4bd8d42a46e311a263a0c0acc018bed6cc3a629b,Python/phate/phate.py,PHATE,von_neumann_entropy,#PHATE#Any#,394

Before Change

            raise NotFittedError("This PHATE instance is not fitted yet. Call "
                                 ""fit" with appropriate arguments before "
                                 "using this method.")
        diff_aff = np.diagflat(
            np.power(np.sum(self.gs_ker, axis=0), 1 / 2))
        diff_aff = np.matmul(np.matmul(diff_aff, self.gs_ker),
                             diff_aff)
        diff_aff = (diff_aff + diff_aff.T) / 2

        _, eigenvalues, _ = svd(diff_aff)
        entropy = []

After Change

            diff_aff = sparse.diags(np.array(diff_aff)[0])
        else:
            diff_aff = np.diagflat(diff_aff)
        diff_aff = diff_aff @ self.gs_ker @ diff_aff
        diff_aff = (diff_aff + diff_aff.T) / 2

        if is_sparse:
            _, eigenvalues, _ = sparse.linalg.svds(
                diff_aff, diff_aff.shape[0] - 1)
        else:
            _, eigenvalues, _ = svd(diff_aff)
        entropy = []
        eigenvalues_t = np.copy(eigenvalues)
        for _ in range(t_max):
            prob = eigenvalues_t / np.sum(eigenvalues_t)

Instances