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CS 506 Spring 2020 - HW1
Clustering and Visualization
Due: October 19, 2020
1 Understanding K-means Clustering
In this exercise, you will implement the K-means clustering algorithm. You will
start on an example 2D dataset that will help you gain an intuition of how the
K-means algorithm works. You will be using k means clustering.py for this part
of the exercise.
1.1 Implementing K-means
The K-means algorithm is a method to automatically cluster similar data examples
together. Concretely, you are given a training set , and want to group the data into a few cohesive clusters. The intuition
behind K -means is an iterative procedure that starts by guessing the initial
centroids, and then refines this guess by repeatedly assigning examples to their
closest centroids and then recomputing the centroids based on the assignments.
The inner loop of the algorithm repeatedly carries out two steps:
• Assigning each training example x to its closest centroid
• Recomputing the mean of each centroid using the points assigned to it.
The K-means algorithm will always converge to some final set of means for
the centroids. Note that the converged solution may not always be ideal and
depends on the initial setting of the centroids. Therefore, in practice the Kmeans
algorithm is usually run a few times with different random initializations.
One way to choose between these different solutions from different random initializations
is to choose the one with the lowest cost function value (distortion).
You will implement the two phases of the K-means algorithm separately in the
next sections.
1.1.1 Finding Closest Centroids
In the cluster assignment phase of the K-means algorithm, the algorithm assigns
every training example x
to its closest centroid, given the current positions of
where c(i) is the index of the centroid that is closest to x
, and j is the position
(index) of the j-th centroid.
Your task is to complete the code in function find closest centroids. This
function takes the data matrix samples and the locations of all centroids inside
centroids and should output a one-dimensional array of clusters that holds the
index (a value in {1, · · · , K}, where K is total number of centroids) of the closest
centroid to every training example. You can implement this using a loop over
every training example and every centroid. Once you have completed the code
in find closest centroids, you can run it and you should see the output [0, 2, 1, ]
corresponding to the centroid assignments for the first 3 examples.
Please take a look at Figure 1 to gain an understanding of the distribution
of the data. It is two dimentional, with x1 and x2.
Figure 1: Result 1
1.1.2 Computing Centroid Means
Given assignments of every point to a centroid, the second phase of the algorithm
recomputes, for each centroid, the mean of the points that were assigned to it.
Specifically, for every centroid k we set
µk :=
where Ck is the set of examples that are assigned to centroid k. Concretely, if
two examples say x
3 and x
5 are assigned to centroid k = 2, then you should
µ2 =
(x(3) + x(5))
Once you have completed the code in get centroids, the k means clustering.py
will run your code and output the centroids after the first step of K-means.
The final centroids should be [[1.95399466 5.02557006] [3.04367119 1.01541041]
[6.03366736 3.00052511]].
When you run the next step, the K-means code will produce a visualization
that steps you through the progress of the algorithm at each iteration. Close
figure multiple times to see how each step of the K-means algorithm changes
the centroids and cluster assignments. At the end, your figure should look as
the one displayed in Figure1
1.2 Random Initialization
The initial assignments of centroids for the example dataset in previous section
were designed so that you will see the same figure as Figure1. In practice, a
good strategy for initializing the centroids is to select random examples from
the training set. In this part of the exercise, you should complete the function
choose random centroids. You should randomly permute the indices of the examples
(using random seed 7). Then, it selects the first K examples based on
the random permutation of the indices. This should allow the examples to be
selected at random without the risk of selecting the same example twice. You
will see how random initialization will affect the first few iterations of clustering,
and also possibly, result in a different cluster assignment.
2 Working with the Algorithms
• In this assignment we will be working with the AirBnB dataset, that you
can also find here. Our goal is to visualize areas of the NYC with respect
to the price of the AirBnb listings in those areas.
From the detailed nyc listings.csv file, you will use longitude and latitude
to cluster closeness and price to cluster for expensiveness.
Note that spatial coordinates and price are in different units, so you may
need to consider scaling in order to avoid arbitrary skewed results.
a) [8 pts.] Find clusters using the 3 different techniques we discussed
in class: k-means++, hierarchical, and GMM. Explain your data
representation and how you determined certain parameters (for example,
the number of clusters in k-means++).
b) [3 pts.] List a few bullet points describing the pros and cons of the various
clustering algorithms.
A few hints:
-Some listings contain missing values. Better strategy for this assignment is to
completely ignore those listings.
-Pay attention to the data type of every column when you read a .csv file and
convert them to the appropriate types (e.g. float or integer).
3 Data visualization
a) [1pt.] Start by producing a Heatmap using the Folium package (you can
install it using pip). You can use the code below to help you (assumes the
use of Pandas Dataframes):
def generateBaseMap ( d e f a u l t l o c a t i o n =[ 4 0. 6 9 3 9 4 3 ,
−7 3. 9 8 5 8 8 0] ) :
base map = f oli um .Map( l o c a t i o n=d e f a u l t l o c a t i o n )
return base map
base map = generateBaseMap ( )
HeatMap ( data=d f [ [ ’ l a t i t u d e ’ , ’ l o n gi t u d e ’ , ’ p r i c e ’ ] ] .
groupby ( [ ’ l a t i t u d e ’ , ’ l o n gi t u d e ’ ] ) . mean ( ) .
r e s e t i n d e x ( ) . v al u e s . t o l i s t ( ) , r a di u s =8, max zoom
=13) . add t o ( base map )
base map . s a ve ( ’ inde x . html ’ )
Is this heatmap useful in order to draw conclusions about the expressiveness
of areas within NYC? If not, why?
b) [2pts.] Visualize the clusters by plotting the longitude/latitude of every
listing in a scatter plot.
c) [2pts.] For every cluster report the average price of the listings within this
d) Bonus points [1pt.] if you provide a plot on an actual NYC map! You
may use Folium or any other package for this.
e) [1pt.] Are the findings in agreement with what you have in mind about
the cost of living for neighborhoods in NYC? If you are unfamiliar with
NYC, you can consult the web.
4 Image Manipulation
a) [8 pts.] Download the image found by clicking here. For this assignment,
you will use the k-means algorithm in the CS506 python package that you
built in class to manipulate this image. The goal is to give this image as
input, and return the image with like pixels combined into 10 clusters.
A few hints:
-There are a number of useful packages for working with images; we recommend
using cv2 (obtained by running pip install opencv). Using this
package, you can use the line img = cv2.imread(“file.jpg”) in order to
load the image as a numpy array (note that this means you will also need
to import numpy).
-If you follow the hint above, your data is no longer being opened from a
file inside your k mean() function so you may need to tweak it a bit.
-To display the image after you have run k-means, you can use the lines
cv2.imshow(‘Display Window’, manipulated img)
-Each pixel is represented by three features: their red, green, and blue
values. You only need to tweak your algorithm to find clusters and then
replace the pixels with the value of their cluster center.
-The more clusters you work with, the slower this algorithm will run, so
for testing it may be useful to work with only 2 clusters.
Here is the starting image:
And here is what your code should return: