High-Dimensional

Data Visualization
 High-Dimensional Data Visualization refers to techniques used to
represent datasets that contain many variables (or features) in a way
that can be understood visually, usually in two or three dimensions.
 Since our visual perception is limited to three dimensions, visualizing
high-dimensional data presents a challenge, which is tackled through
dimensionality reduction and specialized visualization methods.
Techniques for High-Dimensional Data Visualization:

1. Principal Component Analysis (PCA): PCA reduces the

dimensionality of data while retaining most of the variance.
It projects data into a lower-dimensional space (e.g., from
hundreds of dimensions to 2 or 3) so that you can visualize it.
 Example: Suppose you have a dataset of patient health
metrics (e.g., heart rate, blood pressure, glucose levels) with
10 variables.
 Applying PCA might reduce these to 2 or 3 principal
components, which can be plotted to reveal patterns or
clusters in patient health profiles.
 t-SNE
(t-Distributed Stochastic
Neighbor Embedding):
 t-SNE is particularly good for
visualizing clusters in high-dimensional
data by converting similarities
between data points into probabilities
and embedding them in a lower-
dimensional space.
 Example:
 UMAP (Uniform Manifold Approximation
and Projection): UMAP is similar to t-SNE but
tends to preserve more of the global structure
of data, often used for large datasets to
visualize clusters or neighborhoods in the data.
 Example: UMAP can be applied to image data
(like handwritten digits or facial expressions) to
reduce hundreds of features (pixels) into 2D or
3D for visual exploration.
 Parallel Coordinates: This method involves
plotting all the dimensions as parallel axes and
connecting points with lines.
 This technique helps in identifying relationships
between variables.
 Example:
 For a dataset with patient attributes (e.g., age,
weight, cholesterol level), parallel coordinates can
show trends, such as how higher cholesterol tends
to be associated with older patients.
 Radial Plots or Star Plots: Radial plots can
represent each dimension as a spoke from a central
point, and the values of data points are plotted on
these spokes, forming shapes that can be
compared.
 Example:
 Each spoke in a radial plot could represent a
financial metric (e.g., revenue, profit margin), and
plotting multiple companies' financial data could
reveal their strengths and weaknesses.
 Example in Healthcare:
 Let’s consider a PCA example for patient diagnostic data:
• Dataset: Health data with 12 features (e.g., age, blood pressure,
cholesterol, glucose level, heart rate, etc.)
• Objective: Visualize patterns to differentiate patients based on risk
factors.
• PCA Application: Reduce the 12 dimensions to 2 principal
components.
• Result: A 2D scatter plot where each point represents a patient, and
clustering of points might indicate different risk profiles (e.g., high-
risk and low-risk groups).
 t-SNE in Genomic Data Analysis
• Scenario: You are working with high-dimensional genomic data, where
each sample has thousands of gene expressions, and you want to
identify clusters or patterns.
• Steps:
• Prepare the dataset, which contains expression levels of genes across
multiple samples.
• Apply t-SNE to reduce the data from thousands of dimensions to 2 or 3
dimensions.
• Visualize the results using a scatter plot, where each point represents a
sample, and its position reflects the similarity in gene expression.
• Clusters may appear that correspond to different types of cells, tissues, or
conditions (e.g., cancer vs. non-cancer samples).
 UMAP in Customer Segmentation
• Scenario: A retail company wants to visualize and segment its
customers based on purchasing behavior, with hundreds of features
describing each customer's transaction history.
• Steps:
• Gather customer data with features like purchase frequency, average
order value, product categories, etc.
• Use UMAP to reduce the dimensions of the dataset.
• Create a 2D scatter plot where each point is a customer, and customers
with similar behaviors form clusters.
• Identify distinct customer segments, such as "frequent buyers," "discount
seekers," or "luxury shoppers."
 PCA in Credit Risk Analysis
• Scenario: A financial institution wants to visualize its credit risk data,
which contains multiple features for each client (e.g., income, loan
amount, credit score, employment status).
• Steps:
• Gather the dataset with features like credit history, income level, and loan
status.
• Use PCA to reduce the dataset from, say, 15 dimensions to 2 or 3 principal
components.
• Create a 2D scatter plot where each point represents a client, with the axes
representing the principal components.
• Observe the clusters and separations. Clients in certain regions of the plot
may be high-risk or low-risk based on their profile.
 Parallel Coordinates in Healthcare Data
• Scenario: You want to explore relationships between multiple health
metrics (e.g., age, BMI, blood pressure, cholesterol levels) for patients
in a healthcare study.
• Steps:
• Each health metric is represented as a vertical axis in the parallel
coordinates plot.
• Each patient's metrics are connected by lines that cross all axes.
• The lines may reveal relationships between variables. For instance, lines
for patients with high BMI may consistently show higher cholesterol and
blood pressure.
 Radial (Star) Plots in Market Analysis
• Scenario: A company is analyzing the performance of different
products in terms of various features like sales, profit margin,
customer reviews, etc.
• Steps:
• Use a radial plot (also known as a radar chart or star plot) where each
axis represents a product feature.
• Plot the performance of different products on the same chart.
• The shape of each product’s plot gives a visual representation of its
strengths and weaknesses compared to others.
 Heatmaps for High-Dimensional Data in Biology
• Scenario: In a drug discovery study, you have data on how hundreds
of drugs affect thousands of genes. You want to find patterns in the
gene expression changes across different drugs.
• Steps:
• Use a heatmap where rows represent genes and columns represent drugs.
• Each cell in the heatmap is color-coded to represent the level of gene
expression change (e.g., upregulated or downregulated).
• Patterns can emerge that show which drugs affect similar genes or
pathways.
• Benefit: Heatmaps make it easy to spot clusters of similar behavior
across many variables.