bernn 0.1.0__py3-none-any.whl

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Files changed (69) hide show
  1. bernn/__init__.py +44 -0
  2. bernn/dl/__init__.py +39 -0
  3. bernn/dl/models/__init__.py +0 -0
  4. bernn/dl/models/pytorch/__init__.py +11 -0
  5. bernn/dl/models/pytorch/aecnndann.py +1180 -0
  6. bernn/dl/models/pytorch/aedann.py +1057 -0
  7. bernn/dl/models/pytorch/aeekandann.py +1081 -0
  8. bernn/dl/models/pytorch/aekandann.py +1066 -0
  9. bernn/dl/models/pytorch/utils/__init__.py +32 -0
  10. bernn/dl/models/pytorch/utils/dataset.py +1370 -0
  11. bernn/dl/models/pytorch/utils/distributions.py +84 -0
  12. bernn/dl/models/pytorch/utils/loggings.py +1600 -0
  13. bernn/dl/models/pytorch/utils/losses.py +80 -0
  14. bernn/dl/models/pytorch/utils/metrics.py +111 -0
  15. bernn/dl/models/pytorch/utils/plotting.py +80 -0
  16. bernn/dl/models/pytorch/utils/stochastic.py +53 -0
  17. bernn/dl/models/pytorch/utils/utils.py +797 -0
  18. bernn/dl/train/__init__.py +14 -0
  19. bernn/dl/train/aecnndann.py +649 -0
  20. bernn/dl/train/aedacnn.py +1478 -0
  21. bernn/dl/train/data_getters.py +976 -0
  22. bernn/dl/train/dataset.py +1568 -0
  23. bernn/dl/train/pytorch/__init__.py +3 -0
  24. bernn/dl/train/pytorch/aecnndann.py +1180 -0
  25. bernn/dl/train/pytorch/aedann.py +1072 -0
  26. bernn/dl/train/pytorch/aeekandann.py +1635 -0
  27. bernn/dl/train/pytorch/aekandann.py +1017 -0
  28. bernn/dl/train/pytorch/avekandann.py +1173 -0
  29. bernn/dl/train/pytorch/ekan/__init__.py +3 -0
  30. bernn/dl/train/pytorch/ekan/src/__init__.py +0 -0
  31. bernn/dl/train/pytorch/ekan/src/efficient_kan/__init__.py +3 -0
  32. bernn/dl/train/pytorch/ekan/src/efficient_kan/kan.py +339 -0
  33. bernn/dl/train/pytorch/utils/__init__.py +37 -0
  34. bernn/dl/train/pytorch/utils/dataset.py +1370 -0
  35. bernn/dl/train/pytorch/utils/distributions.py +84 -0
  36. bernn/dl/train/pytorch/utils/loggings.py +1615 -0
  37. bernn/dl/train/pytorch/utils/losses.py +80 -0
  38. bernn/dl/train/pytorch/utils/metrics.py +111 -0
  39. bernn/dl/train/pytorch/utils/plotting.py +80 -0
  40. bernn/dl/train/pytorch/utils/stochastic.py +74 -0
  41. bernn/dl/train/pytorch/utils/utils.py +793 -0
  42. bernn/dl/train/train_ae.py +943 -0
  43. bernn/dl/train/train_ae_classifier.py +1346 -0
  44. bernn/dl/train/train_ae_classifier_holdout.py +853 -0
  45. bernn/dl/train/train_ae_classifier_holdout_fixed_hparams.py +773 -0
  46. bernn/dl/train/train_ae_classifier_holdout_less_hparams.py +826 -0
  47. bernn/dl/train/train_ae_then_classifier.py +1274 -0
  48. bernn/dl/train/train_ae_then_classifier_holdout.py +915 -0
  49. bernn/dl/train/train_aecnn_classifier_holdout.py +1471 -0
  50. bernn/dl/train/train_resnet_classifier.py +1122 -0
  51. bernn/dl/train/utils.py +524 -0
  52. bernn/ml/__init__.py +0 -0
  53. bernn/ml/import_data.py +394 -0
  54. bernn/ml/train/__init__.py +0 -0
  55. bernn/ml/train/params_gp.py +137 -0
  56. bernn/ml/train/sklearn_train3_gp2.py +470 -0
  57. bernn/ml/train/sklearn_train_nocv.py +567 -0
  58. bernn/utils/__init__.py +0 -0
  59. bernn/utils/batch_effect_removal.py +436 -0
  60. bernn/utils/data_getters.py +971 -0
  61. bernn/utils/metrics.py +13 -0
  62. bernn/utils/pool_metrics.py +203 -0
  63. bernn/utils/utils.py +524 -0
  64. bernn-0.1.0.dist-info/LICENCE +674 -0
  65. bernn-0.1.0.dist-info/METADATA +298 -0
  66. bernn-0.1.0.dist-info/RECORD +69 -0
  67. bernn-0.1.0.dist-info/WHEEL +5 -0
  68. bernn-0.1.0.dist-info/entry_points.txt +4 -0
  69. bernn-0.1.0.dist-info/top_level.txt +1 -0
bernn/__init__.py ADDED
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+ """BERNN: Batch Effect Removal Neural Networks for Tandem Mass Spectrometry.
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+
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+ This package provides tools for removing batch effects from mass spectrometry data
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+ using deep learning approaches.
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+ """
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+
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+ __version__ = "0.1.0"
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+ __author__ = "Simon Pelletier"
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+ __license__ = "MIT"
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+
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+ # Core training modules
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+ from .dl.train import (
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+ TrainAE,
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+ TrainAEClassifierHoldout,
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+ TrainAEThenClassifierHoldout,
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+ )
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+
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+ # Model definitions
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+ from .dl.models.pytorch import (
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+ AutoEncoder2,
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+ SHAPAutoEncoder2,
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+ KANAutoencoder2,
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+ SHAPKANAutoencoder2,
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+ )
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+
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+ # KAN modules
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+ from .dl.train.pytorch.ekan import KANLinear, KAN
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+
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+ __all__ = [
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+ # Training
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+ "TrainAE",
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+ "TrainAEClassifierHoldout",
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+ "TrainAEThenClassifierHoldout",
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+
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+ # Models
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+ "AutoEncoder2",
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+ "SHAPAutoEncoder2",
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+ "KANAutoencoder2",
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+ "SHAPKANAutoencoder2",
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+
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+ # KAN
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+ "KANLinear",
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+ "KAN"
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+ ]
bernn/dl/__init__.py ADDED
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+ """Deep Learning modules for BERNN.
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+
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+ This subpackage contains the deep learning models and training code.
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+ """
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+
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+ # Model definitions
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+ from .models.pytorch import (
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+ AutoEncoder2,
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+ SHAPAutoEncoder2,
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+ KANAutoencoder2,
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+ SHAPKANAutoencoder2,
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+ )
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+
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+ # Training modules
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+ from .train import (
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+ TrainAE,
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+ TrainAEClassifierHoldout,
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+ TrainAEThenClassifierHoldout,
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+ )
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+
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+ # KAN modules
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+ from .train.pytorch.ekan import KANLinear, KAN
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+
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+ __all__ = [
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+ # Models
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+ "AutoEncoder2",
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+ "SHAPAutoEncoder2",
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+ "KANAutoencoder2",
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+ "SHAPKANAutoencoder2",
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+
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+ # Training
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+ "TrainAE",
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+ "TrainAEClassifierHoldout",
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+ "TrainAEThenClassifierHoldout",
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+
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+ # KAN
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+ "KANLinear",
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+ "KAN"
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+ ]
bernn/dl/models/__init__.py ADDED
File without changes
bernn/dl/models/pytorch/__init__.py ADDED
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+ """PyTorch model definitions for BERNN."""
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+
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+ from .aedann import AutoEncoder2, SHAPAutoEncoder2
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+ from .aeekandann import KANAutoencoder2, SHAPKANAutoencoder2
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+
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+ __all__ = [
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+ "AutoEncoder2",
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+ "SHAPAutoEncoder2",
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+ "KANAutoencoder2",
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+ "SHAPKANAutoencoder2",
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+ ]