Description
Clustering
In this programming assignment you will implement the K-means algorithm and compare it to
agglomerative clustering on the MNIST digit dataset. The MNIST data consists of 20,000 examples
of 28 × 28 images of digits (i.e., numbers from 0-9). There are two files for this assignment.
digits-raw.csv contains the pixel information for each image (first column: image id, second
column: class label, remaining 784 columns: pixel features).
digits-embedding.csv contains a precomputed 2-dimensional embedding of each image using tDistributed Stochastic Neighbor Embedding (tSNE) (first column: image id, second column: class
label, third and fourth columns: image embedding features).
You should implement your solution using Python. You can use supporting libraries like numpy,
scipy as before, but DO NOT use any publicly available code including but not limited to libraries
such as sklearn. As before, you should submit your typed assignment report as a pdf along with
your source code file. (Please don’t forget to put your evaluation and analysis in .pdf
format, make sure to also include the screenshot of the results and/or the output of
the problems in your pdf report.)
In the following sections, we specify a number of steps you are asked to complete for this
assignment. Note that all results in sample outputs are fictitious and for representation
only.
Note: Include the line np.random.seed(0) at the beginning of your code so that it is easier to
compare your answers.
For all the experiments, the definition of Silhoutte Coefficient (SC) is as follows:
For an individual point i:
• A = average distance of ito points in same cluster
• B = average distance of i to points in other clusters
• Si = (B-A) / max(A,B)
SC of clustering = average of Si values for all points i in the dataset.
And, the definition of NMI to be used is: NMI(C, G) = I(C,G)
H(C)+H(G)
. (Please use e as the base of
the log.)
For all metrics that require distance calculation, you should use the Euclidean distance. For
more detail about SC and NMI, please refer to the lecture slides!
1 Exploration (5 pts)
Please put your code for this question in a file called exploration.py, and plots in the report.
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1. Randomly pick one digit from each class in digits-raw.csv and visualize its image as a 28×28
grayscale matrix. In other words, pick one data point from each class (in this dataset, a class
is a “digit” and class membership is given in the second column of the .csv file), and visualize
that data point, utilizing all of its pixel features, as an image (which will be a 28×28 matrix).
2. Visualize 1000 randomly selected examples in 2D from the file digits-embedding.csv, coloring
the points to show their corresponding class labels. Select the examples randomly using the
command np.random.randint(0, N, size=1000), where N is the total number of examples.
2 K-means Clustering
Consider the following setup for questions on K-means Clustering.
• Data/features: Use the digits-embedding.csv data, with the two continuous embedding
features.
• Distance measure: Euclidean distance.
• Starting cluster centers: If there are N points in the dataset, then randomly select K points,
as the starting cluster centroids, using the command np.random.choice(N, K, replace =
False).
• Stopping criteria: Set maximum number of iterations to 50 (In the last iteration, you break
out of the loop after the assignment of points to the cluster and before recomputing the new
centroids). You can also stop when the centroids are not updated.
• Evaluation: You will evaluate the results objectively with (1) within-cluster sum of squared
distances, (2) silhouette coefficient, and (3) normalized mutual information gain (based on
image labels).
2.1 Code (10 pts)
Please put your code for this question in a file called kmeans.py, and include results in the report.
Your python script should take two arguments as input.
1. dataFilename: corresponds to a subset of the embedding data (in the same format as digitsembedding.csv) that should be used as the input data to your algorithm.
2. K: an integer to specify the number of clusters to use.
Your code should read in the data, conduct the k-means algorithm on the data, and print to standard output the within cluster sum of squared distances, silhouette coefficient, and the normalized
mutual information gain for the clustering results. The sample inputs and outputs we expect to
see are as follows (the numbers are fictitious):
$python kmeans.py dataFilename 10
WC-SSD: 1000.524
SC: 0.290
NMI: 0.338
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2.2 Analysis (20 pts)
Consider three versions of the data for each of the questions below:
(i) Dataset 1: use the full dataset digits-embedding.csv;
(ii) Dataset 2: use only the subset of the data consisting of the digits 2, 4, 6 and 7; and
(iii) Dataset 3: use only the subset of the data consisting of the digits 6 and 7.
1. Cluster the data with different values of K ∈ [2, 4, 8, 16, 32] and construct two plots for each
dataset showing the within-cluster sum of squared distances (WC SSD) and silhouette coefficient
(SC) as a function of K.
2. Using the results from Step 1, choose an appropriate K for each dataset and argue why your
choice of K is the best. Discuss how the results compare across the two scores and the three
versions of the data.
3. Repeat Step 1 with 10 times using 10 different random seeds (Note: set the seed using
np.random.seed(x) and you can choose any seed value x as you wish.). Measure and report
the average and standard deviation (for WC SSD and SC) for the different values of K. Discuss
what the results show about k-means sensitivity to initial starting conditions.
4. For the value of K chosen in Step 2, cluster the data again (a single time) and evaluate the
resulting clusters using normalized mutual information gain (NMI). Calculate NMI with respect
to the image class labels. Visualize 1000 randomly selected examples in 2d, coloring the points
to show their corresponding cluster labels. Discuss how both the NMI and visualization results
compare across the three versions of the data.
3 Hierarchical Clustering (15 pts)
Consider the following setup for questions on Hierarchical Clustering.
• Data/features: Use the digits-embedding.csv data, with the two continuous embedding
features.
• Distance measure: Euclidean distance.
1. Put your code for this section in hierarchical.py.
2. Create sub-samples for Dataset 1 in Section 2 by sampling 10 images at random from each
digit group (i.e., 100 images in total). This sample will be used for all the analysis steps of
Hierarchical Clustering. Use the scipy agglomerative clustering method to cluster the data
using single linkage. Plot the dendrogram.
3. Cluster the data again, but this time using (i) complete linkage, and (ii) average linkage. Plot
the associated dendrograms.
4. Consider cutting each of the dendrograms at successive levels of the hierarchy to produce partitions of different sizes (K ∈ [2, 4, 8, 16, 32]). Construct a plot showing the within-cluster sum
of squared distances (WC SSD) and silhouette coefficient (SC) as a function of K.
5. Discuss what value you would choose for K (for each of single, complete, and average linkage)
and whether the results differ from your choice of K using k-means for Dataset 1 in Section 2.
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6. For your choice of K (for each of single, complete, and average linkage), compute and compare
the NMI with respect to the image class labels. Discuss how the NMI obtained compared to the
results from k-means on Dataset 1 in Section 2.
Submission Instructions:
Please submit your assignment through Brightspace:
1. Include in your report which version of Python you are using.
2. Make sure you include in your report all the output / results you get from running your code
for all sub-questions. You may include screen shots to show them.
3. Make a directory named yourF irstN ame yourLastN ame HW5 and copy all of your files to
this directory.
4. DO NOT put the datasets into your directory.
5. Make sure you compress your directory into a zip folder with the same name as described
above, and then upload your zip folder to Brightspace.
Your submission should include the following files:
1. The source code in python.
2. Your evaluation & analysis in .pdf format. Note that your analysis should include visualization
plots as well as a discussion of results, as described in details in the questions above.
3. A README file containing your name, instructions to run your code and anything you would
like us to know about your program (like errors, special conditions, etc).
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