univi 0.3.4__py3-none-any.whl

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Files changed (40) hide show
  1. univi/__init__.py +120 -0
  2. univi/__main__.py +5 -0
  3. univi/cli.py +60 -0
  4. univi/config.py +340 -0
  5. univi/data.py +345 -0
  6. univi/diagnostics.py +130 -0
  7. univi/evaluation.py +632 -0
  8. univi/hyperparam_optimization/__init__.py +17 -0
  9. univi/hyperparam_optimization/common.py +339 -0
  10. univi/hyperparam_optimization/run_adt_hparam_search.py +109 -0
  11. univi/hyperparam_optimization/run_atac_hparam_search.py +109 -0
  12. univi/hyperparam_optimization/run_citeseq_hparam_search.py +137 -0
  13. univi/hyperparam_optimization/run_multiome_hparam_search.py +145 -0
  14. univi/hyperparam_optimization/run_rna_hparam_search.py +111 -0
  15. univi/hyperparam_optimization/run_teaseq_hparam_search.py +146 -0
  16. univi/interpretability.py +399 -0
  17. univi/matching.py +394 -0
  18. univi/models/__init__.py +8 -0
  19. univi/models/decoders.py +249 -0
  20. univi/models/encoders.py +848 -0
  21. univi/models/mlp.py +36 -0
  22. univi/models/tokenizers.py +376 -0
  23. univi/models/transformer.py +249 -0
  24. univi/models/univi.py +1284 -0
  25. univi/objectives.py +46 -0
  26. univi/pipeline.py +194 -0
  27. univi/plotting.py +126 -0
  28. univi/trainer.py +478 -0
  29. univi/utils/__init__.py +5 -0
  30. univi/utils/io.py +621 -0
  31. univi/utils/logging.py +16 -0
  32. univi/utils/seed.py +18 -0
  33. univi/utils/stats.py +23 -0
  34. univi/utils/torch_utils.py +23 -0
  35. univi-0.3.4.dist-info/METADATA +908 -0
  36. univi-0.3.4.dist-info/RECORD +40 -0
  37. univi-0.3.4.dist-info/WHEEL +5 -0
  38. univi-0.3.4.dist-info/entry_points.txt +2 -0
  39. univi-0.3.4.dist-info/licenses/LICENSE +21 -0
  40. univi-0.3.4.dist-info/top_level.txt +1 -0
univi/utils/torch_utils.py ADDED
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+ # univi/utils/torch_utils.py
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+
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+ from __future__ import annotations
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+ from typing import Dict, Any
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+ import numpy as np
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+ import torch
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+
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+
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+ def get_device(prefer: str = "cuda") -> torch.device:
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+ if prefer == "cuda" and torch.cuda.is_available():
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+ return torch.device("cuda")
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+ return torch.device("cpu")
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+
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+
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+ def to_device(batch: Dict[str, torch.Tensor], device: torch.device) -> Dict[str, torch.Tensor]:
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+ return {k: (v.to(device) if v is not None else None)
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+ for k, v in batch.items()}
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+
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+
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+ def to_numpy(x: Any):
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+ if isinstance(x, torch.Tensor):
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+ return x.detach().cpu().numpy()
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+ return np.asarray(x)