Source code for graspologic.cluster.kclust

# Copyright (c) Microsoft Corporation and contributors.
# Licensed under the MIT License.

import numpy as np
from sklearn.cluster import KMeans
from sklearn.metrics import adjusted_rand_score, silhouette_score

from .base import BaseCluster

[docs]class KMeansCluster(BaseCluster): """ KMeans Cluster. It computes all possible models from one component to ``max_clusters``. The best model is given by the lowest silhouette score. Parameters ---------- max_clusters : int, defaults to 1. The maximum number of mixture components to consider. random_state : int, RandomState instance or None, optional (default=None) If int, ``random_state`` is the seed used by the random number generator; If RandomState instance, random_state is the random number generator; If None, the random number generator is the RandomState instance used by `np.random`. Attributes ---------- n_clusters_ : int Optimal number of components. If y is given, it is based on largest ARI. Otherwise, it is based on smallest loss. model_ : KMeans object Fitted KMeans object fitted with optimal n_components. silhouette_ : list List of silhouette scores computed for all possible number of clusters given by ``range(2, max_clusters)``. ari_ : list Only computed when y is given. List of ARI values computed for all possible number of clusters given by ``range(2, max_clusters)``. """ def __init__(self, max_clusters=2, random_state=None): if isinstance(max_clusters, int): if max_clusters <= 1: msg = "n_components must be >= 2 or None." raise ValueError(msg) else: self.max_clusters = max_clusters else: msg = "max_clusters must be an integer, not {}.".format(type(max_clusters)) raise TypeError(msg) self.random_state = random_state
[docs] def fit(self, X, y=None): """ Fits kmeans model to the data. Parameters ---------- X : array-like, shape (n_samples, n_features) List of n_features-dimensional data points. Each row corresponds to a single data point. y : array-like, shape (n_samples,), optional (default=None) List of labels for `X` if available. Used to compute ARI scores. Returns ------- self """ # Deal with number of clusters if self.max_clusters > X.shape[0]: msg = "n_components must be >= n_samples, but got \ n_components = {}, n_samples = {}".format( self.max_clusters, X.shape[0] ) raise ValueError(msg) else: max_clusters = self.max_clusters # Get parameters random_state = self.random_state # Compute all models models = [] silhouettes = [] aris = [] for n in range(2, max_clusters + 1): model = KMeans(n_clusters=n, random_state=random_state) # Fit and compute values predictions = model.fit_predict(X) models.append(model) silhouettes.append(silhouette_score(X, predictions)) if y is not None: aris.append(adjusted_rand_score(y, predictions)) if y is not None: self.ari_ = aris self.silhouette_ = silhouettes self.n_clusters_ = np.argmax(aris) + 1 self.model_ = models[np.argmax(aris)] else: self.ari_ = None self.silhouette_ = silhouettes self.n_clusters_ = np.argmax(silhouettes) + 1 self.model_ = models[np.argmax(silhouettes)] return self