flatnav 0.1.2__cp39-cp39-macosx_10_14_x86_64.whl

flatnav/__init__.py

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+import sys 
+from ._core import (
+    MetricType,
+    data_type,
+    __version__,
+    __doc__
+)
+
+class _DataTypeModule:
+    from ._core.data_type import DataType
+
+
+class _IndexModule:
+    from ._core.index import (
+        IndexL2Float,
+        IndexIPFloat,
+        IndexL2Uint8,
+        IndexIPUint8,
+        IndexL2Int8,
+        IndexIPInt8,
+        create,
+    )
+
+
+index = _IndexModule
+sys.modules['flatnav.index'] = _IndexModule
+sys.modules['flatnav.data_type'] = _DataTypeModule
+
+__all__ = [
+    'MetricType',
+    'data_type',
+    'index',
+    '__version__',
+    '__doc__'
+]

flatnav-0.1.2.dist-info/METADATA

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+Metadata-Version: 2.2
+Name: flatnav
+Version: 0.1.2
+Summary: A performant graph-based kNN search library with re-ordering.
+Home-page: https://flatnav.net
+Author: Benjamin Coleman, Blaise Munyampirwa, Vihan Lakshman
+Author-email: benjamin.ray.coleman@gmail.com, blaisemunyampirwa@gmail.com, vihan@mit.edu
+Maintainer-email: blaisemunyampirwa@gmail.com
+License: Apache License, Version 2.0
+Project-URL: Source Code, https://github.com/BlaiseMuhirwa/flatnav
+Project-URL: Documentation, https://blaisemuhirwa.github.io/flatnav
+Project-URL: Bug Tracker, https://github.com/BlaiseMuhirwa/flatnav/issues
+Keywords: similarity search,vector databases,machine learning
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Other Audience
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: C++
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: System
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Software Development
+Description-Content-Type: text/markdown
+Requires-Dist: numpy<2,>=1.21.0
+Requires-Dist: h5py==3.11.0
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: maintainer-email
+Dynamic: project-url
+Dynamic: requires-dist
+Dynamic: summary
+
+## FlatNav 
+
+FlatNav is a fast and header-only graph-based index for Approximate Nearest Neighbor Search (ANNS). FlatNav is inspired by the influential [Hierarchical Navigable Small World (HNSW) index](https://github.com/nmslib/hnswlib), but with the hierarchical component removed. As detailed in our [research paper](https://arxiv.org/pdf/2412.01940), we found that FlatNav achieved identical performance to HNSW on high-dimensional datasets (dimensionality > 32) with approximately 38% less peak memory consumption and a simplified implementation. 
+
+We hope to maintain this open source library as a resource for broader community. Please consider opening a Github Issue for bugs and feature requests, or get in touch with us directly for discussions.
+
+
+### Installation 
+FlatNav is implemented in C++ with a complete Python extension with [cereal](https://uscilab.github.io/cereal/) as the only external dependency. This is a header-only library, so there is nothing to build. You can just include the necessary headers in your existing code. 
+
+FlatNav is supported on x86-64 machines on linux and MacOS (we can extend this to windows if there is sufficient interest). To get the C++ library working and run examples under the [tools](https://github.com/BlaiseMuhirwa/flatnav/blob/main/tools) directory, you will need
+
+* C++17 compiler with OpenMP support (version >= 2.0)
+* CMake (version >= 3.14)
+
+We provide some helpful scripts for installing the above in the [bin](https://github.com/BlaiseMuhirwa/flatnav/tree/main/bin) directory. 
+
+To generate the library with CMake and compile examples, run 
+
+```shell
+$ git clone https://github.com/BlaiseMuhirwa/flatnav.git --recurse-submodules
+$ cd flatnav
+$ ./bin/build.sh -e
+```
+
+You can get all options available with the `build.sh` script by passing it the `-h` argument.
+
+This will display all available build options:
+
+```shell
+Usage ./build.sh [OPTIONS]
+
+Available Options:
+  -t, --tests:                    Build tests
+  -e, --examples:                 Build examples
+  -v, --verbose:                  Make verbose
+  -b, --benchmark:                Build benchmarks
+  -bt, --build_type:              Build type (Debug, Release, RelWithDebInfo, MinSizeRel)
+  -nmv, --no_simd_vectorization:Disable SIMD instructions
+  -h, --help:                     Print this help message
+
+Example Usage:
+  ./build.sh -t -e -v
+```
+
+To build the Python bindings, follow instructions [here](https://github.com/BlaiseMuhirwa/flatnav/blob/main/flatnav_python/README.md). There are also examples for how to use the library to build an index and run queries on top of it [here](https://github.com/BlaiseMuhirwa/flatnav/blob/main/flatnav_python/unit_tests/test_index.py).
+
+### Support for SIMD Extensions 
+
+We currently support SIMD extensions for certain platforms as detailed below. 
+
+| Operation | x86_64 | arm64v8 | Apple silicon |
+|-----------|--------|---------|-----------------|
+| FP32 Inner product |SSE, AVX, AVX512 | No SIMD support | No SIMD support |
+| FP32 L2 distance |SSE, AVX, AVX512| No SIMD support | No SIMD support |
+| UINT8 L2 distance |AVX512 | No SIMD support | No SIMD support |
+| INT8 L2 distance | SSE | No SIMD support | No SIMD support |
+
+
+### Getting Started in Python
+
+Currently, we support Python wheels for versions 3.8 through 3.12 on x86_64 architectures (Intel, AMD and MacOS). Support for 
+ARM wheels is a future improvement. 
+
+The python library can be installed from PyPI by using 
+```shell
+$ pip install flatnav
+```
+
+Similarly, `flatnav` can be installed from source via [cibuildwheel](https://cibuildwheel.pypa.io/en/stable/), which 
+builds cross-platform wheels. Follow the following steps
+
+```shell
+$ git clone https://github.com/BlaiseMuhirwa/flatnav.git --recurse-submodules
+$ cd flatnav
+$ make install-cibuildwheel
+
+# This will build flatnav for the current version in your environment. If you want to build wheels 
+# for all supported python versions (3.8 to 3.12), remove the --current-version flag.
+$ ./cibuild.sh --current-version
+
+$ pip install wheelhouse/flatnav*.whl --force-reinstall
+```
+
+Once you have the python library installed and you have a dataset you want to index as a numpy array, you can construct the index as shown below. This will allocate memory and create a directed graph with vectors as nodes.
+
+```python
+import numpy as np
+import flatnav
+from flatnav.data_type import DataType 
+
+# Get your numpy-formatted dataset.
+dataset_size = 1_000_000
+dataset_dimension = 128
+dataset_to_index = np.random.randn(dataset_size, dataset_dimension)
+
+# Define index construction parameters.
+distance_type = "l2"
+max_edges_per_node = 32
+ef_construction = 100
+num_build_threads = 16
+
+# Create index configuration and pre-allocate memory
+index = flatnav.index.create(
+    distance_type=distance_type,
+    index_data_type=DataType.float32,
+    dim=dataset_dimension,
+    dataset_size=dataset_size,
+    max_edges_per_node=max_edges_per_node,
+    verbose=True,
+    collect_stats=True,
+)
+index.set_num_threads(num_build_threads)
+
+# Now index the dataset 
+index.add(data=dataset_to_index, ef_construction=ef_construction)
+```
+
+Note that we specified `DataType.float32` to indicate that we want to build an index with vectors represented with `float` type. If you want to use a different precision, such as `uint8_t` or `int8_t` (which are the only other ones currently supported), you can use `DataType.uint8` or `DataType.int8`.
+The distance type can either be `l2` or `angular`. The `collect_stats` flag will record the number of distance evaluations.
+
+To query the index we just created by generating IID vectors from the standard normal distribution, we do it as follows 
+
+```python
+
+# Set query-time parameters 
+k = 100
+ef_search = 100
+
+# Run k-NN query with a single thread.
+index.set_num_threads(1)
+
+queries = np.random.randn(1000, dataset_to_index.shape[1])
+for query in queries:
+  distances, indices = index.search_single(
+    query=query,
+    ef_search=ef_search,
+    K=k,
+  )
+
+```
+
+You can parallelize the search by setting the number of threads to a desired number and using a different API that also returns the exact same results as `search_single`.
+
+```python
+index.set_num_threads(16)
+distances, indices = index.search(queries=queries, ef_search=ef_search, K=k)
+```
+
+### Getting Started in C++
+
+As mentioned earlier, there is nothing to build since this is header-only. We will translate the above Python code in C++ to illustrate how to use the C++ API. 
+
+```c++
+#include <cstdint>
+#include <flatnav/index/Index.h>
+#include <flatnav/distances/SquaredL2Distance.h>
+#include <flatnav/distances/DistanceInterface.h>
+
+template <typename dist_t>
+void run_knn_search(Index<dist_t, int>>* index, float *queries, int* gtruth, 
+        int ef_search, int K, int num_queries, int num_gtruth, int dim) {
+
+  float mean_recall = 0;
+  for (int i = 0; i < num_queries; i++) {
+    float *q = queries + dim * i;
+    int *g = gtruth + num_gtruth * i;
+    std::vector<std::pair<float, int>> result =
+        index->search(q, K, ef_search);
+
+    float recall = 0;
+    for (int j = 0; j < K; j++) {
+      for (int l = 0; l < K; l++) {
+        if (result[j].second == g[l]) {
+          recall = recall + 1;
+        }
+      }
+    }
+    recall = recall / K;
+    mean_recall = mean_recall + recall;
+  }
+}
+
+
+int main(int argc, char** argv) {
+  uint32_t dataset_size = 1000000;
+  uint32_t dataset_dimension = 128;
+
+  // We skip the random data generation, but you can do that with std::mt19937, std::random_device 
+  // and std::normal_distribution
+  // std::vector<float> dataset_to_index; 
+
+  uint32_t max_edges_per_node = 32;
+  uint32_t ef_construction = 100;
+
+  // Create an index with l2 distance 
+  auto distance = SquaredL2Distance<>::create(dataset_dimension);
+  auto* index = new Index<SquaredL2Distance<DataType::float32>>, int>(
+      /* dist = */ std::move(distance), /* dataset_size = */ dataset_size,
+      /* max_edges_per_node = */ max_edges_per_node);
+
+  index->setNumThreads(build_num_threads);
+
+  std::vector<int> labels(dataset_size);
+  std::iota(labels.begin(), labels.end(), 0);
+  index->template addBatch<float>(/* data = */ (void *)dataset_to_index,
+                                  /* labels = */ labels,
+                                  /* ef_construction */ ef_construction);
+
+  // Now query the index and compute the recall 
+  // We assume you have a ground truth (int*) array and a queries (float*) array
+  uint32_t ef_search = 100;
+  uint32_t k = 100;
+  uint32_t num_queries = 1000;
+  uint32_t num_gtruth = 1000;
+  
+  // Query the index and compute the recall. 
+  run_knn_search(index, queries, gtruth, ef_search, k, num_queries, num_gtruth, dataset_dimension);
+}
+
+```
+
+### Datasets from ANN-Benchmarks
+
+ANN-Benchmarks provide HDF5 files for a standard benchmark of near-neighbor datasets, queries and ground-truth results. To index any of these datasets you can use the `construct_npy.cpp` and `query_npy.cpp` files linked above.
+
+To generate the [ANNS benchmark datasets](https://github.com/erikbern/ann-benchmarks?tab=readme-ov-file#data-sets), run the following script
+
+```shell
+$ ./bin/download_anns_datasets.sh <dataset-name> [--normalize]
+```
+
+For datasets that use the angular/cosine similarity, you will need to use `--normalize` option so that the distances are computed correctly. 
+
+Available dataset names include:
+
+```shell
+_ mnist-784-euclidean
+_ sift-128-euclidean
+_ glove-25-angular
+_ glove-50-angular
+_ glove-100-angular
+_ glove-200-angular
+_ deep-image-96-angular
+_ gist-960-euclidean
+_ nytimes-256-angular
+```
+
+### Experimental API and Future Extensions 
+
+You can find the current work under development under the [development-features](https://github.com/BlaiseMuhirwa/flatnav/blob/main/development-features) directory. 
+While some of these features may be usable, they are not guarranteed to be stable. Stable features will be expected to be part of the PyPI releases. 
+The most notable on-going extension that's under development is product quantization.
+
+## Citation
+If you find this library useful, please consider citing our associated paper:
+
+```
+@article{munyampirwa2024down,
+  title={Down with the Hierarchy: The'H'in HNSW Stands for" Hubs"},
+  author={Munyampirwa, Blaise and Lakshman, Vihan and Coleman, Benjamin},
+  journal={arXiv preprint arXiv:2412.01940},
+  year={2024}
+}
+```

flatnav-0.1.2.dist-info/RECORD

@@ -0,0 +1,6 @@
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+flatnav-0.1.2.dist-info/METADATA,sha256=sE_6EUeEaCrgoF2ADwtqIHbM9HFjMExUN0HoZ-3tg0c,12109
+flatnav-0.1.2.dist-info/WHEEL,sha256=iTFmO13zeQqKMhexv916yMBT3HF07MzmsCxsrTHtkmg,104
+flatnav-0.1.2.dist-info/top_level.txt,sha256=FVUKVYK356G2MlNoIaTtjmGUzJNV_2wLRmcHtuSUP3Y,8
+flatnav-0.1.2.dist-info/RECORD,,

flatnav-0.1.2.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: skbuild 0.18.1
+Root-Is-Purelib: false
+Tag: cp39-cp39-macosx_10_14_x86_64
+

flatnav-0.1.2.dist-info/top_level.txt

@@ -0,0 +1 @@
+flatnav