Source code for vaex.ml.cluster

import numpy as np
import traitlets
import vaex.ml.state
import logging
import vaex
import vaex.serialize
from numba import jit
from . import generate
# vaex.set_log_level_debug()

logger_km = logging.getLogger('vaex.ml.kmeans')


def Matrix(type=traitlets.CFloat):
    return traitlets.List(traitlets.List(type()))


# @jit('void(double[:], double[:], double[:])', nopython=True, nogil=True)
@jit(nopython=True, nogil=True, cache=True)
def distances_square(result, centroids, *blocks):
    """
    Function under test.
    """
    k = centroids.shape[0]
    dimensions = centroids.shape[1]
    N = result.shape[1]
    for i in range(k):
        for d in range(dimensions):
            for j in range(N):
                result[i, j] += (blocks[d][j] - centroids[i][d])**2


@jit(nopython=True, nogil=True, cache=True)
def centroid_stats(centroids, counts, sumpos, inertia, *blocks):
    # classes = np.argmin(distances_sq, axis=0)
    # distances_sq = np.choose(classes, distances_sq)
    # inertia = (distances_sq).sum()
    # inertia = 0
    N = blocks[0].shape[0]
    runs = sumpos.shape[0]
    clusters = sumpos.shape[1]
    dimensions = sumpos.shape[2]
    for j in range(N):
        for run in range(runs):
            # if done[run]: ## TODO: bug in numba? seems to crash if included
                best_distance = 1e100
                best_class = 10000
                for cluster in range(clusters):
                    distance = 0
                    for d in range(dimensions):
                        distance += (centroids[run, cluster, d] - blocks[d][j])**2
                    if distance < best_distance:
                        best_class = cluster
                        best_distance = distance
                cls = best_class  # classes[j]
                inertia[run] += best_distance
                for d in range(dimensions):
                    sumpos[run, cls, d] += blocks[d][j]
                counts[run, cls] += 1
#    return inertia
        # for i in range(k):


[docs]@vaex.serialize.register @generate.register class KMeans(vaex.ml.state.HasState): '''The KMeans clustering algorithm. Example: -------- >>> import vaex.ml >>> import vaex.ml.cluster >>> df = vaex.ml.datasets.load_iris() >>> features = ['sepal_width', 'petal_length', 'sepal_length', 'petal_width'] >>> df_train, df_test = vaex.ml.train_test_split(df) >>> cls = vaex.ml.cluster.KMeans(n_clusters=3, features=features, init='random', max_iter=10) >>> df_train = cls.fit_transform(df_train) >>> df_test = cls.transform(df_test) ''' features = traitlets.List(traitlets.Unicode(), help='List of features to cluster.') n_clusters = traitlets.CInt(default_value=2, help='Number of clusters to form.') init = traitlets.Union([Matrix(), traitlets.Unicode()], default_value='random', help='Method for initializing the centroids.') n_init = traitlets.CInt(default_value=1, help='Number of centroid initializations. \ The KMeans algorithm will be run for each initialization, \ and the final results will be the best output of the n_init \ consecutive runs in terms of inertia.') max_iter = traitlets.CInt(default_value=300, help='Maximum number of iterations of the KMeans algorithm for a single run.') random_state = traitlets.CInt(default_value=None, allow_none=True, help='Random number generation for centroid initialization. \ If an int is specified, the randomness becomes deterministic.') verbose = traitlets.CBool(default_value=False, help='If True, enable verbosity mode.') cluster_centers = traitlets.List(traitlets.List(traitlets.CFloat()), help='Coordinates of cluster centers.') inertia = traitlets.CFloat(default_value=None, allow_none=True, help='Sum of squared distances of samples to their closest cluster center.') prediction_label = traitlets.Unicode(default_value='prediction_kmeans', help='The name of the virtual column that houses the cluster labels for each point.') def __call__(self, *blocks): return self._calculate_classes(*blocks) def _calculate_distances_squared(self, *blocks): N = len(blocks[0]) # they are all the same length centroids = np.array(self.cluster_centers) k = centroids.shape[0] dimensions = centroids.shape[1] distances_sq = np.zeros((k, N)) if 1: distances_square(distances_sq, centroids, *blocks) else: for d in range(dimensions): for i in range(k): distances_sq[i] += (blocks[d] - centroids[i][d])**2 return distances_sq def _calculate_classes(self, *blocks): distances_sq = self._calculate_distances_squared(*blocks) classes = np.argmin(distances_sq, axis=0) return classes def generate_cluster_centers_random(self, dataset, rng): indices = rng.randint(0, len(dataset), self.n_clusters) return [[dataset.evaluate(feature, i1=i, i2=i+1)[0] for feature in self.features] for i in indices]
[docs] def transform(self, dataset): ''' Label a dataset with a fitted KMeans model. Parameters: ----------- :param dataset: A vaex dataset. Returns: -------- :return copy: A shallow copy of the dataset that includes the encodings. ''' copy = dataset.copy() lazy_function = copy.add_function('kmean_predict_function', self, unique=True) expression = lazy_function(*self.features) copy.add_virtual_column(self.prediction_label, expression, unique=False) return copy
[docs] def fit(self, dataset): ''' Fit the KMeans model to the dataset. Parameters: ----------- :param dataset: A vaex dataset. Returns: -------- self ''' if self.init == 'random': rng = np.random.RandomState(self.random_state) self.run_cluster_centers = [self.generate_cluster_centers_random(dataset, rng) for k in range(self.n_init)] else: if self.n_init > 1: print("WARNING: n_init > 1 , but init given, only doing one run") self.run_cluster_centers = [self.init] done = [False] * len(self.run_cluster_centers) alldone = False first = True previous_inertias = None iteration = 0 inertias_list = [] while not alldone: new_centers, inertias = self._find_centers_and_inertias(dataset, done) if self.verbose: inertia_msges = [('--' if d else '{: 3}'.format(k)) for k, d in zip(inertias, done)] if len(inertias) == 1: inertia_msg = inertia_msges[0] else: inertia_msg = " | ".join(inertia_msges) print('Iteration {: 4}, inertia {}'.format(iteration, inertia_msg)) if not first: # we can only to a check after the second iteration done = self._is_done(previous_inertias, inertias) alldone = np.all(done) else: first = False iteration += 1 if (iteration >= self.max_iter): logger_km.debug('reached max iterations: %s', self.max_iter) alldone = True previous_inertias = inertias inertias_list.append(inertias) self.run_cluster_centers = new_centers best_run = np.argmin(inertias) self.inertia = inertias[best_run] self.inertias = np.array(inertias_list)[:, best_run] self.cluster_centers = new_centers[best_run]
def _is_done(self, inertias1, inertias2): diffs = [(inertia1 - inertia2) for inertia1, inertia2 in zip(inertias1, inertias2)] return [(diff < 1e-3) for diff in diffs] def _find_centers_and_inertias(self, dataset, done): done = np.array(done, dtype=np.int8) centroids = np.array(self.run_cluster_centers) runs = centroids.shape[0] clusters = centroids.shape[1] dimensions = centroids.shape[2] # print("k =", k) assert dimensions == len(self.features), "nr of dimensions for centroid should equal nr of features" def map(*blocks): # this will be called with a chunk of the data sumpos = np.zeros((runs, clusters, dimensions)) counts = np.zeros((runs, clusters)) inertia = np.zeros((runs)) if 1: centroid_stats(centroids, counts, sumpos, inertia, *blocks) else: # this is the pure python code # although not made for multiple runs yet distances_sq = self._calculate_distances_squared(*blocks) classes = np.argmin(distances_sq, axis=0) distances_sq = np.choose(classes, distances_sq) inertia = (distances_sq).sum() for i in range(k): mask = classes == i counts[i] = np.sum(mask) for d in range(dimensions): sumpos[i, d] += blocks[d][mask].sum() return sumpos, counts, inertia def reduce(x, y): sumpos1, counts1, inertia1 = x sumpos2, counts2, inertia2 = y return sumpos1 + sumpos2, counts1 + counts2, inertia1 + inertia2 sumpos, counts, inertia = dataset.map_reduce(map, reduce, self.features) means = (sumpos/counts[:, :, np.newaxis]) return means.tolist(), inertia
try: from .autogen import cluster as _ del _ except ImportError: pass