bunnech / cellot

Learning Single-Cell Perturbation Responses using Neural Optimal Transport
BSD 3-Clause "New" or "Revised" License
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How to try diiferent drugs? #39

Open Eetenal opened 1 week ago

Eetenal commented 1 week ago

I want to try different drugs, I change the command to

python ./scripts/train.py --outdir ./results/4i/drug-ulixertinib/model-cellot --config ./configs/tasks/4i.yaml --config ./configs/models/cellot.yaml --config.data.target ulixertinib

but I get some error: C:\Anaconda3\Lib\site-packages\anndata__init__.py:52: FutureWarning: anndata.read is deprecated, use anndata.read_h5ad instead. ad.read will be removed in mid 2024. warnings.warn( C:\cellot_main\cellot\data\cell.py:259: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. groups = data.obs.groupby(groupby).groups C:\cellot_main\cellot\data\cell.py:213: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. for key, index in data.obs[split_on].groupby(split_on).groups.items() 0%| | 0/100 [00:00<?, ?it/s]C:\cellot_main\cellot\train\summary.py:67: FutureWarning: Starting with pandas version 3.0 all arguments of to_hdf except for the argument 'path_or_buf' will be keyword-only. df.to_hdf(self.path, self.key, append=True, format='table') 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 100/100 [00:09<00:00, 10.52it/s] Traceback (most recent call last): File "C:\cellot_main\scripts\train.py", line 81, in main(sys.argv) File "C:\cellot_main\scripts\train.py", line 65, in main train(outdir, config) File "C:\cellot_main\cellot\train\train.py", line 165, in train_cellot logger.flush() File "C:\cellot_main\cellot\train\summary.py", line 25, in flush logger.flush() File "C:\cellot_main\cellot\train\summary.py", line 72, in flush self._write() File "C:\cellot_main\cellot\train\summary.py", line 66, in _write df = pd.DataFrame(self.store).set_index('step') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Anaconda3\Lib\site-packages\pandas\core\frame.py", line 6122, in set_index raise KeyError(f"None of {missing} are in the columns") KeyError: "None of ['step'] are in the columns"

Is something wrong with my command? Could you please tell me how to deal with this issues?

Eetenal commented 1 week ago

In addition, I would like to ask if it is OK not to provide feature.txt when training and evaluating the model.