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344 lines
12 KiB
Python
344 lines
12 KiB
Python
"""README, Author - Anurag Kumar(mailto:anuragkumarak95@gmail.com)
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Requirements:
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- sklearn
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- numpy
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- matplotlib
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Python:
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- 3.5
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Inputs:
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- X , a 2D numpy array of features.
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- k , number of clusters to create.
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- initial_centroids , initial centroid values generated by utility function(mentioned
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in usage).
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- maxiter , maximum number of iterations to process.
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- heterogeneity , empty list that will be filled with heterogeneity values if passed
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to kmeans func.
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Usage:
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1. define 'k' value, 'X' features array and 'heterogeneity' empty list
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2. create initial_centroids,
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initial_centroids = get_initial_centroids(
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X,
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k,
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seed=0 # seed value for initial centroid generation,
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# None for randomness(default=None)
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)
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3. find centroids and clusters using kmeans function.
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centroids, cluster_assignment = kmeans(
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X,
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k,
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initial_centroids,
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maxiter=400,
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record_heterogeneity=heterogeneity,
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verbose=True # whether to print logs in console or not.(default=False)
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)
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4. Plot the loss function and heterogeneity values for every iteration saved in
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heterogeneity list.
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plot_heterogeneity(
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heterogeneity,
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k
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)
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5. Transfers Dataframe into excel format it must have feature called
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'Clust' with k means clustering numbers in it.
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"""
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import warnings
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import numpy as np
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import pandas as pd
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from matplotlib import pyplot as plt
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from sklearn.metrics import pairwise_distances
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warnings.filterwarnings("ignore")
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TAG = "K-MEANS-CLUST/ "
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def get_initial_centroids(data, k, seed=None):
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"""Randomly choose k data points as initial centroids"""
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if seed is not None: # useful for obtaining consistent results
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np.random.seed(seed)
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n = data.shape[0] # number of data points
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# Pick K indices from range [0, N).
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rand_indices = np.random.randint(0, n, k)
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# Keep centroids as dense format, as many entries will be nonzero due to averaging.
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# As long as at least one document in a cluster contains a word,
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# it will carry a nonzero weight in the TF-IDF vector of the centroid.
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centroids = data[rand_indices, :]
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return centroids
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def centroid_pairwise_dist(x, centroids):
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return pairwise_distances(x, centroids, metric="euclidean")
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def assign_clusters(data, centroids):
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# Compute distances between each data point and the set of centroids:
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# Fill in the blank (RHS only)
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distances_from_centroids = centroid_pairwise_dist(data, centroids)
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# Compute cluster assignments for each data point:
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# Fill in the blank (RHS only)
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cluster_assignment = np.argmin(distances_from_centroids, axis=1)
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return cluster_assignment
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def revise_centroids(data, k, cluster_assignment):
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new_centroids = []
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for i in range(k):
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# Select all data points that belong to cluster i. Fill in the blank (RHS only)
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member_data_points = data[cluster_assignment == i]
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# Compute the mean of the data points. Fill in the blank (RHS only)
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centroid = member_data_points.mean(axis=0)
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new_centroids.append(centroid)
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new_centroids = np.array(new_centroids)
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return new_centroids
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def compute_heterogeneity(data, k, centroids, cluster_assignment):
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heterogeneity = 0.0
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for i in range(k):
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# Select all data points that belong to cluster i. Fill in the blank (RHS only)
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member_data_points = data[cluster_assignment == i, :]
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if member_data_points.shape[0] > 0: # check if i-th cluster is non-empty
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# Compute distances from centroid to data points (RHS only)
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distances = pairwise_distances(
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member_data_points, [centroids[i]], metric="euclidean"
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)
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squared_distances = distances**2
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heterogeneity += np.sum(squared_distances)
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return heterogeneity
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def plot_heterogeneity(heterogeneity, k):
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plt.figure(figsize=(7, 4))
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plt.plot(heterogeneity, linewidth=4)
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plt.xlabel("# Iterations")
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plt.ylabel("Heterogeneity")
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plt.title(f"Heterogeneity of clustering over time, K={k:d}")
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plt.rcParams.update({"font.size": 16})
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plt.show()
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def kmeans(
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data, k, initial_centroids, maxiter=500, record_heterogeneity=None, verbose=False
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):
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"""Runs k-means on given data and initial set of centroids.
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maxiter: maximum number of iterations to run.(default=500)
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record_heterogeneity: (optional) a list, to store the history of heterogeneity
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as function of iterations
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if None, do not store the history.
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verbose: if True, print how many data points changed their cluster labels in
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each iteration"""
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centroids = initial_centroids[:]
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prev_cluster_assignment = None
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for itr in range(maxiter):
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if verbose:
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print(itr, end="")
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# 1. Make cluster assignments using nearest centroids
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cluster_assignment = assign_clusters(data, centroids)
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# 2. Compute a new centroid for each of the k clusters, averaging all data
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# points assigned to that cluster.
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centroids = revise_centroids(data, k, cluster_assignment)
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# Check for convergence: if none of the assignments changed, stop
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if (
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prev_cluster_assignment is not None
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and (prev_cluster_assignment == cluster_assignment).all()
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):
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break
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# Print number of new assignments
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if prev_cluster_assignment is not None:
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num_changed = np.sum(prev_cluster_assignment != cluster_assignment)
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if verbose:
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print(
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f" {num_changed:5d} elements changed their cluster assignment."
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)
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# Record heterogeneity convergence metric
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if record_heterogeneity is not None:
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# YOUR CODE HERE
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score = compute_heterogeneity(data, k, centroids, cluster_assignment)
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record_heterogeneity.append(score)
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prev_cluster_assignment = cluster_assignment[:]
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return centroids, cluster_assignment
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# Mock test below
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if False: # change to true to run this test case.
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from sklearn import datasets as ds
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dataset = ds.load_iris()
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k = 3
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heterogeneity = []
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initial_centroids = get_initial_centroids(dataset["data"], k, seed=0)
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centroids, cluster_assignment = kmeans(
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dataset["data"],
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k,
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initial_centroids,
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maxiter=400,
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record_heterogeneity=heterogeneity,
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verbose=True,
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)
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plot_heterogeneity(heterogeneity, k)
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def report_generator(
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predicted: pd.DataFrame, clustering_variables: np.ndarray, fill_missing_report=None
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) -> pd.DataFrame:
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"""
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Generate a clustering report given these two arguments:
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predicted - dataframe with predicted cluster column
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fill_missing_report - dictionary of rules on how we are going to fill in missing
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values for final generated report (not included in modelling);
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>>> predicted = pd.DataFrame()
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>>> predicted['numbers'] = [1, 2, 3]
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>>> predicted['col1'] = [0.5, 2.5, 4.5]
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>>> predicted['col2'] = [100, 200, 300]
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>>> predicted['col3'] = [10, 20, 30]
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>>> predicted['Cluster'] = [1, 1, 2]
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>>> report_generator(predicted, ['col1', 'col2'], 0)
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Features Type Mark 1 2
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0 # of Customers ClusterSize False 2.000000 1.000000
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1 % of Customers ClusterProportion False 0.666667 0.333333
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2 col1 mean_with_zeros True 1.500000 4.500000
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3 col2 mean_with_zeros True 150.000000 300.000000
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4 numbers mean_with_zeros False 1.500000 3.000000
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.. ... ... ... ... ...
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99 dummy 5% False 1.000000 1.000000
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100 dummy 95% False 1.000000 1.000000
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101 dummy stdev False 0.000000 NaN
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102 dummy mode False 1.000000 1.000000
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103 dummy median False 1.000000 1.000000
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<BLANKLINE>
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[104 rows x 5 columns]
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"""
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# Fill missing values with given rules
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if fill_missing_report:
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predicted = predicted.fillna(value=fill_missing_report)
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predicted["dummy"] = 1
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numeric_cols = predicted.select_dtypes(np.number).columns
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report = (
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predicted.groupby(["Cluster"])[ # construct report dataframe
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numeric_cols
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] # group by cluster number
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.agg(
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[
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("sum", "sum"),
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("mean_with_zeros", lambda x: np.mean(np.nan_to_num(x))),
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("mean_without_zeros", lambda x: x.replace(0, np.nan).mean()),
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(
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"mean_25-75",
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lambda x: np.mean(
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np.nan_to_num(
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sorted(x)[
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round(len(x) * 25 / 100) : round(len(x) * 75 / 100)
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]
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)
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),
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),
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("mean_with_na", "mean"),
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("min", lambda x: x.min()),
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("5%", lambda x: x.quantile(0.05)),
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("25%", lambda x: x.quantile(0.25)),
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("50%", lambda x: x.quantile(0.50)),
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("75%", lambda x: x.quantile(0.75)),
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("95%", lambda x: x.quantile(0.95)),
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("max", lambda x: x.max()),
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("count", lambda x: x.count()),
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("stdev", lambda x: x.std()),
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("mode", lambda x: x.mode()[0]),
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("median", lambda x: x.median()),
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("# > 0", lambda x: (x > 0).sum()),
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]
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)
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.T.reset_index()
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.rename(index=str, columns={"level_0": "Features", "level_1": "Type"})
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) # rename columns
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# calculate the size of cluster(count of clientID's)
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# avoid SettingWithCopyWarning
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clustersize = report[
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(report["Features"] == "dummy") & (report["Type"] == "count")
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].copy()
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# rename created predicted cluster to match report column names
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clustersize.Type = "ClusterSize"
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clustersize.Features = "# of Customers"
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# calculating the proportion of cluster
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clusterproportion = pd.DataFrame(
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clustersize.iloc[:, 2:].to_numpy() / clustersize.iloc[:, 2:].to_numpy().sum()
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)
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# rename created predicted cluster to match report column names
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clusterproportion["Type"] = "% of Customers"
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clusterproportion["Features"] = "ClusterProportion"
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cols = clusterproportion.columns.tolist()
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cols = cols[-2:] + cols[:-2]
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clusterproportion = clusterproportion[cols] # rearrange columns to match report
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clusterproportion.columns = report.columns
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# generating dataframe with count of nan values
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a = pd.DataFrame(
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abs(
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report[report["Type"] == "count"].iloc[:, 2:].to_numpy()
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- clustersize.iloc[:, 2:].to_numpy()
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)
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)
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a["Features"] = 0
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a["Type"] = "# of nan"
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# filling values in order to match report
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a.Features = report[report["Type"] == "count"].Features.tolist()
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cols = a.columns.tolist()
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cols = cols[-2:] + cols[:-2]
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a = a[cols] # rearrange columns to match report
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a.columns = report.columns # rename columns to match report
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# drop count values except for cluster size
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report = report.drop(report[report.Type == "count"].index)
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# concat report with cluster size and nan values
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report = pd.concat([report, a, clustersize, clusterproportion], axis=0)
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report["Mark"] = report["Features"].isin(clustering_variables)
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cols = report.columns.tolist()
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cols = cols[0:2] + cols[-1:] + cols[2:-1]
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report = report[cols]
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sorter1 = {
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"ClusterSize": 9,
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"ClusterProportion": 8,
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"mean_with_zeros": 7,
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"mean_with_na": 6,
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"max": 5,
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"50%": 4,
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"min": 3,
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"25%": 2,
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"75%": 1,
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"# of nan": 0,
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"# > 0": -1,
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"sum_with_na": -2,
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}
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report = (
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report.assign(
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Sorter1=lambda x: x.Type.map(sorter1),
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Sorter2=lambda x: list(reversed(range(len(x)))),
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)
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.sort_values(["Sorter1", "Mark", "Sorter2"], ascending=False)
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.drop(["Sorter1", "Sorter2"], axis=1)
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)
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report.columns.name = ""
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report = report.reset_index()
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report = report.drop(columns=["index"])
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return report
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if __name__ == "__main__":
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import doctest
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doctest.testmod()
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