Pairwise Similarity and Sorting Samples

Question

The following is a problem from an assignment that I am trying to solve:

Visualization of similarity matrix. Represent every sample with a four-dimension vector (sepal length, sepal width, petal length, petal width). For every two samples, compute their pair-wise similarity. You may do so using the Euclidean distance or other metrics. This leads to a similarity matrix where the element (i,j) stores the similarity between samples i and j. Please sort all samples so that samples from the same category appear together. Visualize the matrix using the function imagesc() or any other function.

Here is the code I have written so far:

load('iris.mat'); % create a table of the data
iris.Properties.VariableNames = {'Sepal_Length' 'Sepal_Width' 'Petal_Length' 'Petal_Width' 'Class'}; % change the variable names to their actual meaning
iris_copy = iris(1:150,{'Sepal_Length' 'Sepal_Width' 'Petal_Length' 'Petal_Width'}); % make a copy of the (numerical) features of the table
iris_distance = table2array(iris_copy); % convert the table to an array

% pairwise similarity
D = pdist(iris_distance); % calculate the Euclidean distance and store the result in D
W = squareform(D); % convert to squareform
figure()
imagesc(W); % visualize the matrix

Now, I think I've got the coding mostly right to answer the question. My issue is how to sort all the samples so that samples from the same category appear together because I got rid of the names when I created the copy. Is it already sorted by converting to squareform? Other suggestions? Thank you!

timbo timbo · Accepted Answer · 2019-03-02T01:24:20

It should be in the same order as the original data. While you could sort it afterwards, the easiest solution is to actually sort your data by class after line 2 and before line 3.

load('iris.mat'); % create a table of the data
iris.Properties.VariableNames = {'Sepal_Length' 'Sepal_Width' 'Petal_Length' 'Petal_Width' 'Class'}; % change the variable names to their actual meaning
% Sort the table here on the "Class" attribute. Don't forget to change the table name
% in the next line too if you need to.
iris_copy = iris(1:150,{'Sepal_Length' 'Sepal_Width' 'Petal_Length' 'Petal_Width'}); % make a copy of the (numerical) features of the table

Consider using sortrows:

tblB = sortrows(tblA,'RowNames') sorts a table based on its row names. Row names of a table label the rows along the first dimension of the table. If tblA does not have row names, that is, if tblA.Properties.RowNames is empty, then sortrows returns tblA.

Pairwise Similarity and Sorting Samples

1 Answers