Exploring Dimensionality Reduction on a Small Dataset

What will you learn?

In this comprehensive guide, you will delve into the world of dimensionality reduction techniques by exploring how to apply them to a small dataset with dimensions 50×20. You will grasp the fundamentals of Principal Component Analysis (PCA) and t-Distributed Stochastic Neighbor Embedding (t-SNE) through practical implementation. By the end, you’ll have a solid understanding of how these methods can simplify complex datasets for visualization and machine learning tasks.

Introduction to the Problem and Solution

When working with datasets containing numerous features, high dimensionality can lead to challenges such as overfitting and increased computational complexity. Dimensionality reduction techniques come to the rescue by streamlining the model through a reduction in input variables while striving to retain crucial information.

In our scenario with a modest dataset size of 50 samples and 20 features, employing dimensionality reduction proves advantageous for enhancing visualization capabilities or preparing data for machine learning algorithms. We will focus on two prominent methods: PCA and t-SNE. These techniques excel at uncovering patterns within data by reducing dimensions while preserving inter-point relationships effectively.


from sklearn.decomposition import PCA
from sklearn.manifold import TSNE
import matplotlib.pyplot as plt

def apply_dimension_reduction(X):
    # Applying PCA
    pca = PCA(n_components=2)
    X_pca = pca.fit_transform(X)

    # Applying t-SNE
    tsne = TSNE(n_components=2, random_state=0)
    X_tsne = tsne.fit_transform(X)

    # Plotting results
    plt.figure(figsize=(12, 6))

    plt.subplot(1, 2, 1)
    plt.title('PCA Result')
    plt.scatter(X_pca[:, 0], X_pca[:, 1])

    plt.subplot(1, 2, 2)
    plt.title('t-SNE Result')
    plt.scatter(X_tsne[:,0], X_tsne[:,1])

apply_dimension_reduction(your_dataset_here) # Replace your_dataset_here with your actual data.

# Copyright PHD


In this section, we break down the essence of each technique:

  • Principal Component Analysis (PCA):

    • Identifies variations and significant patterns in the dataset.
    • Aims to discover principal components that maximize variance.
  • t-Distributed Stochastic Neighbor Embedding (t-SNE):

    • Focuses on keeping similar instances close while separating dissimilar ones.
    • Ideal for visualizing high-dimensional data in lower-dimensional spaces like two or three dimensions.

The provided code snippet demonstrates: – Initialization of PCA and t-SNE from scikit-learn library. – Transformation of the dataset (X) into two components for easy visualization. – Side-by-side plotting of results using matplotlib for comparative analysis.

This visual approach aids in assessing how well each method segregates different classes or clusters within the dataset effectively.

  1. What is Dimensionality Reduction?

  2. Dimensionality reduction involves transforming high-dimensional space into a lower one while retaining essential characteristics to reveal underlying patterns more distinctly.

  3. Why use Dimensionality Reduction?

  4. It helps combat overfitting issues caused by an excessive number of features relative to available samples. Additionally, it significantly reduces computational costs, making analyses more manageable.

  5. When should I choose PCA over t-SNE?

  6. PCA is preferable when aiming to capture maximum variance using fewer components. While computationally less intensive than t-SNE, it may not always offer intuitive cluster separation in cases involving nonlinear feature relationships.

  7. Can I reverse dimensionality reduction process?

  8. While perfect reversal isn’t feasible due to information loss during transformation, PCA allows some reconstruction back into the original space with approximation errors. Conversely, reversing t-SNE transformations poses challenges due its non-linear nature.

  9. How do I choose ‘n_components’?

  10. The selection depends on your objective; for visualization purposes, setting n_components to 2 or 3 is recommended. For preprocessing before modeling, experimentation based on performance evaluation might be necessary to strike a balance between simplicity and retaining critical information.

  11. Is scaling important before applying these techniques?

  12. Yes! Both PCA and t-SNE assume equal importance among features; hence normalizing feature scales beforehand enhances performance by preventing undue influence from variables operating at larger scales compared to others in the dataset.


Dimensionality reduction serves as a vital toolset for managing complexities inherent in vast dimensional spaces. By focusing on what truly matters within your data through visualization enhancements and preprocessing steps before deeper analysis or modeling endeavors; understanding nuances between different approaches ensures selecting the right tool for success when handling small datasets like ours presented here presents an excellent opportunity grasp fundamentals behind powerful concepts reusable skills across wide variety applications future endeavors!

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