plot_swissroll.py

"""
===================================
Swiss Roll And Swiss-Hole Reduction
===================================
This notebook seeks to compare two popular non-linear dimensionality
techniques, T-distributed Stochastic Neighbor Embedding (t-SNE) and
Locally Linear Embedding (LLE), on the classic Swiss Roll dataset.
Then, we will explore how they both deal with the addition of a hole
in the data.
"""
# %%
# Swiss Roll
# ---------------------------------------------------
#
# We start by generating the Swiss Roll dataset.

import matplotlib.pyplot as plt
from sklearn import manifold, datasets


sr_points, sr_color = datasets.make_swiss_roll(n_samples=1500, random_state=0)

# %%
# Now, let's take a look at our data:

fig = plt.figure(figsize=(8, 6))
ax = fig.add_subplot(111, projection="3d")
fig.add_axes(ax)
ax.scatter(
    sr_points[:, 0], sr_points[:, 1], sr_points[:, 2], c=sr_color, s=50, alpha=0.8
)
ax.set_title("Swiss Roll in Ambient Space")
ax.view_init(azim=-66, elev=12)
_ = ax.text2D(0.8, 0.05, s="n_samples=1500", transform=ax.transAxes)

# %%
# Computing the LLE and t-SNE embeddings, we find that LLE seems to unroll the
# Swiss Roll pretty effectively. t-SNE on the other hand, is able
# to preserve the general structure of the data, but, poorly represents the
# continuous nature of our original data. Instead, it seems to unnecessarily
# clump sections of points together.

sr_lle, sr_err = manifold.locally_linear_embedding(
    sr_points, n_neighbors=12, n_components=2
)

sr_tsne = manifold.TSNE(
    n_components=2, learning_rate="auto", perplexity=40, init="pca", random_state=0
).fit_transform(sr_points)

fig, axs = plt.subplots(figsize=(8, 8), nrows=2)
axs[0].scatter(sr_lle[:, 0], sr_lle[:, 1], c=sr_color)
axs[0].set_title("LLE Embedding of Swiss Roll")
axs[1].scatter(sr_tsne[:, 0], sr_tsne[:, 1], c=sr_color)
_ = axs[1].set_title("t-SNE Embedding of Swiss Roll")

# %%
# .. note::
#
#     LLE seems to be stretching the points from the center (purple)
#     of the swiss roll. However, we observe that this is simply a byproduct
#     of how the data was generated. There is a higher density of points near the
#     center of the roll, which ultimately affects how LLE reconstructs the
#     data in a lower dimension.

# %%
# Swiss-Hole
# ---------------------------------------------------
#
# Now let's take a look at how both algorithms deal with us adding a hole to
# the data. First, we generate the Swiss-Hole dataset and plot it:

sh_points, sh_color = datasets.make_swiss_roll(
    n_samples=1500, hole=True, random_state=0
)

fig = plt.figure(figsize=(8, 6))
ax = fig.add_subplot(111, projection="3d")
fig.add_axes(ax)
ax.scatter(
    sh_points[:, 0], sh_points[:, 1], sh_points[:, 2], c=sh_color, s=50, alpha=0.8
)
ax.set_title("Swiss-Hole in Ambient Space")
ax.view_init(azim=-66, elev=12)
_ = ax.text2D(0.8, 0.05, s="n_samples=1500", transform=ax.transAxes)

# %%
# Computing the LLE and t-SNE embeddings, we obtain similar results to the
# Swiss Roll. LLE very capably unrolls the data and even preserves
# the hole. t-SNE, again seems to clump sections of points together, but, we
# note that it preserves the general topology of the original data.


sh_lle, sh_err = manifold.locally_linear_embedding(
    sh_points, n_neighbors=12, n_components=2
)

sh_tsne = manifold.TSNE(
    n_components=2, learning_rate="auto", perplexity=40, init="random", random_state=0
).fit_transform(sh_points)

fig, axs = plt.subplots(figsize=(8, 8), nrows=2)
axs[0].scatter(sh_lle[:, 0], sh_lle[:, 1], c=sh_color)
axs[0].set_title("LLE Embedding of Swiss-Hole")
axs[1].scatter(sh_tsne[:, 0], sh_tsne[:, 1], c=sh_color)
_ = axs[1].set_title("t-SNE Embedding of Swiss-Hole")

# %%
#
# Concluding remarks
# ------------------
#
# We note that t-SNE benefits from testing more combinations of parameters.
# Better results could probably have been obtained by better tuning these
# parameters.
#
# We observe that, as seen in the "Manifold learning on
# handwritten digits" example, t-SNE generally performs better than LLE
# on real world data.