STATS306B STATS306B. Clustering. Jonathan Taylor Department of Statistics Stanford University. June 3, 2010
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1 STATS306B Jonathan Taylor Department of Statistics Stanford University June 3, 2010 Spring 2010
2 Outline K-means, K-medoids, EM algorithm choosing number of clusters: Gap test hierarchical clustering spectral clustering
3 K-means Figure: Simulated data in the plane, clustered into three classes (represented by red, blue and green) by the K-means clustering algorithm. From ESL.
4 K-means Algorithm 1. For each data point, the closest cluster center (in Euclidean distance) is identified; 2. Each cluster center is replaced by the coordinatewise average of all data points that are closest to it. 3. Steps 1. and 2. are alternated until convergence. Algorithm converges to a local minimum of the within-cluster sum of squares. 4. Typically one uses multiple runs from random starting guesses, and chooses the solution with lowest within cluster sum of squares.
5 K-means Figure: Successive iterations of the K-means clustering algorithm for the simulated data.
6 K-means Issues to consider Non-quantitative feature, e.g. categorical variables, are typically coded by dummy variables, and then treated as quantitative. How many centroids k do we use? As k increases, both training and test error decrease!
7 K-means Choosing K Ideally, the within cluster sum of squares flattens out quickly and we might choose the value of K at this elbow. We might also compare the observed within cluster sum of squares to a null model, like uniform on a box containing the data. This is the basis of the gap statistic see ESL.
8 K-means Figure: The Gap statistic ESL
9 K-medoid Algorithm Same as K-means, except that centroid is estimated not by the average, but by the observation having minimum pairwise distance with the other cluster members. Advantage: centroid is one of the observations useful, eg when features are 0 or 1. Also, one only needs pairwise distances for K-medoids rather than the raw observations.
10 K-medoid Example: Country Dissimilarities This example comes from a study in which political science students were asked to provide pairwise dissimilarity measures for 12 countries. BEL BRA CHI CUB EGY FRA IND ISR USA USS YUG BRA 5.58 CHI CUB EGY FRA IND ISR USA USS YUG ZAI
11 Figure: Left panel: dissimilarities reordered and blocked according to 3-medoid clustering. Heat map is coded from most similar (dark red) to least similar (bright red). Right panel: two-dimensional multidimensional scaling plot, with 3-medoid clusters indicated by different colors. STATS306B K-medoid
12 K-means Connection with EM algorithm Earlier, we saw EM algorithm for mixture of two Gaussians. The general case of K Gaussian components is based on the responsibilities γ (t+1) ij = π (t) j f (X i ; µ (t) j, Σ (t) ) K l=1 π(t) l f (X i ; µ (t) l, Σ (t) ) with f (x; µ, Σ) the multivariate Normal density. ˆl (t+1) By choosing labels i = argmax j γ (n+1) ij this yields a clustering algorithm that is almost K-means.
13 This approach produces a hierarchical clustering tree, or dendrogram. Usually a bottom-up (agglomerative); though top-down versions do exist. Starting with single observations as clusters, the closest pair of clusters are joined together and the distance matrix is updated. Different metrics can be used, yielding qualitatively different trees. Important advantage - the dendrogram can be cut at any level, yielding different clusterings of the data.
14 Hierarchical clustering Single linkage The pair of clusters ( C 1, C 2 ) to merge is chosen based on distance matrix D n n and the current clusters (C 1,..., C k ): ( C 1, C 2 ) = argmin (C i,c j ) min x C i,y C j D xy Finding the next cluster involves updating the minimum distances between the unmerged clusters and the new cluster ( C 1, C 2 ), an O(n 2 ) calculation. Tends to result in very few large clusters formed by adding one point at a time to a growing cluster.
15 Hierarchical clustering Complete linkage The pair of clusters ( C 1, C 2 ) to merge is chosen based on distance matrix D n n and the current clusters (C 1,..., C k ): ( C 1, C 2 ) = argmin (C i,c j ) max x C i,y C j D xy Finding the next cluster involves updating the maximum distances between the unmerged clusters and the new cluster ( C 1, C 2 ), an O(n 2 ) calculation. Resulting dendrogram typically has a wider range of interesting cut points than single linkage.
16 Hierarchical clustering Average linkage The pair of clusters ( C 1, C 2 ) to merge is chosen based on distance matrix D n n and the current clusters (C 1,..., C k ): ( C 1, C 2 ) = argmin (C i,c j ) 1 #C i #C j x C i,y C j D xy Finding the next cluster involves updating the mean distances between the unmerged clusters and the new cluster ( C 1, C 2 ). Resulting dendrogram is somewhat intermediate to single and complete linkage.
17 Hierarchical clustering Figure: applied to NCI human tumor data.
18 Hierarchical clustering Issues Allows one to see all numbers of clusters at once. Can use any distance matrix. Algorithm is greedy, clusters are not optimal in any sense Choice of features to use in clustering can make a big difference in the result. data
19 Spectral clustering Connection with EM algorithm In multidimensional scaling, we saw how a distance matrix, D n n leads to an embedding in m dimensions, i.e. a Euclidean matrix X n m. Given this Euclidean matrix, we can apply clustering methods that need Euclidean features, like K-means. If we chose the number of neighbours in such a way that the true clusters are disconnected in the graph and there are m + 1 connected components in the graph, then, in theory, m + 1-means will recover exactly these m + 1 connected components.
20 Spectral clustering Figure: Spectral clustering: 2-means clustering for embedding into 1 dimension, with two clusters disconnected.
21 Spectral clustering Figure: Spectral clustering: 2-means clustering for embedding into 1 dimension, with two clusters connected.
22 Spectral clustering Figure: Spectral clustering: 4-means clustering for embedding into 3 dimensions, with two clusters connected.
23 Spectral clustering Figure: Spectral clustering: 4-means clustering for embedding into 30 dimensions, with two clusters connected.
24 Spectral clustering Figure: Spectral clustering: 2-means clustering for embedding into 1 dimensions.
25 Spectral clustering Figure: Spectral clustering: 2-means clustering for embedding into 1 dimensions.
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