cellarium-ai cellarium-ml issues

cellarium-ai / cellarium-ml

Distributed single-cell data analysis.

BSD 3-Clause "New" or "Revised" License

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issues

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Transforms split into before and after batch transfer

#220 sjfleming closed 3 months ago
3
Filter `save_hyperparameters` warning

#219 ordabayevy closed 3 months ago
0
Filter "Attribute 'model' is an instance of `nn.Module` and is already saved during checkpointing."

#218 ordabayevy closed 3 months ago
0
Your `IterableDataset` has `__len__` defined. In combination with multi-process data loading (when num_workers > 1), `__len__` could be inaccurate if each worker is not configured independently to avoid having duplicate data.

#217 ordabayevy opened 3 months ago
0
FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas.

#216 ordabayevy closed 3 months ago
0
Fix NaN issue in scvi

#215 sjfleming closed 4 months ago
0
Remove reduntant resolve_ckpt method

#214 ordabayevy closed 4 months ago
1
Simplify `AnnDataField`

#213 ordabayevy closed 4 months ago
0
Use `measured_genes_mask` in `OnePassMeanVarStd`

#212 ordabayevy opened 4 months ago
0
NMF - implement consensus NMF

#211 sjfleming opened 4 months ago
0
Add geneformer_demo to the Docs

#210 ordabayevy closed 4 months ago
0
`DDPNoParametersStrategy`

#209 ordabayevy opened 4 months ago
0
Distributed fixes & improvements

#208 ordabayevy closed 4 months ago
0
Support PyTorch Lightning 2.3

#207 ordabayevy closed 4 months ago
0
`DDPNoParametersStrategy`

#206 ordabayevy closed 4 months ago
1
scvi: ensure categorical covariates and continuous covariates work

#205 sjfleming opened 4 months ago
0
scvi: include the option to limit to a specific set of genes

#204 sjfleming closed 1 month ago
7
We might wanna use Millipede for feature selection for CAS

#203 fedorgrab opened 5 months ago
0
Change type of `var_names_g` to `np.ndarray`

#202 ordabayevy closed 5 months ago
0
Add predict method to `LogisticRegression`

#201 ordabayevy closed 4 months ago
0
New pyro version 1.9.1

#200 ordabayevy closed 5 months ago
0
update nmf.py

#199 ImXman closed 4 months ago
1
NMF - add tests

#198 sjfleming opened 5 months ago
0
NMF - implement beta divergence as optional for the loss function

#197 sjfleming opened 5 months ago
0
Non-negative matrix factorization

#196 sjfleming opened 5 months ago
0
Implement contrastive learning model and transforms

#195 bricewang opened 5 months ago
0
Constrain jsonargparse version

#194 ordabayevy closed 5 months ago
0
Parser key "data.batch_keys" error

#193 fedorgrab opened 5 months ago
0
Freeze `CellariumModule` transforms

#192 ordabayevy closed 5 months ago
0
Set `torch.Generator` device in `reset_parameters`

#191 ordabayevy closed 6 months ago
0
RuntimeError: Expected a 'cuda' device type for generator but found 'cpu' when training logistic regression

#190 fedorgrab closed 6 months ago
0
Add `iteration_strategy` option to `IterableDistributedAnnDataCollectionDataset`

#189 ordabayevy closed 6 months ago
0
Add `validation_step`

#188 ordabayevy closed 6 months ago
0
Anndata schema validation descriptive error message

#187 sjfleming closed 4 months ago
0
Freeze parameters for inference with `.freeze()`

#186 ordabayevy closed 5 months ago
0
Add `val_dataloader` method

#185 ordabayevy closed 6 months ago
0
Fix `GatherLayer.backward` and make the test more stringent

#184 ordabayevy closed 6 months ago
0
OSError: Can't synchronously read data (anndata file)

#183 ordabayevy opened 6 months ago
1
Make a docs page out of cli_workflow example

#182 ordabayevy closed 6 months ago
0
Cache throws KeyError for missing entry

#181 bricewang opened 6 months ago
3
AnnDataSchema validate_anndata fix

#180 sjfleming closed 6 months ago
3
AnnDataSchema validate_anndata is over-zealous for obs categoricals

#179 sjfleming closed 6 months ago
6
Refactor negative binomial and add .reconstruct() method

#178 sjfleming closed 7 months ago
0
Fix bugs found during testing

#177 sjfleming closed 7 months ago
0
test_scvi from Yang's starting point

#176 sjfleming closed 7 months ago
0
Add a new `ParallelStrategy` that doesn't require gradient synchronization

#175 ordabayevy opened 7 months ago
1
Fix README

#174 ordabayevy closed 7 months ago
0
Improve error messages

#173 ordabayevy closed 7 months ago
0
Add `GatherLayer` test

#172 ordabayevy closed 7 months ago
2
NegativeBinomial parametrized by `mu` and `theta`

#171 ordabayevy closed 6 months ago
2

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