mlxvs 0.1.0__tar.gz

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+ cmake_minimum_required(VERSION 3.25)
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+ project(mlxvs VERSION 0.1.0 LANGUAGES CXX)
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+
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+ set(CMAKE_CXX_STANDARD 20)
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+ set(CMAKE_CXX_STANDARD_REQUIRED ON)
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+ set(CMAKE_POSITION_INDEPENDENT_CODE ON)
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+ if(NOT CMAKE_BUILD_TYPE)
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+ set(CMAKE_BUILD_TYPE Release)
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+ endif()
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+
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+ option(MLXVS_BUILD_PYTHON "Build the Python bindings (nanobind)" OFF)
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+ option(MLXVS_BUILD_TESTS "Build the C++ tests and benchmarks" ${PROJECT_IS_TOP_LEVEL})
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+
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+ # MLX's C++ library. For the Python bindings, the one the `mlx` wheel ships, so
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+ # that one process holds one libmlx; otherwise an installed MLX (e.g. `brew
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+ # install mlx`), or -DMLX_ROOT. mlxvs pins the MLX version it was built against.
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+ if(MLXVS_BUILD_PYTHON)
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+ find_package(
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+ Python 3.10
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+ COMPONENTS Interpreter Development.Module
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+ REQUIRED)
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+ execute_process(
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+ COMMAND "${Python_EXECUTABLE}" -m mlx --cmake-dir
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+ OUTPUT_STRIP_TRAILING_WHITESPACE
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+ OUTPUT_VARIABLE MLX_ROOT)
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+ endif()
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+ find_package(MLX CONFIG REQUIRED)
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+
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+ add_library(mlxvs STATIC src/knn.cpp src/kmeans.cpp src/nndescent.cpp
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+ src/all_neighbors.cpp src/search.cpp src/cagra.cpp)
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+ target_include_directories(mlxvs PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/include)
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+ target_link_libraries(mlxvs PUBLIC mlx)
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+
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+ if(MLXVS_BUILD_TESTS)
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+ add_executable(test_knn tests/test_knn.cpp)
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+ target_link_libraries(test_knn PRIVATE mlxvs)
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+ add_executable(test_nnd tests/test_nnd.cpp)
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+ target_link_libraries(test_nnd PRIVATE mlxvs)
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+ add_executable(test_all_neighbors tests/test_all_neighbors.cpp)
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+ target_link_libraries(test_all_neighbors PRIVATE mlxvs)
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+ add_executable(bench_knn bench/bench_knn.cpp)
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+ target_link_libraries(bench_knn PRIVATE mlxvs)
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+ enable_testing()
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+ add_test(NAME test_knn COMMAND test_knn)
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+ add_test(NAME test_nnd COMMAND test_nnd)
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+ add_executable(test_search tests/test_search.cpp)
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+ target_link_libraries(test_search PRIVATE mlxvs)
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+ add_test(NAME test_all_neighbors COMMAND test_all_neighbors)
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+ add_test(NAME test_search COMMAND test_search)
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+ add_executable(test_cagra tests/test_cagra.cpp)
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+ target_link_libraries(test_cagra PRIVATE mlxvs)
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+ add_test(NAME test_cagra COMMAND test_cagra)
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+ endif()
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+
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+ if(MLXVS_BUILD_PYTHON)
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+ # nanobind from the `nanobind` wheel (python -m nanobind --cmake_dir)
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+ execute_process(
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+ COMMAND "${Python_EXECUTABLE}" -m nanobind --cmake_dir
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+ OUTPUT_STRIP_TRAILING_WHITESPACE
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+ OUTPUT_VARIABLE nanobind_ROOT)
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+ find_package(nanobind CONFIG REQUIRED)
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+ # NB_DOMAIN mlx: mlx.core's array, Stream and Device types are shared with
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+ # the extension, as MLX's own extension examples do
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+ nanobind_add_module(
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+ _core
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+ NB_STATIC
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+ LTO
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+ NOMINSIZE
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+ NB_DOMAIN
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+ mlx
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+ python/bindings.cpp)
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+ target_link_libraries(_core PRIVATE mlxvs)
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+ install(TARGETS _core LIBRARY DESTINATION mlxvs)
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+ endif()
mlxvs-0.1.0/LICENSE ADDED
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@@ -0,0 +1,5 @@
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+ include CMakeLists.txt LICENSE NOTICE README.md
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+ recursive-include include *.h
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+ recursive-include src *.h *.cpp
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+ include python/bindings.cpp
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+ recursive-include python/tests *.py
mlxvs-0.1.0/NOTICE ADDED
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+ mlxvs
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+ Copyright 2026 mikepapadim
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+
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+ Licensed under the Apache License, Version 2.0.
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+
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+ The NN-Descent kernels (src/nnd_kernels.h, src/nndescent.cpp) are a port to
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+ MLX of the Metal NN-Descent in JVector's jvector-gpu module
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+ (https://github.com/datastax/jvector, Apache License 2.0, Copyright DataStax,
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+ Inc.), from which the algorithm's structure, parameters and kernel design are
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+ taken: random start over permutation blocks, 16 samples per node, 64-member
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+ joins scored with SIMD-group matrices, hashed proposal slots and the bitonic
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+ merge. The prune-side top-k selection in src/kernels.h follows the same
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+ module's exact k-NN selection.
mlxvs-0.1.0/PKG-INFO ADDED
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+ Metadata-Version: 2.4
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+ Name: mlxvs
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+ Version: 0.1.0
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+ Summary: GPU k-NN search and k-NN graph construction on Apple silicon, built on MLX
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+ Author: mikepapadim
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+ License-Expression: Apache-2.0
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+ Project-URL: Homepage, https://github.com/mikepapadim/mlxvs
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+ Project-URL: Issues, https://github.com/mikepapadim/mlxvs/issues
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+ Keywords: nearest-neighbors,knn,knn-graph,nn-descent,vector-search,k-means,gpu,metal,apple-silicon,mlx,cuvs,umap
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+ Classifier: Development Status :: 3 - Alpha
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: Intended Audience :: Developers
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+ Classifier: Programming Language :: C++
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: Operating System :: MacOS :: MacOS X
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+ Classifier: Environment :: GPU
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+ Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
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+ Classifier: Topic :: Database :: Database Engines/Servers
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+ Requires-Python: >=3.10
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+ Description-Content-Type: text/markdown
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+ License-File: LICENSE
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+ License-File: NOTICE
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+ Requires-Dist: mlx<0.33,>=0.32.0
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+ Requires-Dist: numpy>=1.24
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+ Dynamic: license-file
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+
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+ # mlxVS
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+
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+ **cuVS for your Mac: GPU vector search on Apple silicon.**
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+
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+ [![CI](https://github.com/mikepapadim/mlxvs/actions/workflows/ci.yml/badge.svg)](https://github.com/mikepapadim/mlxvs/actions/workflows/ci.yml)
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+ [![License](https://img.shields.io/badge/license-Apache--2.0-blue.svg)](LICENSE)
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+
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+ Index a million vectors in 10 seconds, then answer 70,000 queries per second at 97.6% recall, on a MacBook Pro's
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+ GPU: twice the queries per second of HNSW on all 12 CPU cores at the same recall, from an index built 8 times faster
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+ ([numbers](#benchmarks)). mlxVS brings NVIDIA [cuVS](https://github.com/rapidsai/cuvs)'s operations and parameter
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+ names to the Mac, built on [MLX](https://github.com/ml-explore/mlx): exact k-NN, k-means, NN-Descent, batched
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+ all-neighbors graphs, CAGRA graph pruning and search. NumPy or MLX arrays in, any M-series Mac.
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+
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+ ```python
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+ import mlxvs
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+ graph = mlxvs.cagra_build(vectors, graph_degree=32) # 1M x 128 in ~10 s
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+ ids, dist = mlxvs.graph_search(vectors, graph, queries, k=10) # ~70k queries/s at 97.6% recall
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+ ```
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+
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+ <picture>
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+ <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/mikepapadim/mlxvs/main/docs/img/sift1m-dark.png">
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+ <img alt="SIFT1M on a MacBook Pro M3 Pro: queries per second against recall@10. mlxVS CAGRA degree 32 (built in 10.4 s) reaches 69,500 queries/s at 0.976 recall; hnswlib on 12 CPU cores (built in 88.1 s) reaches 32,200 at 0.964. Numbers in the Benchmarks table." src="https://raw.githubusercontent.com/mikepapadim/mlxvs/main/docs/img/sift1m-light.png" width="720">
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+ </picture>
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+
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+ Use it for approximate nearest-neighbor search, for the k-NN graph behind UMAP, t-SNE, clustering and
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+ deduplication, for exact k-NN ground truth, or as the build step of a graph index (HNSW, Vamana, CAGRA).
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+
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+ ## What's in it
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+
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+ | Function | What it does | cuVS counterpart |
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+ |---|---|---|
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+ | `brute_force_knn(base, queries, k)` | Exact k-NN: matrix multiply and a fused top-k kernel, tiled over the base | `brute_force::search` |
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+ | `kmeans_fit(x, clusters)`, `kmeans_predict(x, centroids, m)` | k-means++ and Lloyd; the `m` nearest centroids per row | `cluster::kmeans` |
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+ | `nn_descent(rows, k)` | Approximate k-NN graph of the rows, FP16 SIMD-group joins | `nn_descent::build` |
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+ | `all_neighbors(rows, k)` | k-NN graph built in overlapping k-means clusters, one on the GPU at a time; reads a NumPy array or memory-mapped file larger than memory where it is | `all_neighbors::build` |
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+ | `cagra_build(rows, graph_degree)` | Search graph: k-NN graph (`all_neighbors`) pruned by `cagra_optimize` | `cagra::build` |
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+ | `cagra_optimize(knn_graph, graph_degree)` | CAGRA's rank-based pruning (fewest two-hop detours) plus reverse edges | `cagra::optimize` |
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+ | `graph_search(base, graph, queries, k)` | Approximate k-NN of queries by beam search of a graph, one threadgroup per query (CAGRA's single-CTA search) | `cagra::search` |
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+ | `NearestNeighbors(n_neighbors).fit(X).kneighbors(Q)` | scikit-learn's interface over the above, NumPy in and out | |
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+
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+ Metrics: `"l2"` (squared), `"cosine"`, `"inner_product"`. Next: Vamana pruning and export to HNSW and JVector; see
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+ [Roadmap](#roadmap).
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+
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+ ## 1. Install
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+
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+ Needs an Apple-silicon Mac on macOS 14 or later (as MLX) and Python 3.10+.
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+
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+ ```bash
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+ pip install mlxvs
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+ ```
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+
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+ Wheels for Python 3.10 to 3.14 on Apple silicon, built against the `mlx` release they pin (MLX has no stable C++
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+ ABI). The latest code from GitHub builds the extension against your `mlx` wheel; that needs the Xcode Command Line
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+ Tools (`xcode-select --install`) and takes about a minute:
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+
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+ ```bash
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+ pip install git+https://github.com/mikepapadim/mlxvs
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+ ```
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+
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+ ## 2. Use
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+
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+ ```python
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+ import numpy as np
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+ import mlxvs
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+
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+ base = np.random.rand(1_000_000, 128).astype(np.float32)
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+ queries = base[:10_000]
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+
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+ # exact k-NN: ids [nq, k], distances [nq, k], nearest first
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+ ids, dist = mlxvs.brute_force_knn(base, queries, k=10, metric="l2")
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+
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+ # approximate k-NN graph: every row's 32 nearest other rows
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+ graph, graph_dist = mlxvs.nn_descent(base, k=32, metric="cosine")
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+
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+ # the same graph in overlapping k-means clusters, as many as the GPU's memory asks for
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+ graph, graph_dist = mlxvs.all_neighbors(base, k=32, metric="cosine")
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+
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+ # a search index: the k-NN graph pruned by CAGRA's rules, then queries searched over it;
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+ # itopk_size trades speed for recall
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+ index = mlxvs.cagra_build(base, graph_degree=32, metric="cosine")
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+ ids, dist = mlxvs.graph_search(base, index, queries, k=10, metric="cosine", itopk_size=64)
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+
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+ graph = np.asarray(graph) # results are mlx arrays; np.asarray converts without a copy
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+ ```
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+
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+ - Inputs: MLX arrays, NumPy arrays, or anything `np.asarray` accepts, in any real dtype (computed in float32).
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+ - Outputs: `int32` ids, `-1` where fewer neighbors exist; `float32` distances, squared for `"l2"`, similarities
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+ (larger is closer) for `"cosine"` and `"inner_product"`.
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+ - `help(mlxvs.nn_descent)` and the others document every parameter.
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+
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+ Data larger than memory: pass a `numpy.memmap`. The rows stay on disk; `all_neighbors` copies one cluster at a time
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+ to the GPU.
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+
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+ ```python
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+ rows = np.memmap("embeddings.f32", dtype=np.float32, mode="r").reshape(-1, 1024)
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+ graph, graph_dist = mlxvs.all_neighbors(rows, k=32, metric="cosine", verbose=True)
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+ ```
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+
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+ Coming from scikit-learn, change the import:
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+
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+ ```python
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+ nn = mlxvs.NearestNeighbors(n_neighbors=10, metric="euclidean").fit(base)
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+ distances, indices = nn.kneighbors(queries) # NumPy arrays, scikit-learn's units
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+ distances, indices = nn.kneighbors() # the base rows' own neighbors
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+ ```
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+
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+ Examples: [UMAP from a GPU k-NN graph](examples/umap_knn.py) and
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+ [exact ground truth for an ANN benchmark](examples/ground_truth.py) (`.fvecs` in, `.ivecs` out).
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+
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+ C++: the same functions in [`include/mlxvs/mlxvs.h`](include/mlxvs/mlxvs.h), taking `mx::array` and a trailing
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+ `mx::StreamOrDevice s = {}` as MLX ops do. In CMake (MLX found through `CMAKE_PREFIX_PATH`, e.g. Homebrew's):
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+
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+ ```cmake
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+ add_subdirectory(mlxvs) # or FetchContent
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+ target_link_libraries(app PRIVATE mlxvs)
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+ ```
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+
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+ ## 3. Run the benchmarks
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+
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+ ```bash
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+ curl -O ftp://ftp.irisa.fr/local/texmex/corpus/sift.tar.gz && tar xzf sift.tar.gz
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+ pip install faiss-cpu pynndescent # optional CPU baselines
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+ python bench/bench_graph.py sift/sift_base.fvecs --k 32 --clusters 1,8 --baselines faiss,pynndescent
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+ ```
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+
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+ It builds the k-NN graph with each method and scores 2,000 random rows against the exact neighbors.
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+
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+ Search: build a graph, then recall@10 against queries per second over a sweep of `itopk_size`, optionally against
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+ hnswlib on the CPU.
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+
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+ ```bash
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+ pip install hnswlib # optional CPU baseline
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+ python bench/bench_search.py sift/sift_base.fvecs sift/sift_query.fvecs --degree 32 --intermediate 64 \
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+ --baselines hnswlib
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+ ```
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+
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+ ### Benchmarks
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+
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+ SIFT1M (985,462 x 128, L2, 10,000 queries in one batch, recall@10), MacBook Pro M3 Pro (18-core GPU, 12-core CPU),
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+ on power. mlxVS 0.1.0; hnswlib 0.8 with `M=16`, `ef_construction=200` on all 12 cores.
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+
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+ | Index | Build | Search setting | Recall@10 | Queries/s |
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+ |---|---:|---|---:|---:|
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+ | mlxVS `cagra_build`, degree 32 (from 64) | 10.4 s | `itopk_size` 32 | 0.932 | 119,800 |
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+ | | | `itopk_size` 64 | 0.976 | 69,500 |
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+ | | | `itopk_size` 128 | 0.993 | 37,800 |
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+ | | | `itopk_size` 256 | 0.998 | 27,000 |
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+ | mlxVS `cagra_build`, degree 64 (from 128) | 19.6 s | `itopk_size` 32 | 0.977 | 79,500 |
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+ | | | `itopk_size` 64 | 0.994 | 43,600 |
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+ | mlxVS `nn_descent` k-NN graph, degree 32 (unpruned) | 8.8 s | `itopk_size` 128 | 0.939 | 42,400 |
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+ | hnswlib (CPU) | 88.1 s | `ef` 32 | 0.904 | 53,300 |
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+ | | | `ef` 64 | 0.964 | 32,200 |
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+ | | | `ef` 128 | 0.990 | 17,600 |
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+ | | | `ef` 256 | 0.998 | 10,200 |
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+
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+ ## Coming from cuVS
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+
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+ | mlxvs | cuVS | Note |
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+ |---|---|---|
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+ | `nn_descent(rows, k, ...)` | `nn_descent::index_params::graph_degree` | cuVS default 64 |
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+ | lists of `max(64, k)` entries | `intermediate_graph_degree` | cuVS default 128 |
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+ | `max_iterations` = 24 | `max_iterations` = 20 | mlxvs samples 16 new neighbors per round and stops early when the lists settle |
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+ | `termination_threshold` = 1e-4 | `termination_threshold` = 1e-3 | tuned for graph quality in JVector; pass 1e-3 for cuVS's behaviour |
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+ | `all_neighbors(..., n_clusters, overlap_factor)` | `all_neighbors::index_params::{n_clusters, overlap_factor}` | overlap 2 as cuVS; `n_clusters` defaults to 0 (chosen from the GPU's memory), cuVS's to 1 |
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+ | `algo="brute_force"` / `"nn_descent"` | `all_neighbors::index_params::graph_build_params` | cuVS also offers IVF-PQ |
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+ | `"cosine"` returns the cosine similarity | `CosineExpanded` returns 1 - cosine | similarities are "larger is closer"; `"l2"` is squared, as `L2Expanded` |
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+ | `cagra_build(rows, graph_degree=32, intermediate_graph_degree=64)` | `cagra::index_params::{graph_degree, intermediate_graph_degree}` | cuVS defaults 64 and 128; NN-Descent here caps the intermediate degree at 128 |
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+ | `cagra_optimize(knn_graph, graph_degree)` | `cagra::optimize` | rank-based pruning and reverse edges, as cuVS; the reverse half fills from the lowest-rank edges |
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+ | `graph_search(base, graph, queries, k, ...)` | `cagra::search` | takes the dataset and graph directly, no index object yet |
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+ | `itopk_size` = 64, `search_width` = 1 | `search_params::{itopk_size, search_width}` | same defaults; `itopk_size` at most 256 |
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+ | `max_iterations` = 0 (automatic) | `search_params::max_iterations` | stops earlier once every list entry is expanded |
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+ | `num_random_samplings` = 1 | `search_params::num_random_samplings` | random start nodes; no seed nodes yet |
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+ | `int32` ids | `int64_t` ids | n < 2^31 rows |
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+
201
+ ## Roadmap
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+
203
+ 1. Vamana alpha pruning; export to HNSW (hnswlib) and JVector layouts (`cagra::serialize_to_hnswlib`).
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+ 2. An index object holding the dataset and graph; float16 and int8 datasets for search.
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+ 3. A C API for other languages (Java via Panama, as cuVS-java does).
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+
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+ How the kernels work: [docs/DESIGN.md](docs/DESIGN.md). Building, testing and code style:
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+ [CONTRIBUTING.md](CONTRIBUTING.md).
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+
210
+ ## License
211
+
212
+ Apache-2.0. The NN-Descent kernels are a port of JVector's `jvector-gpu` module (Apache-2.0, DataStax, Inc.); see
213
+ [NOTICE](NOTICE).