI.setup_anndata(st_adata, layer="counts")
st_model = DestVI.from_rna_model(st_adata, sc_model)
st_model.view_anndata_setup()
st_model.train(max_epochs=2500)
print('Saving a model')
st_model.save("st_model.pt")

```

but scvi.model.DestVI.load still cannot load the model. Code and err msg shown below:

```auto
import pickle;
with open("st_adata.pkl", "rb") as f:
    st_adata = pickle.load(f)
DestVI.setup_anndata(st_adata, layer="counts")
st_model=scvi.model.DestVI.load('./st_model.pt',
                       adata=st_adata
                      )

```

```auto
INFO File ./st_model.pt/model.pt already downloaded                                                            
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
Cell In[17], line 4
     
      3 DestVI.setup_anndata(st_adata, layer="counts")
----> 4 st_model=scvi.model.DestVI.load('./st_model.pt',
      5 adata=st_adata
      6 )

File ~/mambaforge/envs/scvi-env/lib/python3.12/site-packages/scvi/model/base/_base_model.py:733, in BaseModelClass.load(cls, dir_path, adata, accelerator, device, prefix, backup_url)
    731 model = _initialize_model(cls, adata, attr_dict)
    732 model.module.on_load(model)
--> 733 model.module.load_state_dict(model_state_dict)
    735 model.to_device(device)
    736 model.module.eval()

File ~/mambaforge/envs/scvi-env/lib/python3.12/site-packages/torch/nn/modules/module.py:2584, in Module.load_state_dict(self, state_dict, strict, assign)
   2576 error_msgs.insert(
   2577 0,
   2578 "Missing key(s) in state_dict: {}. ".format(
   2579 ", ".join(f'"{k}"' for k in missing_keys)
   2580 ),
   2581 )
   2583 if len(error_msgs) > 0:
-> 2584 raise RuntimeError(
   2585 "Error(s) in loading state_dict for {}:\n\t{}".format(
   2586 self. __class__. __name__ , "\n\t".join(error_msgs)
   2587 )
   2588 )
   2589 return _IncompatibleKeys(missing_keys, unexpected_keys)

RuntimeError: Error(s) in loading state_dict for MRDeconv:
	Unexpected key(s) in state_dict: "pyro_param_store". 

```

could you please help?

---

<div class="post-metadata">

**Author:** ![ori-kron-wis](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/ori-kron-wis/32/1099_2.png) [@ori-kron-wis](https://discourse.scverse.org/u/ori-kron-wis)\
**Post date:** [March 9, 2025, 1:44pm UTC](https://discourse.scverse.org/t/destvi-how-to-load-a-destvi-model-that-was-saved-as-a-pickle/3530/2 "2025-03-09T13:44:59Z")

</div>

Hey @jliu678  
What version of SCVI are you running?  
If its not the latest please update to the most recent version and try again as we had changes in the exact same spot of your error.

You can also save the model with save\_anndata=True,overwrite=True and then wont need to load the adata from pickle.