user2926523 user2926523 -4 years ago 154
Python Question

Sklearn kNN usage with a user defined metric

Currently I'm doing a project which may require using a kNN algorithm to find the top k nearest neighbors for a given point, say P. im using python, sklearn package to do the job, but our predefined metric is not one of those default metrics. so I have to use the user defined metric, from the documents of sklearn, which can be find here and here.

It seems that the latest version of sklearn kNN support the user defined metric, but i cant find how to use it:

import sklearn
from sklearn.neighbors import NearestNeighbors
import numpy as np
from sklearn.neighbors import DistanceMetric
from sklearn.neighbors.ball_tree import BallTree
BallTree.valid_metrics


say i have defined a metric called mydist=max(x-y), then use DistanceMetric.get_metric to make it a DistanceMetric object:

dt=DistanceMetric.get_metric('pyfunc',func=mydist)


from the document, the line should looks like this

nbrs = NearestNeighbors(n_neighbors=4, algorithm='auto',metric='pyfunc').fit(A)
distances, indices = nbrs.kneighbors(A)


but where can i put the
dt
in? Thanks

Answer Source

You pass a metric as metric param, and additional metric arguments as keyword paramethers to NN constructor:

>>> def mydist(x, y):
...     return np.sum((x-y)**2)
...
>>> X = np.array([[-1, -1], [-2, -1], [-3, -2], [1, 1], [2, 1], [3, 2]])

>>> nbrs = NearestNeighbors(n_neighbors=4, algorithm='ball_tree',
...            metric='pyfunc', func=mydist)
>>> nbrs.fit(X)
NearestNeighbors(algorithm='ball_tree', leaf_size=30, metric='pyfunc',
         n_neighbors=4, radius=1.0)
>>> nbrs.kneighbors(X)
(array([[  0.,   1.,   5.,   8.],
       [  0.,   1.,   2.,  13.],
       [  0.,   2.,   5.,  25.],
       [  0.,   1.,   5.,   8.],
       [  0.,   1.,   2.,  13.],
       [  0.,   2.,   5.,  25.]]), array([[0, 1, 2, 3],
       [1, 0, 2, 3],
       [2, 1, 0, 3],
       [3, 4, 5, 0],
       [4, 3, 5, 0],
       [5, 4, 3, 0]]))
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