Implement Tangram #1743
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Implement Tangram #1743
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Codecov ReportBase: 90.84% // Head: 90.85% // Increases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## main #1743 +/- ##
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Coverage 90.84% 90.85%
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Files 115 118 +3
Lines 9758 9969 +211
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+ Hits 8865 9057 +192
- Misses 893 912 +19
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2 tasks
adamgayoso
commented
Oct 19, 2022
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| tensor_dict = self._get_tensor_dict(device=device) | ||
| training_plan = JaxTrainingPlan(self.module, **plan_kwargs) | ||
| module_init = self.module.init(self.module.rngs, tensor_dict) | ||
| state, params = module_init.pop("params") | ||
| training_plan.set_train_state(params, state) | ||
| train_step_fn = JaxTrainingPlan.jit_training_step | ||
| pbar = track(range(max_epochs), style="tqdm", description="Training") | ||
| history = pd.DataFrame(index=np.arange(max_epochs), columns=["loss"]) |
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cc @justjhong it's actually pretty flexible
you can use the training plan just as a shell
adamgayoso
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Oct 19, 2022
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| @dataclass | ||
| class AnnDataManagerValidationCheck: | ||
| """ | ||
| Validation checks for AnnorMudata scvi-tools compat. | ||
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| Parameters | ||
| ---------- | ||
| check_if_view | ||
| If True, checks if AnnData is a view. | ||
| check_fully_paired_mudata | ||
| If True, checks if MuData is fully paired across mods. | ||
| """ | ||
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| check_if_view: bool = True | ||
| check_fully_paired_mudata: bool = True | ||
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@justjhong what do you think?
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seems fine, the user will never interact with this right?
adamgayoso
commented
Oct 19, 2022
adamgayoso
commented
Oct 19, 2022
adamgayoso
commented
Oct 19, 2022
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Fixes #1738
Example on this tutorials PR.
Also fixes an issue with the
to()to device method after removingJaxModuleWrapper