Clustering Solution




Clustering algorithms are unsupervised methods for finding groups of data points that have similar representations in a feature space. Clustering differs from classification in that no a priori labeling (grouping) of the data points is available.

K-means clustering is a simple and popular clustering algorithm. Given a set of data points fx1; : : : ; xN g in multidimensional space, it tries to find K clusters s.t. each data point belongs to one and only one cluster, and the sum of the squares of the distances between each data point and the center of the cluster it belongs to is minimized. If we define k to be the “center” of the kth cluster, and


rnk = 1; if xn is assigned to cluster k ; n = 1; : : : ; N k = 1; : : : ; K 0; otherwise


Then our goal is to find rnk’s and k’s that minimize J = rnk xn k2. The approach

n=1 k=1

of K-means algorithm is to repeatedly perform the following two steps until convergence:

  1. (Re)assign each data point to the cluster whose center is nearest to the data point.

  1. (Re)calculate the position of the centers of the clusters: setting the center of the cluster to the mean of the data points that are currently within the cluster.

The center positions may be initialized randomly.

In this project, the goal includes:

  1. To find proper representations of the data, s.t. the clustering is efficient and gives out reasonable results.

  1. To perform K-means clustering on the dataset, and evaluate the performance of the clus-tering.

  1. To try different preprocessing methods which may increase the performance of the clus-tering.


We work with “20 Newsgroups” dataset that we already explored in Project 1. It is a collection of approximately 20,000 documents, partitioned (nearly) evenly across 20 different


newsgroups, each corresponding to a different category (topic). Each topic can be viewed as a “class”.

In order to define the clustering task, we pretend as if the class labels are not available and aim to find groupings of the documents, where documents in each group are more similar to each other than to those in other groups. We then use class labels as the ground truth to evaluate the performance of the clustering task.

To get started with a simple clustering task, we work with a well separable portion of the data set that we used in Project 1, and see if we can retrieve the known classes. Specifically, let us define two classes comprising of the following categories.

Table 1: Two well-separated classes

Class 1


Class 2

We would like to evaluate how purely the a priori known classes can be reconstructed through clustering. That is, we take all the documents belonging to these two classes and perform unsupervised clustering into two clusters. Then we determine how pure each cluster is when we look at the labels of the documents belonging to each cluster.

Before the following parts, to ensure consistency, please set the random seed as follows:

import numpy as np


import random


Use the settings as in the following code to load the data:

categories = [‘’, ‘’,

‘comp.sys.mac.hardware’, ‘’,

‘’, ‘’,

‘’, ‘’]

dataset = fetch_20newsgroups(subset=‘all’, categories=categories, shuffle=True, random_state=42)

Problem Statement

  1. Building the TF-IDF matrix.

Following the steps in Project 1, transform the documents into TF-IDF vectors. Use min_df = 3, exclude the stopwords (no need to do stemming or lemmatization). QUESTION 1: Report the dimensions of the TF-IDF matrix you get.

  1. Apply K-means clustering with k = 2 using the TF-IDF data. Note that the KMeans class in sklearn has parameters named random_state, max_iter and n_init. Please use random_state=0, max_iter 1000 and n_init 301. Compare the clustering results

  • If you have enough computation power, the larger the better


with the known class labels. (you can refer to sklearn – Clustering text documents using k-means for a basic work flow)

  1. Given the clustering result and ground truth labels, contingency table A is the matrix whose entries Aij is the number of data points that belong to both the class Ci the cluster Kj.

QUESTION 2: Report the contingency table of your clustering result.

  1. In order to evaluate clustering results, there are various measures for a given partition of the data points with respect to the ground truth. We will use the measures ho-mogeneity score, completeness score, V-measure, adjusted Rand score and adjusted mutual info score, all of which can be calculated by the corresponding functions provided in sklearn.metrics.

    • Homogeneity is a measure of how “pure” the clusters are. If each cluster con-tains only data points from a single class, the homogeneity is satisfied.

    • On the other hand, a clustering result satisfies completeness if all data points of a class are assigned to the same cluster. Both of these scores span between 0 and 1; where 1 stands for perfect clustering.

    • The V-measure is then defined to be the harmonic average of homogeneity score and completeness score.

    • The adjusted Rand Index is similar to accuracy measure, which computes similarity between the clustering labels and ground truth labels. This method counts all pairs of points that both fall either in the same cluster and the same class or in different clusters and different classes.

    • Finally, the adjusted mutual information score measures the mutual infor-mation between the cluster label distribution and the ground truth label distri-butions.

QUESTION 3: Report the 5 measures above for the K-means clustering results you get.

  1. Dimensionality reduction

As you may have observed, high dimensional sparse TF-IDF vectors do not yield a good clustering result. One of the reasons is that in a high-dimensional space, the Euclidean distance is not a good metric anymore, in the sense that the distances between data points tends to be almost the same (see [1]).

K-means clustering has other limitations. Since its objective is to minimize the sum of within-cluster l2 distances, it implicitly assumes that the clusters are isotropically shaped, i.e. round-shaped. When the clusters are not round-shaped, K-means may fail to identify the clusters properly. Even when the clusters are round, K-means algorithm may also fail when the clusters have unequal variances. A direct visualization for these problems can be found at sklearn – Demonstration of k-means assumptions.

In this part we try to find a “better” representation tailored to the way that K-means clustering algorithm works, by reducing the dimension of our data before clustering.

We will use Singular Value Decomposition (SVD) and Non-negative Matrix Factorization (NMF) that you are already familiar with for dimensionality reduction.

    1. First we want to find the effective dimension of the data through inspection of the top singular values of the TF-IDF matrix and see how many of them are significant in reconstructing the matrix with the truncated SVD representation. A guideline is to see what ratio of the variance of the original data is retained after the dimensionality reduction.


QUESTION 4: Report the plot of the percent of variance the top r principle compo-nents can retain v.s. r, for r = 1 to 1000.

Hint: explained_variance_ratio_ of TruncatedSVD objects. See sklearn docu-ment.

  1. Now, use the following two methods to reduce the dimension of the data. Sweep over the dimension parameters for each method, and choose one that yields better results in terms of clustering purity metrics.

Truncated SVD / PCA

Note that you don’t need to perform SVD multiple times: performing SVD with r = 1000 gives you the data projected on all the top 1000 principle components, so for smaller r’s, you just need to exclude the least important features.



Let r be the dimension that we want to reduce the data to (i.e. n_components).

Try r = 1; 2; 3; 5; 10; 20; 50; 100; 300, and plot the 5 measure scores v.s. r for both SVD and NMF.

Report the best r choice for SVD and NMF respectively.

Note: what is “best” after all? What if some measures contradict with each other? Here you are faced with this challenge that you need to decide which measure you value the most, and design your own standard of “best”.

Please explain your standard and justify it.

QUESTION 6: How do you explain the non-monotonic behavior of the measures as r increases?

4. (a) Visualization.

We can visualize the clustering results by projecting the dim-reduced data points onto 2-D plane with SVD, and coloring the points according to

  • Ground truth class label

  • Clustering label


QUESTION 7: Visualize the clustering results for:

    • SVD with its best r

    • NMF with its best r

  1. Now try the transformation methods below to see whether they increase the clustering performance. Perform transformation on SVD-reduced data and NMF-reduced data, respectively. Still use the best r we had in previous parts.

    • Scaling features s.t. each feature has unit variance, i.e. each column of the reduced-dimensional data matrix has unit variance (if we use the convention that rows correspond to documents).

    • Applying a non-linear transformation to the data vectors. Here we use logarithm transformation below as an example (try c = 0:01):


) (



xi > 0

f(x) = sign(x)


xi = 0

j j




xi < 0



Try combining both transformations (in both orders).

To sum up, you are asked to try 2 (2 + 2) = 8 combinations.

QUESTION 8: Visualize the transformed data as in part (a).

QUESTION 9: Can you justify why the “logarithm transformation” may improve the clustering results?

QUESTION 10: Report the new clustering measures (except for the contingency ma-trix) for the clustering results of the transformed data.

  1. Expand Dataset into 20 categories

In this part we want to examine how purely we can retrieve all 20 original sub-class labels with clustering. Therefore, we need to include all the documents and the corresponding terms in the data matrix and find proper representation through dimensionality reduction of the TF-IDF representation.

QUESTION 11: Repeat the following for 20 categories using the same parameters as in

2-class case:

    • Transform corpus to TF-IDF matrix;

    • Directly perform K-means and report the 5 measures and the contingency matrix;

QUESTION 12: Try different dimensions for both truncated SVD and NMF dimensional-ity reduction techniques and the different transformations of the obtained feature vectors as outlined in above parts.

You don’t need to report everything you tried, which will be tediously long. You are asked, however, to report your best combination, and quantitatively report how much better it is compared to other combinations. You should also include typical combinations showing what choices are desirable (or undesirable).


Please submit a zip file containing your report, and your codes with a readme file on how to run your code to CCLE. The zip file should be named as “Project2_UID1_UID2_…” where UIDx’s are student ID numbers of the team members. If you had any questions, please ask on Piazza or through email.


  1. Why is Euclidean distance not a good metric in high dimensions? [online].