Description
Three datasets (Iris, Cho, Iyer) with cluster labels are provided. In each dataset file, the
last column is the cluster label, and the remaining columns are attributes.
In this assignment, you need to implement Principle Component Analysis (PCA) algorithm
to map high-dimensional data to 2 dimensions, and plot the 2-dimensional data points. You
are not allowed to call existing PCA libraries directly. If you are not sure about whether it
is OK to use a certain function, please post your question on Piazza.
Please take the following steps:
1. The template based on Python is provided. You are asked to complete the required
functions (pca and plot) in that template. Please do not change the input and output
provided in the template. The details of the template are explained as follows:
There are four functions in the template: loadDataSet, pca, plot and the main function.
The loadDataSet function is to load the dataset from the csv file. The input of this function
is the filename of the dataset and the outputs are the data matrix (dataMat) and
corresponding labels (labelMat). Each row in the dataMat represents an observation and
each column in the dataMat represents an attribute. Each entry of labelMat is the label
corresponding to each row of dataMat.
You need to implement PCA algorithm in the pca function. The input of the pca function
is dataMat obtained from the loadDataSet function and the number of dimensions after
PCA transformation which is set to be 2. The output of the pca function is the twodimensional data(lowDDataMat) after PCA transformation.
In the plot function you need to plot all observations as scatter plots and color the data
points according to their labels. You also need to save the figure. The input to the plot
function is the data matrix after PCA transformation (lowDDataMat) obtained from the
pca function, the label vector (labelMat) obtained from the loadDataSet function and the
name of the saved figure (figname).
The aforementioned functions are called in the main function. To run the template, you can
use the command line and then type the following command:
Python pca_template.py [filename]
You can also run the template in an IDE and specify the configuration.
The parameter filename is an optional parameter to specify the name of the data file you
want to read. If it is not specified, the default value (‘iris_with_cluster.csv’) will be used.
2. Apply PCA on the Iris dataset and get the two-dimensional data points. Draw them in a
scatter plot, and color them according to their cluster labels. Compare the scatter plot with
the given plots below and see if you get the plot correctly. If your plot matches either of
the following plots, it is correct.
Iris Data
3. If Step 2 works fine, then apply PCA on the Cho and Iyer datasets and draw a scatter
plot for each dataset following the same procedure discussed in Step 2.
4. Prepare your submission. Your final submission should be a zip file named as
Assignment1.zip. In the zip file, you should include:
• The python code.
• Report: A doc or pdf file named as Assignment1.doc or Assignment1.docx or
Assignment1.pdf. The report should consist of the following parts: 1) Two scatter plots
obtained by running PCA on Cho and Iyer datasets. Please label them properly by the dataset
names and have tick marks along both axes in each plot. 2) The codes of PCA and plot
drawing.
5. Submit the zip file under Assignment 1 on Brightspace.
Please refer to Course Syllabus for late submission policy and academic integrity policy. This
assignment must be done independently. Running your submitted code should be able to reproduce
the plots in the report.