Clustering on Python and Bokeh; select widget which allows user to change clustering algorithm

Question

I am trying to build a feature in a Bokeh dashboard which allows the user to cluster data. I am using the following example as a template, here is the link:- Clustering in Bokeh example

Here is the code from this example:-

import numpy as np
from sklearn import cluster, datasets
from sklearn.preprocessing import StandardScaler

from bokeh.layouts import column, row
from bokeh.plotting import figure, output_file, show

print("\n\n*** This example may take several seconds to run before displaying. ***\n\n")

N = 50000
PLOT_SIZE = 400

# generate datasets.
np.random.seed(0)
noisy_circles = datasets.make_circles(n_samples=N, factor=.5, noise=.04)
noisy_moons = datasets.make_moons(n_samples=N, noise=.05)
centers = [(-2, 3), (2, 3), (-2, -3), (2, -3)]
blobs1 = datasets.make_blobs(centers=centers, n_samples=N, cluster_std=0.4, random_state=8)
blobs2 = datasets.make_blobs(centers=centers, n_samples=N, cluster_std=0.7, random_state=8)

colors = np.array([x for x in ('#00f', '#0f0', '#f00', '#0ff', '#f0f', '#ff0')])
colors = np.hstack([colors] * 20)

# create clustering algorithms
dbscan   = cluster.DBSCAN(eps=.2)
birch    = cluster.Birch(n_clusters=2)
means    = cluster.MiniBatchKMeans(n_clusters=2)
spectral = cluster.SpectralClustering(n_clusters=2, eigen_solver='arpack', affinity="nearest_neighbors")
affinity = cluster.AffinityPropagation(damping=.9, preference=-200)

# change here, to select clustering algorithm (note: spectral is slow)
algorithm = dbscan  # <- SELECT ALG

plots =[]
for dataset in (noisy_circles, noisy_moons, blobs1, blobs2):
    X, y = dataset
    X = StandardScaler().fit_transform(X)

    # predict cluster memberships
    algorithm.fit(X)
    if hasattr(algorithm, 'labels_'):
        y_pred = algorithm.labels_.astype(int)
    else:
        y_pred = algorithm.predict(X)

    p = figure(output_backend="webgl", title=algorithm.__class__.__name__,
               width=PLOT_SIZE, height=PLOT_SIZE)

    p.circle(X[:, 0], X[:, 1], color=colors[y_pred].tolist(), alpha=0.1,)

    plots.append(p)

# generate layout for the plots
layout = column(row(plots[:2]), row(plots[2:]))

output_file("clustering.html", title="clustering with sklearn")

show(layout)

The example allows the user to cluster data. Within the code, you can specify which algorithm to use; in the code pasted above, the algorithm is dbscan. I tried to modify the code so that I can add in a widget which would allow the user to specify the algorithm to use :-

from bokeh.models.annotations import Label
import numpy as np
from sklearn import cluster, datasets
from sklearn.preprocessing import StandardScaler

from bokeh.layouts import column, row
from bokeh.plotting import figure, output_file, show
from bokeh.models import CustomJS, Select
print("\n\n*** This example may take several seconds to run before displaying. ***\n\n")

N = 50000
PLOT_SIZE = 400

# generate datasets.
np.random.seed(0)
noisy_circles = datasets.make_circles(n_samples=N, factor=.5, noise=.04)
noisy_moons = datasets.make_moons(n_samples=N, noise=.05)
centers = [(-2, 3), (2, 3), (-2, -3), (2, -3)]
blobs1 = datasets.make_blobs(centers=centers, n_samples=N, cluster_std=0.4, random_state=8)
blobs2 = datasets.make_blobs(centers=centers, n_samples=N, cluster_std=0.7, random_state=8)

colors = np.array([x for x in ('#00f', '#0f0', '#f00', '#0ff', '#f0f', '#ff0')])
colors = np.hstack([colors] * 20)

# create clustering algorithms
dbscan   = cluster.DBSCAN(eps=.2)
birch    = cluster.Birch(n_clusters=2)
means    = cluster.MiniBatchKMeans(n_clusters=2)
spectral = cluster.SpectralClustering(n_clusters=2, eigen_solver='arpack', affinity="nearest_neighbors")
affinity = cluster.AffinityPropagation(damping=.9, preference=-200)
kmeans   = cluster.KMeans(n_clusters=2)

############################select widget for different clustering algorithms############


menu     =[('DBSCAN','dbscan'),('Birch','birch'),('MiniBatchKmeans','means'),('Spectral','spectral'),('Affinity','affinity'),('K-means','kmeans')]
select = Select(title="Option:", value="DBSCAN", options=menu)
select.js_on_change("value", CustomJS(code="""
    console.log('select: value=' + this.value, this.toString())
"""))

# change here, to select clustering algorithm (note: spectral is slow)
algorithm = select.value  

############################################################
plots =[]
for dataset in (noisy_circles, noisy_moons, blobs1, blobs2):
    X, y = dataset
    X = StandardScaler().fit_transform(X)

    # predict cluster memberships
    algorithm.fit(X)
    if hasattr(algorithm, 'labels_'):
        y_pred = algorithm.labels_.astype(int)
    else:
        y_pred = algorithm.predict(X)

    p = figure(output_backend="webgl", title=algorithm.__class__.__name__,
               width=PLOT_SIZE, height=PLOT_SIZE)

    p.circle(X[:, 0], X[:, 1], color=colors[y_pred].tolist(), alpha=0.1,)

    plots.append(p)

# generate layout for the plots
layout = column(select,row(plots[:2]), row(plots[2:]))

output_file("clustering.html", title="clustering with sklearn")

show(layout)

However, I get this error when I try to run it:-

AttributeError: 'str' object has no attribute 'fit'

Can anyone tell me what I am missing in order to fix this?

Also, and if not too hard to do, I would like to add in a numeric input widget which allows the user to select the number of clusters for each algorithm to find. Suggestions?

Many thanks :)

EDIT

Here is the current state of the code with @Tony solution.

''' Example inspired by an example from the scikit-learn project:
http://scikit-learn.org/stable/auto_examples/cluster/plot_cluster_comparison.html
'''
#https://github.com/bokeh/bokeh/blob/branch-2.4/examples/webgl/clustering.py
from bokeh.models.annotations import Label
import numpy as np
from sklearn import cluster, datasets
from sklearn.preprocessing import StandardScaler

from bokeh.layouts import column, row
from bokeh.plotting import figure, output_file, show
from bokeh.models import CustomJS, Select
print("\n\n*** This example may take several seconds to run before displaying. ***\n\n")

N = 50000
PLOT_SIZE = 400

# generate datasets.
np.random.seed(0)
noisy_circles = datasets.make_circles(n_samples=N, factor=.5, noise=.04)
noisy_moons = datasets.make_moons(n_samples=N, noise=.05)
centers = [(-2, 3), (2, 3), (-2, -3), (2, -3)]
blobs1 = datasets.make_blobs(centers=centers, n_samples=N, cluster_std=0.4, random_state=8)
blobs2 = datasets.make_blobs(centers=centers, n_samples=N, cluster_std=0.7, random_state=8)

colors = np.array([x for x in ('#00f', '#0f0', '#f00', '#0ff', '#f0f', '#ff0')])
colors = np.hstack([colors] * 20)

# create clustering algorithms
dbscan   = cluster.DBSCAN(eps=.2)
birch    = cluster.Birch(n_clusters=2)
means    = cluster.MiniBatchKMeans(n_clusters=2)
spectral = cluster.SpectralClustering(n_clusters=2, eigen_solver='arpack', affinity="nearest_neighbors")
affinity = cluster.AffinityPropagation(damping=.9, preference=-200)
kmeans   = cluster.KMeans(n_clusters=2)

menu     =[('DBSCAN','dbscan'),('Birch','birch'),('MiniBatchKmeans','means'),('Spectral','spectral'),('Affinity','affinity'),('K-means','kmeans')]
select = Select(title="Option:", value="DBSCAN", options=menu)
select.js_on_change("value", CustomJS(code="""
    console.log('select: value=' + this.value, this.toString())
"""))

# change here, to select clustering algorithm (note: spectral is slow)
#algorithm = select.value  

algorithm = None

if select.value == 'dbscan':
    algorithm = dbscan # use dbscan algorithm function
elif select.value == 'birch':
      algorithm = birch  # use birch algorithm function
elif select.value == 'means':
      algorithm = means  # use means algorithm function
elif select.value == 'spectral':
      algorithm = spectral
elif select.value == 'affinity':
      algorithm = affinity
elif select.value == 'kmeans':
      algorithm = 'kmeans'


if algorithm is not None:
    plots =[]
for dataset in (noisy_circles, noisy_moons, blobs1, blobs2):
    X, y = dataset
    X = StandardScaler().fit_transform(X)

    # predict cluster memberships
    algorithm.fit(X)           ######################This is what appears to be the problem######################
    if hasattr(algorithm, 'labels_'):
        y_pred = algorithm.labels_.astype(int)
    else:
        y_pred = algorithm.predict(X)

    p = figure(output_backend="webgl", title=algorithm.__class__.__name__,
               width=PLOT_SIZE, height=PLOT_SIZE)

    p.circle(X[:, 0], X[:, 1], color=colors[y_pred].tolist(), alpha=0.1,)

    plots.append(p)
else:
   print('Please select an algorithm first')
    


# generate layout for the plots
layout = column(select,row(plots[:2]), row(plots[2:]))

output_file("clustering.html", title="clustering with sklearn")

show(layout)

See algorithm.fit(X) this is where the error occurs. Error message:-

AttributeError: 'NoneType' object has no attribute 'fit'
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
m:\bokehdash\clusteringbokeh.py in 
     67 
     68     # predict cluster memberships
---> 69     algorithm.fit(X)
     70     if hasattr(algorithm, 'labels_'):
     71         y_pred = algorithm.labels_.astype(int)

AttributeError: 'NoneType' object has no attribute 'fit'

Answer 1

I don't know sklearn but comparing both your examples I can see the following:

1. the Select is a Bokeh model which has value attribute of type string. So select.value is a string
2. the dbscan is an algorithm function

So when you do algorithm = dbscan you assign an algorithm function to your algorithm variable and when you do algorithm = select.value in your second example you assign just a string to it so it won't work because string doesn't have the fit() function. You should do something like this:

algorithm = None

if select.value == 'DBSCAN':
    algorithm = dbscan # use dbscan algorithm function
elif select.value == 'Birch':
      algorithm = birch  # use birch algorithm function
elif select.value == 'MiniBatchKmeans':
      algorithm = means  # use means algorithm function
etc...

if algorithm is not None:
    plots =[]
    for dataset in (noisy_circles, noisy_moons, blobs1, blobs2):
        ...
else:
   print('Please select an algorithm first')