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CIS 520: Machine Learning Due: Apr 14, 2020 (10:29 AM)
Problem Set 4
Submission Instructions:
Unless otherwise announced, all problem sets require submission of two components on Gradescope and
Canvas:
• PDF Submission: This is your main submission, and must contain your solutions to all problems
that you are attempting, including both mathematical problems and programming prob-
lems. It must be submitted as a single PDF file to Gradescope and Canvas, compiled in LATEX
using the LATEX template provided on Canvas. Each problem should be on a new page. Mathematical
problems can be either typed in LATEX or written by hand and scanned into images included in your
LATEX solution, but it must be readable by our staff to be graded; we recommend that you not take
photos of your hand-written solutions. For programming problems, in addition to including any plots,
observations, or explanations as requested, be sure to include a snippet of your code in your LATEX
solution; for this, we encourage you to use mcode or listings packages for LATEX.
Special instruction for submitting on Gradescope: For each problem, select the pages containing your
solution for that problem.
• Code Submission: Submit all your (Matlab) code in a single zip file under the problem set’s code
submission component on Canvas. Submit all your (Matlab) code files (unzipped .m files) to the
problem set’s code submission component on Gradescope. Note that these are in addition to writing
your code inline in the PDF file above.
Summary: The PDF file should be submitted to both Gradescope and Canvas. Matlab code files should
be submitted to Canvas in a single zip file. Also, Matlab code files should be submitted to Gradescope
unzipped. All components of problem set must be received in the right places and in the right formats
before the submission deadline. Plan to submit early!
Collaboration Policy:
You are allowed to discuss problems in groups, but you must write all your solutions and code individually,
on your own. All collaborators with whom problems were discussed must be listed in your PDF submission.
1
2 CIS 520: Machine Learning, Spring 2020, Problem Set 4
1. (20 points) Principal Component Analysis. In this exercise, you are provided part of the MNIST
digit data set, containing 3,600 images of handwritten digits (data is provided in X_train.mat). Each
example is a 28 × 28 grayscale image, leading to 784 pixels. These images correspond to 3 different
digits (’3’, ’6’, and ’9’), although you do not have the labels for them. You will perform PCA in an
unsupervised manner.
(a) To get familiar with what the data looks like, generate the last example (the 3, 600th row of
X_train) as an image. Provide your code and the resulting image. (Hint: You can reshape
the data back into a 28 × 28 image using reshape in MATLAB, and you can use imagesc and
colormap gray to see the picture. Make sure you are able to get the picture to face the right
way, which should look like a ”9”.)
(b) Run PCA on the data. You can use the built-in pca function in MATLAB. (Reminder: Make sure
you understand the MATLAB function you used, especially whether the function standardizes the
data set before running PCA. Make sure that the data is mean-centered.) Just like in the previous
part, generate the first principal component vector as an image. Repeat for the second and third.
Do these images make sense? Explain.
(c) Create a 2D scatter plot showing all the data points projected in the first 2 PC dimensions,
clearly labeling your axes. Make sure the data points are mean-centered before projecting onto
the principal components. Now create a similar plot showing the same data points projected in
the 100th and 101st PC dimensions. What do you observe? Can you explain why you might
expect this?
(d) Graph the (in-sample) fractional reconstruction accuracy as a function of the number of principal
components that are included. Also give a table listing the number of principal components
needed to achieve each of 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, and 10% reconstruction
accuracy (i.e., to explain X% of the variance).
(e) Using the numbers you found in the previous part, reconstruct the 1000th, 2000th, and 3000th
examples using each of the different numbers of principal components. (Hint: We have provided a
function plot_reconstruction.m for your convenience. Make sure you read the documentation
within this function to understand it’s input arguments.) For instance, the last example looks
like:
CIS 520: Machine Learning, Spring 2020, Problem Set 4 3
2. (20 points) EM Practice: Red and Blue Coins. Your friend has two coins: a red coin and a blue
coin, with biases pr and pb, respectively (i.e. the red coin comes up heads with probability pr, and the
blue coin does so with probability pb). She also has an inherent preference pi for the red coin. She
conducts a sequence of m coin tosses: for each toss, she first picks either the red coin with probability
pi or the blue coin with probability 1− pi, and then tosses the corresponding coin; the process for each
toss is carried out independently of all other tosses. You don’t know which coin was used on each toss;
all you are told are the outcomes of the m tosses (heads or tails). In particular, for each toss i, define
a random variable Xi as
Xi =
{
1 if the i-th toss results in heads
0 otherwise.
Then the data you see are the values x1, . . . , xm taken by these m random variables. Based on this
data, you want to estimate the parameters θ = (pi, pr, pb). To help with this, for each toss i, define a
latent (unobserved) random variable Zi as follows:
Zi =
{
1 if the i-th toss used the red coin
0 otherwise.
(a) Let X be a random variable denoting the outcome of a coin toss according to the process described
above, and let Z be the corresponding latent random variable indicating which coin was used,
also as described above (both X and Z take values in {0, 1} as above). Write an expression for
the joint distribution of X and Z. Give your answer in the form
p(x, z; θ) = .
(b) Write an expression for the complete-data log-likelihood, lnLc(θ) =
∑m
i=1 ln p(xi, zi; θ).
(c) Suppose you knew the values zi taken by the latent variables Zi. What would be the maximum-
likelihood parameter estimates θ?? Give expressions for pi, p?r, and p?b (in terms of xi and zi). Show
your calculations.
(d) In the absence of knowledge of zi, one possibility for estimating θ is to use the EM algorithm.
Recall that the algorithm starts with some initial parameter estimates θ0, and then on each
iteration t, performs an E-step followed by an M-step. Let θt denote the parameter estimates
at the start of iteration t. In the E-step, for each toss i, the algorithm requires computing the
posterior distribution of the latent variable Zi under the current parameters θ
t. Calculate the
posterior probability P(Zi = 1 |Xi = xi; θt).
(e) For each toss i, denote the posterior probability computed in part (d) above by γti (so that
γti = P(Zi = 1 |Xi = xi; θt)). Then the expected complete-data log-likelihood with respect to
these posterior distributions is
m∑
i=1
(
γti · ln p(xi, 1; θt) + (1− γti ) · ln p(xi, 0; θt)
)
.
The M-step of the EM algorithm requires finding parameters θt+1 that maximize this expected
complete-data log-likelihood. Determine the updated parameters θt+1. Give expressions for pit+1,
pt+1r , and p
t+1
b (in terms of xi and γ
t
i ). Show your calculations.
3. (25 points) Programming Exercise: Gaussian Mixture Models. Write a piece of MATLAB code
to implement the EM algorithm for learning a Gaussian mixture model (GMM) given a data set X,
where X is an m× d matrix (m instances, each of dimension d), and a target number of Gaussians K:
your program should take the training data X and the target number of Gaussians K as input and
should output estimated parameters of a mixture of K Gaussians (specifically, it should output mixing
4 CIS 520: Machine Learning, Spring 2020, Problem Set 4
coefficients p?i ∈ ?K , mean vectors µ?1, . . . , µ?K ∈ Rd, and covariance matrices Σ?1, . . . , Σ?K ∈ Rd×d).
For this problem, you are provided a 2-dimensional data set generated from a mixture of (3) Gaussians.
The data set is divided into training and test sets; the training set has 480 data points and the test
set has 120 data points. The goal is to learn a GMM from the training data; the quality of the learned
GMM will be measured via its log-likelihood on the test data.
EM initialization and stopping criterion: Initialize the mixing coefficients to a uniform distribu-
tion, and each of the covariance matrices to be the d× d identity matrix: pi0 = (1/K, . . . , 1/K)>, and
Σ01 = . . . = Σ
0
K = Id. Initializations for the means will be provided to you (if you like, you can write
your program to take the mean initialization as an additional input). For the stopping criterion, on each
iteration t, keep track of the (incomplete-data) log-likelihood on the training data,
∑m
i=1 ln p(xi; θ
t);
stop when either the change in log-likelihood,
∑m
i=1 ln p(xi; θ
t+1)−∑mi=1 ln p(xi; θt), becomes smaller
than 10−6, or when the number of iterations reaches 1000 (whichever occurs earlier; here θt denotes
the parameter estimates on iteration t).
(a) Known K. For this part, assume you are given K = 3.
i. Learning curve. Use your implementation of EM for GMMs to learn a mixture of 3 Gaus-
sians from increasing fractions of the training data (10% of the training data, then 20% of
the training data, then 30% and so on upto 100%). You must use the subsets provided
in the folder TrainSubsets; in each case, to initialize the means of the Gaussians, use the
initializations provided in the folder MeanInitialization. In each case, calculate the nor-
malized (incomplete-data) log-likelihood of the learned model on the training data, as well
as the normalized log-likelihood on the test data (here normalizing means dividing the log-
likelihood by the number of data points); you can use the provided file compute llh.m to
compute the log-likelihood. In a single plot, give curves showing the normalized train and
test log-likelihoods (on the y-axis) as a function of the fraction of data used for training (on
the x-axis). (Note: the training log-likelihood should be calculated only on the subset of
examples used for training, not on all the training examples available in the given data set.)
ii. Analysis of learned models. For each of the learned models (corresponding to the different
subsets of the training data), show a plot of the Gaussians in the learned GMM overlaid on
the test data. What do you observe? For the final model (learned from 100% of the training
data), also write down all the parameters of the learned GMM, together with the (normalized)
train and test log-likelihoods.
Hints:
i. You may use the function we provide in plot contours.m to assist in plotting the density
curves. Be sure to carefully read the function header, so you know how to structure your
inputs. If you choose to do this, you may find it convenient to format the parameters output
by your GMM function in the data structures expected by plot contours.m
(b) Unknown K. Now suppose you do not know the right number of Gaussians in the mixture
model to be learned. Select the number of Gaussians K from the range {1, . . . , 5} using 5-fold
cross-validation on the full training data (use the folds provided in the folder CrossValidation).
For each K, to initialize the means of the K Gaussians, use the initializations provided in the
folder MeanInitialization. In a single plot, draw 3 curves showing the (normalized) train, test,
and cross-validation log-likelihoods (on the y-axis) as a function of number of Gaussians K (on
the x-axis); again, you can use the provided file compute llh.m to compute the normalized log-
likelihood. Write down the chosen value of K (with the highest cross-validation log-likelihood).
4. (35 points) Hidden Markov Models. On any given day, Alice is in one of two states: happy or sad.
You do not know her internal state, but get to observe her activities in the evening. Each evening, she
either sings, goes for a walk, or watches TV.
CIS 520: Machine Learning, Spring 2020, Problem Set 4 5
Alice’s state on any day is random. Her state Z1 on day 1 is equally likely to be happy or sad:
P (Z1 = happy) = 1/2 .
Given her state Zt on day t, her state Zt+1 on the next day is governed by the following probabilities
(and is conditionally independent of her previous states and activities):
P (Zt+1 = happy |Zt = happy) = 4/5 P (Zt+1 = happy |Zt = sad) = 1/2 .
Alice’s activities are also random. Her activities vary based on her state; given her state Zt on day t,
her activity Xt on that day is governed by the following probabilities (and is conditionally independent
of everything else):
P (Xt = sing |Zt = happy) = 5/10 P (Xt = sing |Zt = sad) = 1/10
P (Xt = walk |Zt = happy) = 3/10 P (Xt = walk |Zt = sad) = 2/10
P (Xt = TV |Zt = happy) = 2/10 P (Xt = TV |Zt = sad) = 7/10 .
(a) (15 points) Suppose you observe Alice singing on day 1 and watching TV on day 2, i.e. you
observe x1:2 = (sing,TV). Find the joint probability of this observation sequence together with
each possible hidden state sequence that could be associated with it, i.e. find the four probabilities
below. Show your calculations.
P
(
X1:2 = (sing,TV), Z1:2 = (happy, happy)
)
P
(
X1:2 = (sing,TV), Z1:2 = (happy, sad)
)
P
(
X1:2 = (sing,TV), Z1:2 = (sad, happy)
)
P
(
X1:2 = (sing,TV), Z1:2 = (sad, sad)
)
Based on these probabilities, what is the most likely hidden state sequence z1:2? What is the
individually most likely hidden state on day 2 ?
(b) (20 points) Write a small piece of Matlab code to implement the Viterbi algorithm, and use this
to calculate both the most likely hidden state sequence z1:10 and the corresponding maximal joint
probability p(x1:10, z1:10) for each of the following observation sequences:
x1:10 = (sing,walk,TV, sing,walk,TV, sing,walk,TV, sing)
x1:10 = (sing, sing, sing,TV,TV,TV,TV,TV,TV,TV)
x1:10 = (TV,walk,TV, sing, sing, sing,walk,TV, sing, sing)
In your code, rather than multiplying probabilities (which can lead to underflow), you may find
it helpful to add their logarithms (and later exponentiate to obtain the final result). Include a
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