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Approximate Nearest Neighbor Search for Sparse Data in Python! This library is well suited to finding nearest neighbors in sparse, high dimensional spaces (like text documents).

Out of the box, PySparNN supports Cosine Distance (i.e. 1 - cosine_similarity).

PySparNN benefits:

  • Designed to be efficient on sparse data (memory & cpu).
  • Implemented leveraging existing python libraries (scipy & numpy).
  • Easily extended with other metrics: Manhattan, Euclidian, Jaccard, etc.
  • Supports incremental insertion of elements.

If your data is NOT SPARSE - please consider faiss or annoy. They use similar methods and I am a big fan of both. You should expect better performance on dense vectors from both of those projects.

The most comparable library to PySparNN is scikit-learn's LSHForest module. As of this writing, PySparNN is ~4x faster on the 20newsgroups dataset (as a sparse vector). A more robust benchmarking on sparse data is desired. Here is the comparison. Here is another comparison on the larger Enron email dataset.

Example Usage

Simple Example

import pysparnn.cluster_index as ci

import numpy as np
from scipy.sparse import csr_matrix

features = np.random.binomial(1, 0.01, size=(1000, 20000))
features = csr_matrix(features)

# build the search index!
data_to_return = range(1000)
cp = ci.MultiClusterIndex(features, data_to_return)[:5], k=1, return_distance=False)
>> [[0], [1], [2], [3], [4]]

Text Example

import pysparnn.cluster_index as ci

from sklearn.feature_extraction.text import TfidfVectorizer

data = [
    'hello world',
    'oh hello there',
    'Play it',
    'Play it again Sam',

tv = TfidfVectorizer()

features_vec = tv.transform(data)

# build the search index!
cp = ci.MultiClusterIndex(features_vec, data)

# search the index with a sparse matrix
search_data = [
    'oh there',
    'Play it again Frank'

search_features_vec = tv.transform(search_data), k=1, k_clusters=2, return_distance=False)
>> [['oh hello there'], ['Play it again Sam']]


PySparNN requires numpy and scipy. Tested with numpy 1.11.2 and scipy 0.18.1.


# clone pysparnn
cd pysparnn 
pip install -r requirements.txt 
python install

How PySparNN works

Searching for a document in an collection of D documents is naively O(D) (assuming documents are constant sized).

However! we can create a tree structure where the first level is O(sqrt(D)) and each of the leaves are also O(sqrt(D)) - on average.

We randomly pick sqrt(D) candidate items to be in the top level. Then -- each document in the full list of D documents is assigned to the closest candidate in the top level.

This breaks up one O(D) search into two O(sqrt(D)) searches which is much much faster when D is big!

This generalizes to h levels. The runtime becomes: O(h * h_root(D))

Further Information

See the CONTRIBUTING file for how to help out.


PySparNN is BSD-licensed. We also provide an additional patent grant.


Approximate Nearest Neighbor Search for Sparse Data in Python!




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