Unleashing the Power of Data Visualization with t-SNE and Python

Posted by Nova April 4, 2023
t-SNE and Python

Introduction

t-Distributed Stochastic Neighbor Embedding (t-SNE) is a popular machine learning algorithm used for data visualization. It is commonly used to display high-dimensional data in a low-dimensional space, making it easier to analyze and interpret complex data. In this article, we will provide an introduction to t-SNE and walk through a Python example of how to use it.

What is t-SNE?

t-SNE is a dimensionality reduction technique that is commonly used to visualize high-dimensional data. It was introduced in 2008 by Laurens van der Maaten and Geoffrey Hinton as an improvement over other techniques like PCA (Principal Component Analysis) and LLE (Locally Linear Embedding).

t-SNE works by taking a set of high-dimensional data points and mapping them to a low-dimensional space while preserving their pairwise similarities. It does this by minimizing the divergence between two probability distributions: a distribution that measures pairwise similarities between the high-dimensional data points and a distribution that measures pairwise similarities between the corresponding low-dimensional points.

How does t-SNE work?

t-SNE works in two main steps:

  1. Compute the pairwise similarities between the high-dimensional data points
  2. Map the data points to a low-dimensional space in a way that preserves the pairwise similarities

To compute the pairwise similarities, t-SNE uses a Gaussian kernel to convert the Euclidean distances between data points into similarities. This kernel has a bandwidth parameter that determines the width of the kernel and thus how similar two data points need to be to be considered similar.

Once the pairwise similarities have been computed, t-SNE tries to find a low-dimensional embedding of the data that preserves these similarities. It does this by minimizing the Kullback-Leibler divergence between two probability distributions: a distribution over pairs of high-dimensional data points that measures their similarity and a distribution over pairs of low-dimensional points that measures their similarity. The algorithm does this by using a gradient descent method to optimize the embedding.

Python Example

Let’s walk through a Python example of how to use t-SNE to visualize high-dimensional data.

First, we’ll need to install the required libraries:

pip install numpy
pip install matplotlib
pip install scikit-learn

Once the libraries are installed, we can load in our data. For this example, we’ll use the iris dataset, which is a popular dataset that contains measurements of different iris flowers.

from sklearn.datasets import load_iris
import pandas as pd

iris = load_iris()
df = pd.DataFrame(data=iris.data, columns=iris.feature_names)
df['target'] = iris.target

Next, we’ll use t-SNE to reduce the dimensionality of the data and plot it in two dimensions.

from sklearn.manifold import TSNE

tsne = TSNE(n_components=2, perplexity=30.0, random_state=42)
X_tsne = tsne.fit_transform(df.drop('target', axis=1))

df['tsne-2d-one'] = X_tsne[:,0]
df['tsne-2d-two'] = X_tsne[:,1]

import matplotlib.pyplot as plt

plt.figure(figsize=(10,10))
plt.scatter(
    X_tsne[:,0], X_tsne[:,1],
    c=df.target,
    cmap='rainbow'
)
plt.xlabel("t-SNE 1")
plt.ylabel("t-SNE 2")
plt.show()

This code will produce a scatter plot of the iris dataset in two dimensions, with different colors representing different types of iris flowers.

Conclusion

t-SNE is a powerful technique for visualizing high-dimensional data. It works by mapping data points to a low-dimensional space while preserving their pairwise similarities, making it easy to identify patterns and clusters in complex data.

In this article, we provided an introduction to t-SNE, including how it works and its benefits in visualizing high-dimensional data. We also walked through a Python example of how to use t-SNE to reduce the dimensionality of the iris dataset and plot it in two dimensions.

By using t-SNE, data scientists and analysts can more easily explore complex data and identify patterns and relationships that might otherwise be difficult to discern. With its ability to map high-dimensional data to a low-dimensional space while preserving pairwise similarities, t-SNE is a powerful tool for data visualization.

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