# Clustering Hierarchical clustering and k-mean clustering

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1 Clustering Hierarchical clustering and k-mean clustering Genome 373 Genomic Informatics Elhanan Borenstein

2 The clustering problem: A quick review partition genes into distinct sets with high homogeneity and high separation Many different representations Many possible distance metrics Metric matters Homogeneity vs separation

3 The clustering problem A good clustering solution should have two features: 1. High homogeneity: homogeneity measures the similarity between genes assigned to the same cluster. 2. High separation: separation measures the distance/dissimilarity between clusters. (If two clusters have similar expression patterns, then they should probably be merged into one cluster).

4 The philosophy of clustering Unsupervised learning problem No single solution is necessarily the true/correct! There is usually a tradeoff between homogeneity and separation: More clusters increased homogeneity but decreased separation Less clusters Increased separation but reduced homogeneity Method matters; metric matters; definitions matter; There are many formulations of the clustering problem; most of them are NP-hard (why?). In most cases, heuristic methods or approximations are used.

5 One problem, numerous solutions Many algorithms: Hierarchical clustering k-means self-organizing maps (SOM) Knn PCC CAST CLICK The results (i.e., obtained clusters) can vary drastically depending on: Clustering method Parameters specific to each clustering method (e.g. number of centers for the k-mean method, agglomeration rule for hierarchical clustering, etc.)

6 Hierarchical clustering

7 object 1 object 2 object 3 object 4 object 5 Hierarchical clustering An agglomerative clustering method Takes as input a distance matrix Progressively regroups the closest objects/groups The result is a tree - intermediate nodes represent clusters Branch lengths represent distances between clusters Tree representation Distance matrix branch node c3 c1 object 1 object 5 object object object object object root c4 c2 object 4 object 2 object 3 leaf nodes

8 mmm Déjà vu anyone?

9 Hierarchical clustering algorithm 1. Assign each object to a separate cluster. 2. Find the pair of clusters with the shortest distance, and regroup them into a single cluster. 3. Repeat 2 until there is a single cluster.

10 Hierarchical clustering algorithm 1. Assign each object to a separate cluster. 2. Find the pair of clusters with the shortest distance, and regroup them into a single cluster. 3. Repeat 2 until there is a single cluster.

11 Hierarchical clustering 1. Assign each object to a separate cluster. 2. Find the pair of clusters with the shortest distance, and regroup them into a single cluster. 3. Repeat 2 until there is a single cluster. One needs to define a (dis)similarity metric between two groups. There are several possibilities Average linkage: the average distance between objects from groups A and B Single linkage: the distance between the closest objects from groups A and B Complete linkage: the distance between the most distant objects from groups A and B

12 Impact of the agglomeration rule These four trees were built from the same distance matrix, using 4 different agglomeration rules. Single-linkage typically creates nesting clusters Complete linkage create more balanced trees. Note: these trees were computed from a matrix of random numbers. The impression of structure is thus a complete artifact.

13 Hierarchical clustering result Five clusters 13

14 K-mean clustering Divisive Non-hierarchical

15 K-mean clustering An algorithm for partitioning n observations/points into k clusters such that each observation belongs to the cluster with the nearest mean/center cluster_1 mean cluster_2 mean Note that this is a somewhat strange definition: Assignment of a point to a cluster is based on the proximity of the point to the cluster mean But the cluster mean is calculated based on all the points assigned to the cluster.

16 K-mean clustering: Chicken and egg An algorithm for partitioning n observations/points into k clusters such that each observation belongs to the cluster with the nearest mean/center The chicken and egg problem: I do not know the means before I determine the partitioning into clusters I do not know the partitioning into clusters before I determine the means Key principle - cluster around mobile centers: Start with some random locations of means/centers, partition into clusters according to these centers, and then correct the centers according to the clusters (somewhat similar to expectation-maximization algorithm)

17 K-mean clustering algorithm The number of centers, k, has to be specified a-priori Algorithm: 1. Arbitrarily select k initial centers 2. Assign each element to the closest center 3. Re-calculate centers (mean position of the assigned elements) 4. Repeat 2 and 3 until.

18 K-mean clustering algorithm The number of centers, k, has to be specified a-priori Algorithm: 1. Arbitrarily select k initial centers 2. Assign each element to the closest center 3. Re-calculate centers (mean position of the assigned elements) 4. Repeat 2 and 3 until one of the following termination conditions is reached: i. The clusters are the same as in the previous iteration ii. iii. The difference between two iterations is smaller than a specified threshold The maximum number of iterations has been reached How can we do this efficiently?

19 Partitioning the space Assigning elements to the closest center B A

20 Partitioning the space Assigning elements to the closest center closer to A than to B B closer to B than to A A

21 Partitioning the space Assigning elements to the closest center closer to B than to A closer to A than to B B closer to B than to C A C

22 Partitioning the space Assigning elements to the closest center closest to A B closest to B A C closest to C

23 Partitioning the space Assigning elements to the closest center B A C

24 Voronoi diagram Decomposition of a metric space determined by distances to a specified discrete set of centers in the space Each colored cell represents the collection of all points in this space that are closer to a specific center s than to any other center Several algorithms exist to find the Voronoi diagram.

25 K-mean clustering algorithm The number of centers, k, has to be specified a priori Algorithm: 1. Arbitrarily select k initial centers 2. Assign each element to the closest center (Voronoi) 3. Re-calculate centers (mean position of the assigned elements) 4. Repeat 2 and 3 until one of the following termination conditions is reached: i. The clusters are the same as in the previous iteration ii. iii. The difference between two iterations is smaller than a specified threshold The maximum number of iterations has been reached

26 K-mean clustering example Two sets of points randomly generated 200 centered on (0,0) 50 centered on (1,1)

27 K-mean clustering example Two points are randomly chosen as centers (stars)

28 K-mean clustering example Each dot can now be assigned to the cluster with the closest center

29 K-mean clustering example First partition into clusters

30 K-mean clustering example Centers are re-calculated

31 K-mean clustering example And are again used to partition the points

32 K-mean clustering example Second partition into clusters

33 K-mean clustering example Re-calculating centers again

34 K-mean clustering example And we can again partition the points

35 K-mean clustering example Third partition into clusters

36 K-mean clustering example After 6 iterations: The calculated centers remains stable

37 K-mean clustering: Summary The convergence of k-mean is usually quite fast (sometimes 1 iteration results in a stable solution) K-means is time- and memory-efficient Strengths: Simple to use Fast Can be used with very large data sets Weaknesses: The number of clusters has to be predetermined The results may vary depending on the initial choice of centers

38 K-mean clustering: Variations Expectation-maximization (EM): maintains probabilistic assignments to clusters, instead of deterministic assignments, and multivariate Gaussian distributions instead of means. k-means++: attempts to choose better starting points. Some variations attempt to escape local optima by swapping points between clusters

39 The take-home message Hierarchical clustering K-mean clustering? D haeseleer, 2005

40

41 What else are we missing?

42 What else are we missing? What if the clusters are not linearly separable?

43 Clustering in both dimensions We can cluster genes, conditions (samples), or both.

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