Assignment 3
Due: Saturday, May 12 Due:
Wednesday, May 16
For this assignment you will experiment with various regression approaches
and you'll get your feet wet with some clustering. We will rely on subsets of
some realworld data sets and on tools from the
Scikitlearn machine learning
package for Python as well as modules from the textbook code (Machine Learning
in Action, Chapters 8 and 10).
 Linear Regression [Dataset:
communities.zip]
For this problem you will experiment with linear regression models to
make predictions with numerical data. You will also explore more systematic
methods for feature selection and for optimizing model parameters (model
selection). The data set you will use is a subset
of the "Communities and Crime" data set that combines information from the
1990 census data as well as FBI crime data from 1995. Please read the
full description of the data,
including the description and statistics on different variables. The target
attribute for regression purposes is "ViolentCrimesPerPop". The two
identifier attributes "state" and "community name" should be excluded for
the regression task.
Your tasks in this problem are the following [Note: for these
tasks you will use the available linearmodels from scikitlearn as
well as the
implementations of the relevant approaches from the Ch. 8 of MLA] .
 Load and preprocess the data using Pandas or Numpy and, if
necessary, preprocessing functions
from scikitlearn. The provided data is already normalized (see
description), so there is no
need for additional normalization. Compute and display basic statistics
(mean, standard deviation, min, max, etc.) for each of the variables in the
data set. Separate the target attribute for regression.
 Perform standard linear regression on data
using the implementation for Ch. 8 of MLA. Compute the RMSE value on the full training data. Also, plot the correlation
between the predicted and actual values of the target attribute. Display the
obtained regression coefficients (weights). Finally, perform 10fold
crossvalidation and compare the crossvalidation RMSE to the
training RMSE (for cross validation, you should use the KFold
module from sklearn.cross_validation).
 Feature Selection:
use the scikitlearn regression model from
sklearn.linear_model with a subset of features to
perform linear regression. For feature selection, write a script or function
that takes as
input the training data, target variable; the model; and any other
parameters you find necessary, and returns the optimal percentage of the
most informative features to use. Your approach should use kfold
crossvalidation on the training data (you can use k=5). You can use
feature_selection.SelectPercentile
to find the most informative variables. Show the list of most informative
variables and their weights [Note: since this is regression
not classification, you should use
feature_selection.f_regression as scoring function rather
than
chi2). Next, plot the model's mean
absolute error
values on crossvalidation relative to the percentage of selected features
(See scikitlearn's
metrics.mean_absolute_error).
In order to use
cross_validation.cross_val_score with regression you'll need
to pass to it
scoring='mean_absolute_error' as a parameter.
[Hint: for an example of a similar feature selection
process please review the
class example notebook. Also, review
scikitlearn documentation for feature selection.]
 Next, perform Ridge Regression and Lasso Regression using the modules from
sklearn.linear_model. In each case, perform systematic model
selection to identify the optimal alpha
parameter. First, create a 20%80% randomized split of the data. Set aside
the test portion; the model selection process should be performed using the
80% training data partition. You should create a function that takes as
input the data and target variable; the parameter to vary and a list of its
values; the model to be trained; and any other relevant input needed to
determine the optimal value for the specified parameter. The model selection
process should perform kfold cross validation (k should be a parameter,
but you can select k=5 for this problem). You should also plot the error
values on the training and crossvalidation splits across the specified
values of the alpha parameter. Finally,
using the best alpha value, run the model on the setaside test data.
Discuss your observation and conclusions. [Hint: for an
example of a similar model selection process please review the
class example notebook.]
 Next, perform regression using
Stochastic Gradient Descent for regression. For this part, you should use
the
SGDRegessor module from
sklearn.linear_model.
Again, start by a creating randomized 80%20% traintest split. SGDRegessor requires that features be standardized (with 0 mean and scaled
by standard deviation). Prior to fiting the model, perform the scaling using
StandardScaler from
sklearn.preprocessing. For this problem, perform a grid search (using
GridSearchCV from
sklearn.grid_search) Your grid search should compare combinations of
two penalty parameters ('l2', 'l1') and different values of alpha (alpha
could vary from 0.0001 which is the default to relatively large values, say
10).
Using the best parameters, apply the model to the setaside test data.
Finally, perform model selection (similar to part d, above) to find the best
"l1_ratio" parameter using SGDRegressor with the "elasticnet" penalty
parameter. [Note: "l1_ratio" is The Elastic Net mixing
parameter, with 0 <= l1_ratio <= 1; l1_ratio=0 corresponds to L2
penalty, l1_ratio=1 to L1 penalty; defaults to 0.15.] Using the best mixing
ratio, apply the Elastic Net model to the setaside test data. Provide a summary of your findings
from the above experiments.
 Automatic Document Clustering [Dataset:
newsgroups5.zip]
For this problem you will use a different subset of the 20 Newsgroup data set
that you used in Assignment 2 (see the
description of the full
dataset). The subset for this assignment includes 2,500 documents
(newsgroup posts), each belonging to one of 5 categories windows (0),
crypt (1), christian (2), hockey (3), forsale
(4). The documents are represented by 9328 terms (stems). The dictionary
(vocabulary) for the data set is given in the file "terms.txt" and the full
termbydocument matrix is given in "matrix.txt" (comma separated values).
The actual category labels for the documents are provided in the file "classes.txt".
Your goal in this assignment is to perform clustering on the documents and
compare the clusters to the actual categories.
Your tasks in this problem are the following [Note: for the
clustering part of this assignment you should use the
kMeans module form Ch. 10 of MLA (use the
version provided here as it includes some corrections to the book version).
You may also use Pandas and other modules from scikitlearn that you may
need for preprocessing or evaluation.]
 Create your own distance function that, instead
of using Euclidean distance, uses Cosine similarity. This is the distance
function you will use to pass to the kMeans function.
 Load the data set [Note: the data matrix provided
has terms as rows and documents as columns. Since you will be clustering
documents, you'll need to take the transpose of this matrix so that your
main data matrix is a document x term matrix. In Numpy, you may use the ".T"
operation to obtain the transpose.] Then, split the data set (the document x term matrix) and set aside 20% for later use (see
below). Use the 80% segment for clustering in the next part. The 20% portion
must be a random subset.
 Perform Kmeans clustering on the training data. Write a function
to display the top N terms in each cluster along with the cluster DF values
for each term and the size of the cluster. The cluster DF value for a term
t in a cluster C is the percentage of docs in cluster
C in which term t appears (so, if a
cluster has 500 documents, and term "game" appears in 100 of those 500
documents, then DF value of "game" in that cluster is 0.2 or 20%). Sort the terms
for each cluster in decreasing order of the DF
percentage. Here is an example of how this
output might look like (here the top 10 terms for 3 of the 5 clusters
are displayed in decreasing order of cluster DF values, but the mean
frequnecy from the cluster centroid is also shown). [Extra Credit: use your favorite third party tool,
ideally with a Python based API, to create a word cloud for each cluster.]
 Using the cluster assignments from Kmeans clustering,
compare your 5 clusters to the 5 preassigned classes by computing the
Completeness and Homogeneity values.
 Finally, using your cluster assignments as class labels,
categorize each of the documents in the 20% setaside data into each of the
appropriate cluster. Your categorization should be based on Cosine
similarity between each test document and cluster centroids. For each test
document show the predicted class label as well as Cosine similarity to the
corresponding cluster.
Notes on Submission: You must submit your Jupyter Notebook
(similar to examples in class) which includes your documented code, results of
your interactions, and any discussions or explanations of the results. Please
organize your notebook so that it's clear what parts of the notebook correspond
to which problems in the assignment. Please submit the notebook in both IPYNB
and HTML formats (along with any auxiliary files). Your assignment should be submitted
via D2L.
