The Tutorial of

Principal Component Analysis, Hierarchical

Clustering, and Multidimensional Scaling
Wenshan Wang
Multi-dimensional Scaling (MDS)

Multi-dimensional scaling (MDS) is a method that represents measurements
of similarity (or dissimilarity) among pairs of objects as distances between
points of a low-dimensional multidimensional space.

------------ Ingwer Borg and Patrick J.F. Groenen
From <<Modern Multidimensional Scaling: Theory and Applications>>
Purposes of using MDS
Exploratory technique
Testing Structural Hypotheses
Similarity Judgments
Principal Component Analysis (PCA)
Principal Component Analysis is a method of
identifying the pattern of data set by a much
smaller number of new variables, named as
principal components.
Objectives of using PCA
Explaining correlations between designs (row)
and original variables (column) in the data set.
Explore the proximities of designs or variables
Using a lower dimensional space that is
sufficient to represent most of variances of
data.
Compare PCA and MDS
PCA using covariance matrix to
analyze the correlation
between designs and variables.
Thus, the correlation reflects on
the plot are dot products.
MDS using distance and loss-function
to analyze the proximities of designs,
which is represented by cross products
How to read PCA charts?
1. PCA eigenvalues & cumulative weight
Eigenvalues are the explained variances of principal components and its
cumulative weights (blue line).
How to read PCA charts?
2. PCA score charts
2-D chart plots the projections of original variables
on a reduced two dimensions by first two principal
components.
Arrows represent the relative contribution of the
original variables to the variability along the first
two PCs. The longer the arrow, the higher the
strength of the contribution. Arrows orthogonal to
PC1 (PC2) have null contribution along PC1 (PC2).
Arrows collinear with PC1 (PC2) contribute only on
PC1 (PC2).
---------------modeFRONTIER help document
3-D chart plots the projections of original
variables and designs on a reduced three
dimensions by first three principal components.
All others are similar as those in 2-D chart
How to read PCA charts?
3. PCA loading charts
An Geometric Programming Example
Geometric Programming Problem:
Usually, the row vectors in the data table are named as observations or designs,
and the columns are named as variables, including inputs and outputs.
An Geometric Programming Example
Principal Component Analysis (PCA)
Part 1: Correlations between variables and PCs
An Geometric Programming Example
Principal Component Analysis (PCA)
Part 2: Designs and Variables
Figure 1. Loading Chart
Figure 2. Score Chart Figure 3. Parallel Coordination Chart
An Geometric Programming Example
Principal Component Analysis (PCA)
Part 2: (continue) Designs and Variables
How do designs influence other design variables?
Figure 1. Loading Chart
**Hint**: software automatically chooses necessary number of principal components, which is
showed in the loading chart.

**Bug**: Direction and Magnitude of
variables originally showed in the software are
incorrect if not choosing PC1 VS. PC2.
Figure 2. Score Chart Figure 3. Parallel Coordination Chart
An Geometric Programming Example
Principal Component Analysis (PCA)
Part 2: (continue) PCA & Correlation Matrix
Run Log: Selected Variables = [x1, x2, x3, y] , Eigenvalue 1 = 1.998E0, Eigenvalue 2 = 1.003E0, Eigenvalue 3 = 9.992E-1, Eigenvalue 4
= 8.882E-16, Percentage of Explained Variance: PC1 : 50.0%, PC2 : 25.1%, PC3 : 25.0%, PC4 : 0.0%
Normally, when looking at a bi-dimensional PCA chart, if a variable is collinear to PC1(PC2), it contributes
to PC1(PC2) only, while if this variable is orthogonal to PC1(PC2), it has no influence on PC1(PC2).
Moreover, if a variable has a larger projection along PC1(PC2) than PC2(PC1), it contributes more to
PC1(PC2) than PC2(PC1). Usually, PC1 is more important than PC2, or the same, thus variables
contributes more to PC1 should be the interesting variables that customers needs to analysis.

The correlation between variables showed in the PCA chart can also be verified by the correlation matrix.
An Geometric Programming Example
Hierachical Clustering (HC)
Part 2: Quality and Property of Current Clusters
Clustering Analysis is the procedure of grouping designs into new groups, called clusters by their
proximities. Hierarchical Clustering, or in detail, Agglomerative Hierarchical Clustering, merge designs into
various groups using a linage criterion, which is a function calculating a pairwise distance between
designs. In order to know how well the current clustering represents the proximity of designs, Descriptive
and Discriminating Features table is provided for further evaluation. Please click x Cluster to see the
table.
An Geometric Programming Example
Hierachical Clustering
Part 1: PCA & Hierarchical Clustering
Usually, using uncategorized designs are still difficult to predict the influences on variables. Therefore, employing other
multivariate methods are necessary for users to accomplish a decision making. Hierarchical Clustering is available in
modeFRONTIER 4.2.1, which groups designs into clusters with a bottom-up strategy. Conduct hierarchical clustering is a
simple procedure and we assume readers know how to implement it now.
Colors in charts represent different clusters. We pick different variables to conduct analysis, and find that the clusters are
organized by a bottom-up strategy following the direction of the vector product of all arrows chosen.
An Geometric Programming Example
Hierachical Clustering
Part 2: Conduct A DM with HC
Parallel charts are useful to discover which variables determinate cluster structure as
indicated by internal and external similarity values.
----------- modeFRONTIER help document
From left parallel charts show that if the target is to minimize all design variables, then
decision making (DM) should consider the yellow cluster would be better. Moreover,
customers can also depend on various to choose designs that fit the requirement.
An Geometric Programming Example
Hierachical Clustering
Part 3: Check the Similarity
How should we check the similarity between clusters with a straightforward view? Mountain View Plot
shows it. Users are recommended to look at three parts:
1. Relative position of the peaks, which
reflects the similarity between clusters. It
is calculated by Multidimensional Scaling
on cluster centroids.
2. The sigma of each peak is proportional to
the size of the corresponding cluster
3. The height of each peak is proportional to
the Internal Similarity of the
corresponding cluster (as calculated in
Descriptive and Discriminating table)
An Geometric Programming Example
Multidimensional Scaling (MDS)
Part 1: A Lower-dimensional Measurement
Similar to hierarchical clustering, multidimensional scaling also shows the similarity
between a pair of designs into a distance measure, but distinction of this method is in a
lower-dimensional space by minimizing the stress function, or called as loss function.
Usually, a two dimensional or three dimensional space is usually used for visualizing the
similarity of designs.
1. Inputs projections
on a bi-dimensional
space
2. Decay of stress
function
3. Run Log
An Geometric Programming Example
Multidimensional Scaling (MDS)
Part 2: Reduced Bi-dimensional Space
MDS can be generalized using various design variables. Designs are categorized by hierarchical
clustering, and the following charts show the projections of designs on a reduced two dimensional
space.
An Geometric Programming Example
Multidimensional Scaling (MDS)
Part 3: Shepard Plot
Shepard Plot shows the distances between projections in the reduced 2-D space (y
axis) against those between samples in the original space (x axis).
Narrow linear distribution of points indicates a good MDS.
Is better than
An Geometric Programming Example
Multidimensional Scaling (MDS)
Part 4: 3-D Score Plot
MDS 3D plots display projections of designs on the x-y coordination, and z axis shows the value of
parameter selected by the user.
An Geometric Programming Example
Multidimensional Scaling (MDS)
Part 5: Hierarchical Clustering & MDS
Click on Paint Categorized, hierarchical clustering results are displayed on the chart. Unlike PCA or
MDS, hierarchical clustering depends on all dimensions, therefore, this method is able to be
combined with other multivariate analysis. By using hierarchical clustering, customers can discretize
designs clearly.