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DuckDB-VSS

Vector Similarity Search for DuckDB

This is an experimental extension for DuckDB that adds indexing support to accelerate Vector Similarity Search using DuckDB's new fixed-size ARRAY type added in version v0.10.0. This extension is based on the usearch library and serves as a proof of concept for providing a custom index type, in this case a HNSW index, from within an extension and exposing it to DuckDB.

Usage

To create a new HNSW index on a table with an ARRAY column, use the CREATE INDEX statement with the USING HNSW clause. For example:

CREATE TABLE my_vector_table (vec FLOAT[3]);
INSERT INTO my_vector_table SELECT array_value(a,b,c) FROM range(1,10) ra(a), range(1,10) rb(b), range(1,10) rc(c);
CREATE INDEX my_hnsw_index ON my_vector_table USING HNSW (vec);

The index will then be used to accelerate queries that use a ORDER BY clause evaluating one of the supported distance metric functions against the indexed columns and a constant vector, followed by a LIMIT clause. For example:

SELECT * FROM my_vector_table ORDER BY array_distance(vec, [1,2,3]::FLOAT[3]) LIMIT 3;

# We can verify that the index is being used by checking the EXPLAIN output 
# and looking for the HNSW_INDEX_SCAN node in the plan

EXPLAIN SELECT * FROM my_vector_table ORDER BY array_distance(vec, [1,2,3]::FLOAT[3]) LIMIT 3;

┌───────────────────────────┐
│         PROJECTION        │
│   ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─   │
│             #0            │
└─────────────┬─────────────┘                             
┌─────────────┴─────────────┐
│         PROJECTION        │
│   ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─   │
│            vec            │
│array_distance(vec, [1.0, 2│
│         .0, 3.0])         │
└─────────────┬─────────────┘                             
┌─────────────┴─────────────┐
│      HNSW_INDEX_SCAN      │
│   ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─   │
│   t1 (HNSW INDEX SCAN :   │
│           my_idx)         │
│   ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─   │
│            vec            │
│   ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─   │
│           EC: 3           │
└───────────────────────────┘

By default the HNSW index will be created using the euclidean distance l2sq (L2-norm squared) metric, matching DuckDBs array_distance function, but other distance metrics can be used by specifying the metric option during index creation. For example:

CREATE INDEX my_hnsw_cosine_index ON my_vector_table USING HNSW (vec) WITH (metric = 'cosine');

The following table shows the supported distance metrics and their corresponding DuckDB functions

Description Metric Function
Euclidean distance l2sq array_distance
Cosine similarity cosine array_cosine_distance
Inner product ip array_negative_inner_product

Inserts, Updates, Deletes and Re-Compaction

The HNSW index does support inserting, updating and deleting rows from the table after index creation. However, there are two things to keep in mind:

  • Its faster to create the index after the table has been populated with data as the initial bulk load can make better use of parallelism on large tables.
  • Deletes are not immediately reflected in the index, but are instead "marked" as deleted, which can cause the index to grow stale over time and negatively impact query quality and performance.

To address this, you can call the PRAGMA hnsw_compact_index('<index name>') pragma function to trigger a re-compaction of the index pruning deleted items, or re-create the index after a significant number of updates.

Limitations

  • Only vectors consisting of FLOATs are supported at the moment.
  • The index itself is not buffer managed and must be able to fit into RAM memory.

With that said, the index will be persisted into the database if you run DuckDB with a disk-backed database file. But there is no incremental updates, so every time DuckDB performs a checkpoint the entire index will be serialized to disk and overwrite its previous blocks. Similarly, the index will be deserialized back into main memory in its entirety after a restart of the database, although this will be deferred until you first access the table associated with the index. Depending on how large the index is, the deserialization process may take some time, but it should be faster than simply dropping and re-creating the index.

Building the extension

Build steps

To build the extension, run:

make

The main binaries that will be built are:

./build/release/duckdb
./build/release/test/unittest
./build/release/extension/vss/vss.duckdb_extension
  • duckdb is the binary for the duckdb shell with the extension code automatically loaded.
  • unittest is the test runner of duckdb. Again, the extension is already linked into the binary.
  • vss.duckdb_extension is the loadable binary as it would be distributed.

Running the extension

To run the extension code, simply start the shell with ./build/release/duckdb.

Running the tests

Thes SQL tests can be run using:

make test