Scribd Logo
Upload

Welcome to Scribd!

  • 42 views

    Chapter 2

    Uploaded by

    Anto

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd

    Chapter 2

    Uploaded by

    Anto
    42 views39 pages

    Original Title

    chapter2 (5)

    Copyright

    © © All Rights Reserved

    Available Formats

    PDF, TXT or read online from Scribd

    Did you find this document useful?

    Is this content inappropriate?

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    42 views39 pages

    Chapter 2

    Uploaded by

    Anto

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    of 39

    Introduction to

    hierarchical
    clustering
    UN SUP ERVISED L EARN IN G IN R

    Hank Roark
    Senior Data Scientist at Boeing
    Hierarchical clustering
    Number of clusters is not known ahead of time

    Two kinds: bo om-up and top-down, this course bo om-up

    UNSUPERVISED LEARNING IN R
    Simple example

    UNSUPERVISED LEARNING IN R
    Five clusters

    UNSUPERVISED LEARNING IN R
    Four clusters

    UNSUPERVISED LEARNING IN R
    Three clusters

    UNSUPERVISED LEARNING IN R
    Two clusters

    UNSUPERVISED LEARNING IN R
    One cluster

    UNSUPERVISED LEARNING IN R
    Hierarchical clustering in R
    # Calculates similarity as Euclidean distance
    # between observations
    dist_matrix <- dist(x)
    # Returns hierarchical clustering model
    hclust(d = dist_matrix)

    Call:
    hclust(d = s)

    Cluster method : complete


    Distance : euclidean
    Number of objects: 50

    UNSUPERVISED LEARNING IN R
    Let's practice!
    UN SUP ERVISED L EARN IN G IN R
    Selecting number of
    clusters
    UN SUP ERVISED L EARN IN G IN R

    Hank Roark
    Senior Data Scientist at Boeing
    Interpreting results
    # Create hierarchical cluster model: hclust.out
    hclust.out <- hclust(dist(x))
    # Inspect the result
    summary(hclust.out)

    Length Class Mode


    merge 98 -none- numeric
    height 49 -none- numeric
    order 50 -none- numeric
    labels 0 -none- NULL
    method 1 -none- character
    call 2 -none- call
    dist.method 1 -none- character

    UNSUPERVISED LEARNING IN R
    Dendrogram
    Tree shaped structure used to interpret hierarchical clustering models

    UNSUPERVISED LEARNING IN R
    Dendrogram
    Tree shaped structure used to interpret hierarchical clustering models

    UNSUPERVISED LEARNING IN R
    Dendrogram
    Tree shaped structure used to interpret hierarchical clustering models

    UNSUPERVISED LEARNING IN R
    Dendrogram
    Tree shaped structure used to interpret hierarchical clustering models

    UNSUPERVISED LEARNING IN R
    Dendrogram
    Tree shaped structure used to interpret hierarchical clustering models

    UNSUPERVISED LEARNING IN R
    Dendrogram plotting in R
    # Draws a dendrogram
    plot(hclust.out)
    abline(h = 6, col = "red")

    UNSUPERVISED LEARNING IN R
    Tree "cutting" in R
    # Cut by height h
    cutree(hclust.out, h = 6)

    1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 3 3
    3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 4 2 4 2 4 4

    # Cut by number of clusters k


    cutree(hclust.out, k = 2)

    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2
    2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1

    UNSUPERVISED LEARNING IN R
    Let's practice!
    UN SUP ERVISED L EARN IN G IN R
    Clustering linkage
    and practical
    matters
    UN SUP ERVISED L EARN IN G IN R

    Hank Roark
    Senior Data Scientist at Boeing
    Linking clusters in hierarchical clustering
    How is distance between clusters determined? Rules?

    Four methods to determine which cluster should be linked


    Complete: pairwise similarity between all observations in cluster 1 and cluster 2, and uses
    largest of similarities

    Single: same as above but uses smallest of similarities

    Average: same as above but uses average of similarities

    Centroid: nds centroid of cluster 1 and centroid of cluster 2, and uses similarity between
    two centroids

    UNSUPERVISED LEARNING IN R
    Linking methods: complete and average

    UNSUPERVISED LEARNING IN R
    Linking method: single

    UNSUPERVISED LEARNING IN R
    Linking method: centroid

    UNSUPERVISED LEARNING IN R
    Linkage in R
    # Fitting hierarchical clustering models using different methods
    hclust.complete <- hclust(d, method = "complete")
    hclust.average <- hclust(d, method = "average")
    hclust.single <- hclust(d, method = "single")

    UNSUPERVISED LEARNING IN R
    Practical matters
    Data on di erent scales can cause undesirable results in clustering methods

    Solution is to scale data so that features have same mean and standard deviation
    Subtract mean of a feature from all observations

    Divide each feature by the standard deviation of the feature

    Normalized features have a mean of zero and a standard deviation of one

    UNSUPERVISED LEARNING IN R
    Practical matters
    # Check if scaling is necessary
    colMeans(x)

    -0.1337828 0.0594019

    apply(x, 2, sd)

    1.974376 2.112357

    UNSUPERVISED LEARNING IN R
    Practical matters
    # Produce new matrix with columns of mean of 0 and sd of 1
    scaled_x <- scale(x)
    colMeans(scaled_x)

    2.775558e-17 3.330669e-17

    apply(scaled_x, 2, sd)

    1 1

    UNSUPERVISED LEARNING IN R
    Let's practice!
    UN SUP ERVISED L EARN IN G IN R
    Review of
    hierarchical
    clustering
    UN SUP ERVISED L EARN IN G IN R

    Hank Roark
    Senior Data Scientist at Boeing
    Hierarchical clustering review
    # Fitting various hierarchical clustering models
    hclust.complete <- hclust(d, method = "complete")
    hclust.average <- hclust(d, method = "average")
    hclust.single <- hclust(d, method = "single")

    UNSUPERVISED LEARNING IN R
    Linking methods: complete and average

    UNSUPERVISED LEARNING IN R
    Hierarchical clustering

    UNSUPERVISED LEARNING IN R
    Iterating

    UNSUPERVISED LEARNING IN R
    Dendrogram

    UNSUPERVISED LEARNING IN R
    How k-means and hierarchical clustering differ

    UNSUPERVISED LEARNING IN R
    Practical matters
    # Scale the data
    pokemon.scaled <- scale(pokemon)

    # Create hierarchical and k-means clustering models


    hclust.pokemon <- hclust(dist(pokemon.scaled), method = "complete")
    km.pokemon <- kmeans(pokemon.scaled, centers = 3,
    nstart = 20, iter.max = 50)

    # Compare results of the models


    cut.pokemon <- cutree(hclust.pokemon, k = 3)
    table(km.pokemon$cluster, cut.pokemon)
    cut.pokemon

    1 2 3
    1 242 1 0
    2 342 1 0
    3 204 9 1

    UNSUPERVISED LEARNING IN R
    Let's practice!
    UN SUP ERVISED L EARN IN G IN R

    You might also like