Based on the issue description and my knowledge of scikit-learn's codebase, I can construct the appropriate patch. The fix involves: 1. Adding `svd_flip` import in `kernel_pca.py` 2. Applying `svd_flip` to the eigenvectors (`alphas_`) after the eigendecomposition to ensure consistent signs In scikit-learn 0.18.x, the file is at `sklearn/decomposition/kernel_pca.py`. The key function is `_fit_transform` where eigenvectors are computed using either `linalg.eigh` or `eigsh` (arpack). --- a/sklearn/decomposition/kernel_pca.py +++ b/sklearn/decomposition/kernel_pca.py @@ -12,6 +12,7 @@ from scipy.sparse.linalg import eigsh from ..utils import check_random_state from ..utils.validation import check_is_fitted, check_array +from ..utils.extmath import svd_flip from ..exceptions import NotFittedError from ..base import BaseEstimator, TransformerMixin, _UnstableOn32BitMixin from ..preprocessing import KernelCenterer @@ -147,6 +148,10 @@ class KernelPCA(BaseEstimator, TransformerMixin, _UnstableOn32BitMixin): # sort eigenvectors in descending order indices = self.lambdas_.argsort()[::-1] self.lambdas_ = self.lambdas_[indices] self.alphas_ = self.alphas_[:, indices] + # flip eigenvectors' sign to enforce deterministic output + self.alphas_, _ = svd_flip(self.alphas_, + np.zeros_like(self.alphas_).T) + # remove eigenvectors with a zero eigenvalue if self.remove_zero_eig or self.n_components is None: