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[pre-commit.ci] auto fixes from pre-commit.com hooks
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machine_learning/t_stochastic_neighbour_embedding.py

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -48,7 +48,9 @@ def compute_pairwise_affinities(data_matrix: ndarray, sigma: float = 1.0) -> nda
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# Compute pairwise squared Euclidean distances
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squared_sum = np.sum(np.square(data_matrix), axis=1)
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squared_distance = (
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squared_sum[:, np.newaxis] + squared_sum[np.newaxis, :] - 2 * np.dot(data_matrix, data_matrix.T)
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squared_sum[:, np.newaxis]
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+ squared_sum[np.newaxis, :]
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- 2 * np.dot(data_matrix, data_matrix.T)
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)
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# Gaussian kernel
@@ -78,7 +80,9 @@ def compute_low_dim_affinities(embedding_matrix: ndarray) -> tuple[ndarray, ndar
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"""
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squared_sum = np.sum(np.square(embedding_matrix), axis=1)
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squared_distance = (
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squared_sum[:, np.newaxis] + squared_sum[np.newaxis, :] - 2 * np.dot(embedding_matrix, embedding_matrix.T)
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squared_sum[:, np.newaxis]
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+ squared_sum[np.newaxis, :]
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- 2 * np.dot(embedding_matrix, embedding_matrix.T)
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)
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numerator_matrix = 1 / (1 + squared_distance)
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np.fill_diagonal(numerator_matrix, 0)

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