combatlearn 1.1.1__py3-none-any.whl → 1.1.2__py3-none-any.whl

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Files changed (8) hide show
  1. combatlearn/__init__.py +1 -1
  2. combatlearn/combat.py +4 -6
  3. {combatlearn-1.1.1.dist-info → combatlearn-1.1.2.dist-info}/METADATA +1 -2
  4. combatlearn-1.1.2.dist-info/RECORD +7 -0
  5. combatlearn-1.1.1.dist-info/RECORD +0 -7
  6. {combatlearn-1.1.1.dist-info → combatlearn-1.1.2.dist-info}/WHEEL +0 -0
  7. {combatlearn-1.1.1.dist-info → combatlearn-1.1.2.dist-info}/licenses/LICENSE +0 -0
  8. {combatlearn-1.1.1.dist-info → combatlearn-1.1.2.dist-info}/top_level.txt +0 -0
combatlearn/__init__.py CHANGED
@@ -1,5 +1,5 @@
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  from .combat import ComBat
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  __all__ = ["ComBat"]
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- __version__ = "1.1.1"
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+ __version__ = "1.1.2"
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  __author__ = "Ettore Rocchi"
combatlearn/combat.py CHANGED
@@ -828,8 +828,7 @@ class ComBatModel:
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  """Chen et al. (2022) CovBat."""
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  self._fit_fortin(X, batch, disc, cont)
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  X_meanvar_adj = self._transform_fortin(X, batch, disc, cont)
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- X_centered = X_meanvar_adj - X_meanvar_adj.mean(axis=0)
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- pca = PCA(svd_solver="full", whiten=False).fit(X_centered)
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+ pca = PCA(svd_solver="full", whiten=False).fit(X_meanvar_adj)
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  # Determine number of components based on threshold type
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  if isinstance(self.covbat_cov_thresh, int):
@@ -841,7 +840,7 @@ class ComBatModel:
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  self._covbat_pca = pca
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  self._covbat_n_pc = n_pc
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- scores = pca.transform(X_centered)[:, :n_pc]
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+ scores = pca.transform(X_meanvar_adj)[:, :n_pc]
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  scores_df = pd.DataFrame(scores, index=X.index, columns=[f"PC{i + 1}" for i in range(n_pc)])
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  self._batch_levels_pc = self._batch_levels
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  n_per_batch = self._n_per_batch
@@ -1091,8 +1090,7 @@ class ComBatModel:
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  ) -> pd.DataFrame:
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  """Chen transform implementation."""
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  X_meanvar_adj = self._transform_fortin(X, batch, disc, cont)
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- X_centered = X_meanvar_adj - self._covbat_pca.mean_
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- scores = self._covbat_pca.transform(X_centered)
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+ scores = self._covbat_pca.transform(X_meanvar_adj)
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  n_pc = self._covbat_n_pc
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  scores_adj = scores.copy()
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@@ -1109,7 +1107,7 @@ class ComBatModel:
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  else:
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  scores_adj[idx, :n_pc] = (scores_adj[idx, :n_pc] - g) / np.sqrt(d)
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- X_recon = self._covbat_pca.inverse_transform(scores_adj) + self._covbat_pca.mean_
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+ X_recon = self._covbat_pca.inverse_transform(scores_adj)
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  return pd.DataFrame(X_recon, index=X.index, columns=X.columns)
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{combatlearn-1.1.1.dist-info → combatlearn-1.1.2.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: combatlearn
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- Version: 1.1.1
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+ Version: 1.1.2
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  Summary: Batch-effect harmonization for machine learning frameworks.
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  Author-email: Ettore Rocchi <ettoreroc@gmail.com>
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  License: MIT
@@ -36,7 +36,6 @@ Dynamic: license-file
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  [![Python versions](https://img.shields.io/badge/python-%3E%3D3.10-blue?logo=python)](https://www.python.org/)
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  [![Test](https://github.com/EttoreRocchi/combatlearn/actions/workflows/test.yaml/badge.svg)](https://github.com/EttoreRocchi/combatlearn/actions/workflows/test.yaml)
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  [![Documentation](https://readthedocs.org/projects/combatlearn/badge/?version=latest)](https://combatlearn.readthedocs.io)
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- [![PyPI Downloads](https://static.pepy.tech/badge/combatlearn)](https://pepy.tech/projects/combatlearn)
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  [![PyPI Version](https://img.shields.io/pypi/v/combatlearn?cacheSeconds=300)](https://pypi.org/project/combatlearn/)
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  [![License](https://img.shields.io/github/license/EttoreRocchi/combatlearn)](https://github.com/EttoreRocchi/combatlearn/blob/main/LICENSE)
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combatlearn-1.1.2.dist-info/RECORD ADDED
@@ -0,0 +1,7 @@
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+ combatlearn/__init__.py,sha256=pxEMfuu86HIeV9w-7ODj__98E66YVgD_Zv9iNPKaVKk,100
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+ combatlearn/combat.py,sha256=Bk1qlJe2THui1WMMyIzOAAR9x655MiSu93hnhl1PGUk,58852
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+ combatlearn-1.1.2.dist-info/licenses/LICENSE,sha256=O34CBRTmdL59PxDYOa6nq1N0-2A9xyXGkBXKbsL1NeY,1070
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+ combatlearn-1.1.2.dist-info/METADATA,sha256=q8cO7ftorW5ESGU9QnDk4F0FJ6_cC_Nl9NZoMVo1Q_I,8978
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+ combatlearn-1.1.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ combatlearn-1.1.2.dist-info/top_level.txt,sha256=3cFQv4oj2sh_NKra45cPy8Go0v8W9x9-zkkUibqZCMk,12
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+ combatlearn-1.1.2.dist-info/RECORD,,
combatlearn-1.1.1.dist-info/RECORD DELETED
@@ -1,7 +0,0 @@
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- combatlearn/__init__.py,sha256=ETYsrj1yK76UxKS8bfnTkzx5XPnk18XsNEgr-6tu6YY,100
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- combatlearn/combat.py,sha256=oiDtJv87PWRJHsWZVZfZ9_uLZbmzS0zl7j128kxIKdY,58992
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- combatlearn-1.1.1.dist-info/licenses/LICENSE,sha256=O34CBRTmdL59PxDYOa6nq1N0-2A9xyXGkBXKbsL1NeY,1070
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- combatlearn-1.1.1.dist-info/METADATA,sha256=ujWyvXi1loi_9Y6Qp-uP9HXUmrM_PPrKaM6Bnc1UfOU,9082
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- combatlearn-1.1.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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- combatlearn-1.1.1.dist-info/top_level.txt,sha256=3cFQv4oj2sh_NKra45cPy8Go0v8W9x9-zkkUibqZCMk,12
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- combatlearn-1.1.1.dist-info/RECORD,,