Clustering (pt I)

Clustering of unlabeled data can be performed with the module sklearn.cluster.

Each clustering algorithm comes in two variants: a class, that implements the fit method to learn the clusters on train data, and a function, that, given train data, returns an array of integer labels corresponding to the different clusters. For the class, the labels over the training data can be found in the labels_ attribute.

Input data

One important thing to note is that the algorithms implemented in this module can take different kinds of matrix as input. All the methods accept standard data matrices of shape [n_samples, n_features]. These can be obtained from the classes in the sklearn.feature_extraction module. For AffinityPropagation, SpectralClustering and DBSCAN one can also input similarity matrices of shape [n_samples, n_samples]. These can be obtained from the functions in the sklearn.metrics.pairwise module.

Overview of clustering methods

A comparison of the clustering algorithms in scikit-learn

Method name Parameters Scalability Usecase Geometry (metric used)
K-Means number of clusters Very large n_samples, medium, n_clusters with MiniBatch code General-purpose,even cluster size, flat geometry, not too many clusters Distances between points
Affinity propagation damping, sample preference Not scalable with n_samples Many clusters, uneven cluster size, non-flat geometry  Graph distance (e.g. nearest-neighbor graph)
Mean-shift bandwidth Not scalable with n_samples Many clusters, uneven cluster size, non-flat geometry  Distances between points
Spectral clustering number of clusters Medium n_samples, small n_clusters Few clusters, even cluster size, non-flat geometry Graph distance (e.g. nearest-neighbor graph)
Ward hierarchical clustering number of clusters Large n_samples and n_clusters Many clusters possibly connectivity constraints Distances between points
Agglomerative clustering number of clusters, linkage type, distance Large n_samples and n_clusters Many clusters possibly connectivity constraints, non Euclidean distances Any pairwise distance
DBSCAN neighborhood size Very large n_samples, medium, n_clusters Non-flat geometry, uneven cluster sizes Distances between nearest points
Gaussian mixtures many Not scalable Flat geometry, good for density estimation Mahalanobis distances to centers
Birch branching factor, threshold, optimal global clusterer  Large n_samples and n_clusters Large dataset, outlier removal, data reduction. Euclidean distance between points

Non-flat geometry clustering is useful when the clusters have a specific shape, i.e. a non-flat manifold, and the standard euclidean distance is not the right metric. This case arises in the two top rows of the figure above.

Gaussian mixture models, useful for clustering, are described in another chapter of the documentation dedicated to mixture models. KMeans can be seen as a special case of Gaussian mixture model with equal covariance per component.


The KMeans algorithm clusters data by trying to separate samples in n groups of equal variance, minimizing a criterion known as the inertia or within-cluster sum-of-squares. This algorithm requires the number of clusters to be specified. It scales well to large number of samples and has been used across a large range of application areas in many different fields.

The k-means algorithm divides a set of samples into disjoint clusters , each described by the mean of the samples in the cluster. The means are commonly called the cluster “centroids”; note that they are not, in general, points from , although they live in the same space. The K-means algorithm aims to choose centroids that minimise the inertia, or within-cluster sum of squared criterion:

Inertia, or the within-cluster sum of squares criterion, can be recognized as a measure of how internally coherent clusters are. It suffers from various drawbacks:

  • Inertia makes the assumption that clusters are convex and isotropic, which is not always the case. It responds poorly to elongated clusters, or manifolds with irregular shapes.
  • Inertia is not a normalized metric: we just know that lower values are better and zero is optimal. But in very high-dimensional spaces, Euclidean distances tend to become inflated (this is an instance of the so-called “curse of dimensionality”). Running a dimensionality reduction algorithm such as PCA prior to k-means clustering can alleviate this problem and speed up the computations.

K-means is often referred to as Lloyd’s algorithm. In basic terms, the algorithm has three steps. The first step chooses the initial centroids, with the most basic method being to choose samples from the dataset . After initialization, K-means consists of looping between the two other steps. The first step assigns each sample to its nearest centroid. The second step creates new centroids by taking the mean value of all of the samples assigned to each previous centroid. The difference between the old and the new centroids are computed and the algorithm repeats these last two steps until this value is less than a threshold. In other words, it repeats until the centroids do not move significantly.

K-means is equivalent to the expectation-maximization algorithm with a small, all-equal, diagonal covariance matrix.

The algorithm can also be understood through the concept of Voronoi diagrams. First the Voronoi diagram of the points is calculated using the current centroids. Each segment in the Voronoi diagram becomes a separate cluster. Secondly, the centroids are updated to the mean of each segment. The algorithm then repeats this until a stopping criterion is fulfilled. Usually, the algorithm stops when the relative decrease in the objective function between iterations is less than the given tolerance value. This is not the case in this implementation: iteration stops when centroids move less than the tolerance.

Given enough time, K-means will always converge, however this may be to a local minimum. This is highly dependent on the initialization of the centroids. As a result, the computation is often done several times, with different initializations of the centroids. One method to help address this issue is the k-means++ initialization scheme, which has been implemented in scikit-learn (use the init='k-means++' parameter). This initializes the centroids to be (generally) distant from each other, leading to provably better results than random initialization, as shown in the reference.

The algorithm supports sample weights, which can be given by a parameter sample_weight. This allows to assign more weight to some samples when computing cluster centers and values of inertia. For example, assigning a weight of 2 to a sample is equivalent to adding a duplicate of that sample to the dataset .

A parameter can be given to allow K-means to be run in parallel, called n_jobs. Giving this parameter a positive value uses that many processors (default: 1). A value of -1 uses all available processors, with -2 using one less, and so on. Parallelization generally speeds up computation at the cost of memory (in this case, multiple copies of centroids need to be stored, one for each job).

Warning: The parallel version of K-Means is broken on OS X when numpy uses the Accelerate Framework. This is expected behavior: Accelerate can be called after a fork but you need to execv the subprocess with the Python binary (which multiprocessing does not do under posix).

K-means can be used for vector quantization. This is achieved using the transform method of a trained model of KMeans.

Mini Batch K-Means

The MiniBatchKMeans is a variant of the KMeans algorithm which uses mini-batches to reduce the computation time, while still attempting to optimise the same objective function. Mini-batches are subsets of the input data, randomly sampled in each training iteration. These mini-batches drastically reduce the amount of computation required to converge to a local solution. In contrast to other algorithms that reduce the convergence time of k-means, mini-batch k-means produces results that are generally only slightly worse than the standard algorithm.

The algorithm iterates between two major steps, similar to vanilla k-means. In the first step,  samples are drawn randomly from the dataset, to form a mini-batch. These are then assigned to the nearest centroid. In the second step, the centroids are updated. In contrast to k-means, this is done on a per-sample basis. For each sample in the mini-batch, the assigned centroid is updated by taking the streaming average of the sample and all previous samples assigned to that centroid. This has the effect of decreasing the rate of change for a centroid over time. These steps are performed until convergence or a predetermined number of iterations is reached.

MiniBatchKMeans converges faster than KMeans, but the quality of the results is reduced. In practice this difference in quality can be quite small, as shown in the example and cited reference.

Affinity Propagation

AffinityPropagation creates clusters by sending messages between pairs of samples until convergence. A dataset is then described using a small number of exemplars, which are identified as those most representative of other samples. The messages sent between pairs represent the suitability for one sample to be the exemplar of the other, which is updated in response to the values from other pairs. This updating happens iteratively until convergence, at which point the final exemplars are chosen, and hence the final clustering is given.

Affinity Propagation can be interesting as it chooses the number of clusters based on the data provided. For this purpose, the two important parameters are the preference, which controls how many exemplars are used, and the damping factor which damps the responsibility and availability messages to avoid numerical oscillations when updating these messages.

The main drawback of Affinity Propagation is its complexity. The algorithm has a time complexity of the order , where is the number of samples and is the number of iterations until convergence. Further, the memory complexity is of the order if a dense similarity matrix is used, but reducible if a sparse similarity matrix is used. This makes Affinity Propagation most appropriate for small to medium sized datasets.

Algorithm description: The messages sent between points belong to one of two categories. The first is the responsibility , which is the accumulated evidence that sample should be the exemplar for sample . The second is the availability which is the accumulated evidence that sample should choose sample to be its exemplar, and considers the values for all other samples that should be an exemplar. In this way, exemplars are chosen by samples if they are (1) similar enough to many samples and (2) chosen by many samples to be representative of themselves.

More formally, the responsibility of a sample to be the exemplar of sample is given by:

Where is the similarity between samples and . The availability of sample to be the exemplar of sample is given by:

To begin with, all values for and are set to zero, and the calculation of each iterates until convergence. As discussed above, in order to avoid numerical oscillations when updating the messages, the damping factor is introduced to iteration process:

where indicates the iteration times.

Mean Shift

MeanShift clustering aims to discover blobs in a smooth density of samples. It is a centroid based algorithm, which works by updating candidates for centroids to be the mean of the points within a given region. These candidates are then filtered in a post-processing stage to eliminate near-duplicates to form the final set of centroids.

Given a candidate centroid for iteration , the candidate is updated according to the following equation:

Where is the neighborhood of samples within a given distance around and is the mean shift vector that is computed for each centroid that points towards a region of the maximum increase in the density of points. This is computed using the following equation, effectively updating a centroid to be the mean of the samples within its neighborhood:

The algorithm automatically sets the number of clusters, instead of relying on a parameter bandwidth, which dictates the size of the region to search through. This parameter can be set manually, but can be estimated using the provided estimate_bandwidth function, which is called if the bandwidth is not set.

The algorithm is not highly scalable, as it requires multiple nearest neighbor searches during the execution of the algorithm. The algorithm is guaranteed to converge, however the algorithm will stop iterating when the change in centroids is small.

Labelling a new sample is performed by finding the nearest centroid for a given sample.

Spectral clustering

SpectralClustering does a low-dimension embedding of the affinity matrix between samples, followed by a KMeans in the low dimensional space. It is especially efficient if the affinity matrix is sparse and the pyamg module is installed. SpectralClustering requires the number of clusters to be specified. It works well for a small number of clusters but is not advised when using many clusters.

For two clusters, it solves a convex relaxation of the normalised cuts problem on the similarity graph: cutting the graph in two so that the weight of the edges cut is small compared to the weights of the edges inside each cluster. This criteria is especially interesting when working on images: graph vertices are pixels, and edges of the similarity graph are a function of the gradient of the image.

Warning Transforming distance to well-behaved similarities

Note that if the values of your similarity matrix are not well distributed, e.g. with negative values or with a distance matrix rather than a similarity, the spectral problem will be singular and the problem not solvable. In which case it is advised to apply a transformation to the entries of the matrix. For instance, in the case of a signed distance matrix, is common to apply a heat kernel:

	 similarity = np.exp(-beta * distance / distance.std())

See the examples for such an application.

Different label assignment strategies

Different label assignment strategies can be used, corresponding to the assign_labels parameter of SpectralClustering. The "kmeans" strategy can match finer details of the data, but it can be more unstable. In particular, unless you control the random_state, it may not be reproducible from run-to-run, as it depends on a random initialization. On the other hand, the "discretize" strategy is 100% reproducible, but it tends to create parcels of fairly even and geometrical shape.



Spectral Clustering Graphs

Spectral Clustering can also be used to cluster graphs by their spectral embeddings. In this case, the affinity matrix is the adjacency matrix of the graph, and SpectralClustering is initialized with affinity=’precomputed’:

>>> from sklearn.cluster import SpectralClustering
>>> sc = SpectralClustering(3, affinity='precomputed', n_init=100,
... assign_labels='discretize') 
>>> sc.fit_predict(adjacency_matrix)  

Hierarchical clustering

Hierarchical clustering is a general family of clustering algorithms that build nested clusters by merging or splitting them successively. This hierarchy of clusters is represented as a tree (or dendrogram). The root of the tree is the unique cluster that gathers all the samples, the leaves being the clusters with only one sample. See the Wikipedia page for more details.

The AgglomerativeClustering object performs a hierarchical clustering using a bottom up approach: each observation starts in its own cluster, and clusters are successively merged together. The linkage criteria determines the metric used for the merge strategy:

  • Ward minimizes the sum of squared differences within all clusters. It is a variance-minimizing approach and in this sense is similar to the k-means objective function but tackled with an agglomerative hierarchical approach.
  • Maximum or complete linkage minimizes the maximum distance between observations of pairs of clusters.
  • Average linkage minimizes the average of the distances between all observations of pairs of clusters.
  • Single linkage minimizes the distance between the closest observations of pairs of clusters.

AgglomerativeClustering can also scale to large number of samples when it is used jointly with a connectivity matrix, but is computationally expensive when no connectivity constraints are added between samples: it considers at each step all the possible merges.


The FeatureAgglomeration uses agglomerative clustering to group together features that look very similar, thus decreasing the number of features. It is a dimensionality reduction tool, see Unsupervised dimensionality reduction.

Different linkage type: Ward, complete, average, and single linkage

AgglomerativeClustering supports Ward, single, average, and complete linkage strategies.

Agglomerative cluster has a “rich get richer” behavior that leads to uneven cluster sizes. In this regard, single linkage is the worst strategy, and Ward gives the most regular sizes. However, the affinity (or distance used in clustering) cannot be varied with Ward, thus for non Euclidean metrics, average linkage is a good alternative. Single linkage, while not robust to noisy data, can be computed very efficiently and can therefore be useful to provide hierarchical clustering of larger datasets. Single linkage can also perform well on non-globular data.

Adding connectivity constraints

An interesting aspect of AgglomerativeClustering is that connectivity constraints can be added to this algorithm (only adjacent clusters can be merged together), through a connectivity matrix that defines for each sample the neighboring samples following a given structure of the data. For instance, in the swiss-roll example below, the connectivity constraints forbid the merging of points that are not adjacent on the swiss roll, and thus avoid forming clusters that extend across overlapping folds of the roll.

These constraint are useful to impose a certain local structure, but they also make the algorithm faster, especially when the number of the samples is high.

The connectivity constraints are imposed via an connectivity matrix: a scipy sparse matrix that has elements only at the intersection of a row and a column with indices of the dataset that should be connected. This matrix can be constructed from a-priori information: for instance, you may wish to cluster web pages by only merging pages with a link pointing from one to another. It can also be learned from the data, for instance using sklearn.neighbors.kneighbors_graph to restrict merging to nearest neighbors as in this example, or using sklearn.feature_extraction.image.grid_to_graph to enable only merging of neighboring pixels on an image, as in the coin example.

Warning: Connectivity constraints with single, average and complete linkage
Connectivity constraints and single, complete or average linkage can enhance the ‘rich getting richer’ aspect of agglomerative clustering, particularly so if they are built with sklearn.neighbors.kneighbors_graph. In the limit of a small number of clusters, they tend to give a few macroscopically occupied clusters and almost empty ones. (see the discussion in Agglomerative clustering with and without structure). Single linkage is the most brittle linkage option with regard to this issue.

Varying the metric

Single, average and complete linkage can be used with a variety of distances (or affinities), in particular Euclidean distance (l2), Manhattan distance (or Cityblock, or l1), cosine distance, or any precomputed affinity matrix.

  • l1 distance is often good for sparse features, or sparse noise: i.e. many of the features are zero, as in text mining using occurrences of rare words.
  • cosine distance is interesting because it is invariant to global scalings of the signal.

The guidelines for choosing a metric is to use one that maximizes the distance between samples in different classes, and minimizes that within each class.


The DBSCAN algorithm views clusters as areas of high density separated by areas of low density. Due to this rather generic view, clusters found by DBSCAN can be any shape, as opposed to k-means which assumes that clusters are convex shaped. The central component to the DBSCAN is the concept of core samples, which are samples that are in areas of high density. A cluster is therefore a set of core samples, each close to each other (measured by some distance measure) and a set of non-core samples that are close to a core sample (but are not themselves core samples). There are two parameters to the algorithm, min_samples and eps, which define formally what we mean when we say dense. Higher min_samples or lower eps indicate higher density necessary to form a cluster.

More formally, we define a core sample as being a sample in the dataset such that there exist min_samples other samples within a distance of eps, which are defined as neighbors of the core sample. This tells us that the core sample is in a dense area of the vector space. A cluster is a set of core samples that can be built by recursively taking a core sample, finding all of its neighbors that are core samples, finding all of their neighbors that are core samples, and so on. A cluster also has a set of non-core samples, which are samples that are neighbors of a core sample in the cluster but are not themselves core samples. Intuitively, these samples are on the fringes of a cluster.

Any core sample is part of a cluster, by definition. Any sample that is not a core sample, and is at least eps in distance from any core sample, is considered an outlier by the algorithm.

In the figure below, the color indicates cluster membership, with large circles indicating core samples found by the algorithm. Smaller circles are non-core samples that are still part of a cluster. Moreover, the outliers are indicated by black points below.


The DBSCAN algorithm is deterministic, always generating the same clusters when given the same data in the same order. However, the results can differ when data is provided in a different order. First, even though the core samples will always be assigned to the same clusters, the labels of those clusters will depend on the order in which those samples are encountered in the data. Second and more importantly, the clusters to which non-core samples are assigned can differ depending on the data order. This would happen when a non-core sample has a distance lower than eps to two core samples in different clusters. By the triangular inequality, those two core samples must be more distant than eps from each other, or they would be in the same cluster. The non-core sample is assigned to whichever cluster is generated first in a pass through the data, and so the results will depend on the data ordering.

The current implementation uses ball trees and kd-trees to determine the neighborhood of points, which avoids calculating the full distance matrix (as was done in scikit-learn versions before 0.14). The possibility to use custom metrics is retained; for details, see NearestNeighbors.

Memory consumption for large sample sizes

This implementation is by default not memory efficient because it constructs a full pairwise similarity matrix in the case where kd-trees or ball-trees cannot be used (e.g. with sparse matrices). This matrix will consume n^2 floats. A couple of mechanisms for getting around this are:

  • A sparse radius neighborhood graph (where missing entries are presumed to be out of eps) can be precomputed in a memory-efficient way and dbscan can be run over this with metric='precomputed'. See sklearn.neighbors.NearestNeighbors.radius_neighbors_graph.
  • The dataset can be compressed, either by removing exact duplicates if these occur in your data, or by using BIRCH. Then you only have a relatively small number of representatives for a large number of points. You can then provide a sample_weight when fitting DBSCAN.


The Birch builds a tree called the Characteristic Feature Tree (CFT) for the given data. The data is essentially lossy compressed to a set of Characteristic Feature nodes (CF Nodes). The CF Nodes have a number of subclusters called Characteristic Feature subclusters (CF Subclusters) and these CF Subclusters located in the non-terminal CF Nodes can have CF Nodes as children.

The CF Subclusters hold the necessary information for clustering which prevents the need to hold the entire input data in memory. This information includes:

  • Number of samples in a subcluster.
  • Linear Sum - A n-dimensional vector holding the sum of all samples
  • Squared Sum - Sum of the squared L2 norm of all samples.
  • Centroids - To avoid recalculation linear sum / n_samples.
  • Squared norm of the centroids.

The Birch algorithm has two parameters, the threshold and the branching factor. The branching factor limits the number of subclusters in a node and the threshold limits the distance between the entering sample and the existing subclusters.

This algorithm can be viewed as an instance or data reduction method, since it reduces the input data to a set of subclusters which are obtained directly from the leaves of the CFT. This reduced data can be further processed by feeding it into a global clusterer. This global clusterer can be set by n_clusters. If n_clusters is set to None, the subclusters from the leaves are directly read off, otherwise a global clustering step labels these subclusters into global clusters (labels) and the samples are mapped to the global label of the nearest subcluster.

Algorithm description:

  • A new sample is inserted into the root of the CF Tree which is a CF Node. It is then merged with the subcluster of the root, that has the smallest radius after merging, constrained by the threshold and branching factor conditions. If the subcluster has any child node, then this is done repeatedly till it reaches a leaf. After finding the nearest subcluster in the leaf, the properties of this subcluster and the parent subclusters are recursively updated.
  • If the radius of the subcluster obtained by merging the new sample and the nearest subcluster is greater than the square of the threshold and if the number of subclusters is greater than the branching factor, then a space is temporarily allocated to this new sample. The two farthest subclusters are taken and the subclusters are divided into two groups on the basis of the distance between these subclusters.
  • If this split node has a parent subcluster and there is room for a new subcluster, then the parent is split into two. If there is no room, then this node is again split into two and the process is continued recursively, till it reaches the root.

Birch or MiniBatchKMeans?

  • Birch does not scale very well to high dimensional data. As a rule of thumb if n_features is greater than twenty, it is generally better to use MiniBatchKMeans.
  • If the number of instances of data needs to be reduced, or if one wants a large number of subclusters either as a preprocessing step or otherwise, Birch is more useful than MiniBatchKMeans.

How to use partial_fit?

To avoid the computation of global clustering, for every call of partial_fit the user is advised

  1. To set n_clusters=None initially
  2. Train all data by multiple calls to partial_fit.
  3. Set n_clusters to a required value using brc.set_params(n_clusters=n_clusters).
  4. Call partial_fit finally with no arguments, i.e. brc.partial_fit() which performs the global clustering.
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