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Hnswlib - fast approximate nearest neighbor search

Header-only C++ HNSW implementation with python bindings, insertions and updates.

NEWS:

version 0.8.0

Full list of changes: https://github.com/nmslib/hnswlib/pull/523

version 0.7.0

Highlights:

  1. Lightweight, header-only, no dependencies other than C++ 11
  2. Interfaces for C++, Python, external support for Java and R (https://github.com/jlmelville/rcpphnsw).
  3. Has full support for incremental index construction and updating the elements (thanks to the contribution by Apoorv Sharma). Has support for element deletions (by marking them in index, later can be replaced with other elements). Python index is picklable.
  4. Can work with custom user defined distances (C++).
  5. Significantly less memory footprint and faster build time compared to current nmslib's implementation.

Description of the algorithm parameters can be found in ALGO_PARAMS.md.

Python bindings

Supported distances:

DistanceparameterEquation
Squared L2'l2'd = sum((Ai-Bi)^2)
Inner product'ip'd = 1.0 - sum(Ai*Bi)
Cosine similarity'cosine'd = 1.0 - sum(Ai*Bi) / sqrt(sum(Ai*Ai) * sum(Bi*Bi))

Note that inner product is not an actual metric. An element can be closer to some other element than to itself. That allows some speedup if you remove all elements that are not the closest to themselves from the index.

For other spaces use the nmslib library https://github.com/nmslib/nmslib.

API description

hnswlib.Index methods:

Read-only properties of hnswlib.Index class:

Properties of hnswlib.Index that support reading and writing:

Python bindings examples

See more examples here:

An example of creating index, inserting elements, searching and pickle serialization:

import hnswlib
import numpy as np
import pickle

dim = 128
num_elements = 10000

# Generating sample data
data = np.float32(np.random.random((num_elements, dim)))
ids = np.arange(num_elements)

# Declaring index
p = hnswlib.Index(space = 'l2', dim = dim) # possible options are l2, cosine or ip

# Initializing index - the maximum number of elements should be known beforehand
p.init_index(max_elements = num_elements, ef_construction = 200, M = 16)

# Element insertion (can be called several times):
p.add_items(data, ids)

# Controlling the recall by setting ef:
p.set_ef(50) # ef should always be > k

# Query dataset, k - number of the closest elements (returns 2 numpy arrays)
labels, distances = p.knn_query(data, k = 1)

# Index objects support pickling
# WARNING: serialization via pickle.dumps(p) or p.__getstate__() is NOT thread-safe with p.add_items method!
# Note: ef parameter is included in serialization; random number generator is initialized with random_seed on Index load
p_copy = pickle.loads(pickle.dumps(p)) # creates a copy of index p using pickle round-trip

### Index parameters are exposed as class properties:
print(f"Parameters passed to constructor:  space={p_copy.space}, dim={p_copy.dim}") 
print(f"Index construction: M={p_copy.M}, ef_construction={p_copy.ef_construction}")
print(f"Index size is {p_copy.element_count} and index capacity is {p_copy.max_elements}")
print(f"Search speed/quality trade-off parameter: ef={p_copy.ef}")

An example with updates after serialization/deserialization:

import hnswlib
import numpy as np

dim = 16
num_elements = 10000

# Generating sample data
data = np.float32(np.random.random((num_elements, dim)))

# We split the data in two batches:
data1 = data[:num_elements // 2]
data2 = data[num_elements // 2:]

# Declaring index
p = hnswlib.Index(space='l2', dim=dim)  # possible options are l2, cosine or ip

# Initializing index
# max_elements - the maximum number of elements (capacity). Will throw an exception if exceeded
# during insertion of an element.
# The capacity can be increased by saving/loading the index, see below.
#
# ef_construction - controls index search speed/build speed tradeoff
#
# M - is tightly connected with internal dimensionality of the data. Strongly affects memory consumption (~M)
# Higher M leads to higher accuracy/run_time at fixed ef/efConstruction

p.init_index(max_elements=num_elements//2, ef_construction=100, M=16)

# Controlling the recall by setting ef:
# higher ef leads to better accuracy, but slower search
p.set_ef(10)

# Set number of threads used during batch search/construction
# By default using all available cores
p.set_num_threads(4)

print("Adding first batch of %d elements" % (len(data1)))
p.add_items(data1)

# Query the elements for themselves and measure recall:
labels, distances = p.knn_query(data1, k=1)
print("Recall for the first batch:", np.mean(labels.reshape(-1) == np.arange(len(data1))), "\n")

# Serializing and deleting the index:
index_path='first_half.bin'
print("Saving index to '%s'" % index_path)
p.save_index("first_half.bin")
del p

# Re-initializing, loading the index
p = hnswlib.Index(space='l2', dim=dim)  # the space can be changed - keeps the data, alters the distance function.

print("\nLoading index from 'first_half.bin'\n")

# Increase the total capacity (max_elements), so that it will handle the new data
p.load_index("first_half.bin", max_elements = num_elements)

print("Adding the second batch of %d elements" % (len(data2)))
p.add_items(data2)

# Query the elements for themselves and measure recall:
labels, distances = p.knn_query(data, k=1)
print("Recall for two batches:", np.mean(labels.reshape(-1) == np.arange(len(data))), "\n")

C++ examples

See examples here:

Bindings installation

You can install from sources:

apt-get install -y python-setuptools python-pip
git clone https://github.com/nmslib/hnswlib.git
cd hnswlib
pip install .

or you can install via pip: pip install hnswlib

For developers

Contributions are highly welcome!

Please make pull requests against the develop branch.

When making changes please run tests (and please add a test to tests/python in case there is new functionality):

python -m unittest discover --start-directory tests/python --pattern "bindings_test*.py"

Other implementations

200M SIFT test reproduction

To download and extract the bigann dataset (from root directory):

python tests/cpp/download_bigann.py

To compile:

mkdir build
cd build
cmake ..
make all

To run the test on 200M SIFT subset:

./main

The size of the BigANN subset (in millions) is controlled by the variable subset_size_millions hardcoded in sift_1b.cpp.

Updates test

To generate testing data (from root directory):

cd tests/cpp
python update_gen_data.py

To compile (from root directory):

mkdir build
cd build
cmake ..
make

To run test without updates (from build directory)

./test_updates

To run test with updates (from build directory)

./test_updates update

HNSW example demos

References

HNSW paper:

@article{malkov2018efficient,
  title={Efficient and robust approximate nearest neighbor search using hierarchical navigable small world graphs},
  author={Malkov, Yu A and Yashunin, Dmitry A},
  journal={IEEE transactions on pattern analysis and machine intelligence},
  volume={42},
  number={4},
  pages={824--836},
  year={2018},
  publisher={IEEE}
}

The update algorithm supported in this repository is to be published in "Dynamic Updates For HNSW, Hierarchical Navigable Small World Graphs" US Patent 15/929,802 by Apoorv Sharma, Abhishek Tayal and Yury Malkov.