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Improved line formatting
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machine_learning/t_stochastic_neighbour_embedding.py

Lines changed: 20 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -12,12 +12,11 @@ def collect_dataset() -> tuple[ndarray, ndarray]:
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Returns:
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tuple[ndarray, ndarray]: Feature matrix and target labels.
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Example:
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>>> features, targets = collect_dataset()
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>>> features.shape
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(150, 4)
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>>> targets.shape
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(150,)
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>>> features, targets = collect_dataset()
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>>> features.shape
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(150, 4)
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>>> targets.shape
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(150,)
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"""
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iris_dataset = load_iris()
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return np.array(iris_dataset.data), np.array(iris_dataset.target)
@@ -34,11 +33,10 @@ def compute_pairwise_affinities(data_matrix: ndarray, sigma: float = 1.0) -> nda
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Returns:
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ndarray: Symmetrized probability matrix.
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37-
Example:
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>>> x = np.array([[0.0, 0.0], [1.0, 0.0]])
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>>> probabilities = compute_pairwise_affinities(x)
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>>> float(round(probabilities[0, 1], 3))
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0.25
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>>> x = np.array([[0.0, 0.0], [1.0, 0.0]])
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>>> probabilities = compute_pairwise_affinities(x)
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>>> float(round(probabilities[0, 1], 3))
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0.25
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"""
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n_samples = data_matrix.shape[0]
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squared_sum = np.sum(np.square(data_matrix), axis=1)
@@ -63,11 +61,10 @@ def compute_low_dim_affinities(embedding_matrix: ndarray) -> tuple[ndarray, ndar
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Returns:
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tuple[ndarray, ndarray]: (Q probability matrix, numerator matrix).
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Example:
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>>> y = np.array([[0.0, 0.0], [1.0, 0.0]])
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>>> q_matrix, numerators = compute_low_dim_affinities(y)
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>>> q_matrix.shape
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(2, 2)
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>>> y = np.array([[0.0, 0.0], [1.0, 0.0]])
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>>> q_matrix, numerators = compute_low_dim_affinities(y)
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>>> q_matrix.shape
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(2, 2)
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"""
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squared_sum = np.sum(np.square(embedding_matrix), axis=1)
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numerator_matrix = 1 / (
@@ -101,11 +98,10 @@ def apply_tsne(
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Returns:
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ndarray: Low-dimensional embedding of the data.
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Example:
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>>> features, _ = collect_dataset()
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>>> embedding = apply_tsne(features, n_components=2, n_iter=50)
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>>> embedding.shape
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(150, 2)
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>>> features, _ = collect_dataset()
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>>> embedding = apply_tsne(features, n_components=2, n_iter=50)
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>>> embedding.shape
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(150, 2)
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"""
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if n_components < 1 or n_iter < 1:
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raise ValueError("n_components and n_iter must be >= 1")
@@ -147,10 +143,9 @@ def main() -> None:
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"""
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Run t-SNE on the Iris dataset and display the first 5 embeddings.
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Example:
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>>> main() # doctest: +ELLIPSIS
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t-SNE embedding (first 5 points):
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[[...
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>>> main() # doctest: +ELLIPSIS
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t-SNE embedding (first 5 points):
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[[...
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"""
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features, _labels = collect_dataset()
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embedding = apply_tsne(features, n_components=2, n_iter=300)

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