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#402 in Data structures

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QWT: Rust Quad Wavelet Tree

The wavelet tree [1] is a compact data structure that for a sequence $S$ of length $n$ over an alphabet of size $\sigma$ requires only $n\lceil\log \sigma \rceil (1+o(1))$ bits of space and can answer rank and select queries in $\Theta(\log \sigma)$ time.

A rank query counts the number of occurrences of a symbol up to a given position in the sequence. A select query finds the position in the sequence of a symbol with a given rank. These queries have applications in, e.g., compression, computational geometry, and pattern matching in the form of the backward search---the backbone of many compressed full-text indices.

This repository provides a very fast implementation of wavelet trees in Rust. A companion C++ implementation is available here. More precisely, we implement here a variant called wavelet matrix [2], which gives a more elegant implementation.

The Quad Wavelet Tree (QWT) improves query performance by using a 4-ary tree instead of a binary tree as the basis of the wavelet tree. The 4-ary tree layout of a wavelet tree helps to halve the number of cache misses during queries and thus reduces the query latency.

An experimental evaluation shows that the quad wavelet tree improves the latency of access, rank and select queries by a factor of $\approx$ 2 compared to other implementations of wavelet trees (e.g., the implementation in the widely used C++ Succinct Data Structure Library (SDSL)). For more details, see Benchmarks and the paper [3].

Even faster rank query

As previously highlighted, the Quad Wavelet Tree (QWT) enhances query performance by replacing the conventional binary tree structure in the wavelet tree with a 4-ary tree.

When working with moderately large sequences, the primary factor affecting query performance is the cost of the cache misses, which occur at each level of the wavelet tree. However, by utilizing a 4-ary tree structure, we effectively reduce the tree's height by half. Consequently, this reduction in height leads to a proportional decrease in the number of cache misses, resulting in the ~2x improvement in query time.

The rank queries can be further improved by means of a small prediction model designed to anticipate and pre-fetch the cache lines required for rank queries. This could give a further improvement up to a factor 1.6 for rank query.

Benchmarks

We report here a few experiments to compare our implementation with other state-of-the-art implementations. The experiments use a single thread on a server machine with 8 Intel i9-9900KF cores with base frequencies of 3.60 GHz running Ubuntu 23.04 LTS kernel version 6.2.0-36. The code is compiled with Rust 1.73.0. Each core has a dedicated L1 cache of size 32 KiB, a dedicated L2 cache of size 256 KiB, a shared L3 cache of size 16 MiB, and 64 GiB of RAM. A more detailed experimental evaluation (on different machines) can be found in [3].

The dataset, named Big English, is the concatenation of all 35,750 English text files from the Gutenberg Project that are encoded in ASCII. Headers related to the project were removed, leaving only the actual text. The prefix of size 4 GiB was used. The text has an alphabet with 168 distinct symbols. Below we report details to download the dataset.

Implementation access (ns) rank (ns) select (ns) space (MiB) Language
SDSL 2.1.1 1178 1223 2900 6089 C++
Pasta 1598 1729 5197 4112 C++
Sucds 0.8.1 967 1015 2727 5376 Rust
SimpleS 933 1005 2558 6383 Rust
Qwt256 516 542 1226 4616 C++/Rust
Qwt256Pfs 515 363 1226 4626 Rust
Qwt512 525 569 1196 4360 C++/Rust
Qwt512Pfs 526 398 1197 4369 Rust

We note that the results for the rank query depend on how we generate the symbols to rank in the query set. Here for every rank query, we choose a symbol at random by following the distribution of symbols in the text, i.e., more frequent symbols are selected more frequently. All the data structures have more or less the same performance in ranking rare symbols. The reason is that the portion of the last layers for those rare symbols is likely to fit in the cache.

There are four instances of our proposed wavelet trees, Qwt256 and Qwt512, which are quad wavelet trees with block sizes of 256 and 512 symbols, respectively. The suffix pfs in Qwt256pfs and Qwt512pfs indicates that they utilize additional space to store a predicting model, which is able to further accelerate 'rank' queries. Please refer to our full paper [3] for more details.

To run the experiments, we need to compile the binary executables with

RUSTFLAGS="-C target-cpu=native" cargo build --release

This produces the two executables perf_rs_quat_vector and perf_wavelet_tree in \target\release\.

The former is used to measure the performance of QuadVectors, which are the building block of our implementation of Wavelet Trees. You can safely ignore it.

The latter is used to measure the performance of a Quad Wavelet Tree built on a given input text.

We can now download and uncompress in the current directory the Big English. Then, we take its prefix of length 4 GiB.

wget http://pages.di.unipi.it/rossano/big_english.gz
gunzip big_english.gz
head -c 4294967296 english > big_english.4GiB

The following command builds the wavelet trees (QWT 256 and 512 with or without prefetching support) on this input text and runs 10 million random access, rank, and select queries.

./target/release/perf_wavelet_tree --input-file big_english.4GiB --access --rank --select

We can use the flag --test-correctness to perform some extra tests for the correctness of the index. We can also specify the number of queries with n_queries (default is 10,000,000 queries).

The code measures the latency of the queries by forcing the input of each query to depend on the output of the previous one. This is consistent with the use of the queries in a real setting. For example, the more advanced queries supported by compressed text indexes (e.g., CSA or FM-index) decompose into several dependent queries on the underlying wavelet tree.

To repeat the comparison against other Rust libraries, please check out the branch benchmark. Then, run the benchmark perf_wt_bench using the following command:

/target/release/perf_wt_bench --input-file big_english.4GiB --rank --select --access

Examples

Run the following Cargo command in your project directory

cargo add qwt

to add the library.

Once the crate has been added, we can easily build a Quad Wavelet Tree with the following code.

use qwt::QWT256;

let data = vec![1u8, 0, 1, 0, 2, 4, 5, 3];

let qwt = QWT256::from(data);

assert_eq!(qwt.len(), 8);

We can print the space usage of the wavelet tree with

use qwt::QWT256;
use qwt::SpaceUsage;

let data = vec![1u8, 0, 1, 0, 2, 4, 5, 3];

let qwt = QWT256::from(data);

println!("{}", qwt.space_usage_byte() );

A wavelet tree implements FromIterator and, thus, we can use .collect().

use qwt::QWT256;

let qwt: QWT256<_> = (0..10_u8).into_iter().cycle().take(1000).collect();

assert_eq!(qwt.len(), 1000);

The data structure supports three operations:

  • get(i) accesses the i-th symbols of the indexed sequence;
  • rank(c, i) counts the number of occurrences of symbol c up to position i excluded;
  • select(c, i) returns the position of the i-th occurrence of symbol c.

Here is an example of the three operations.

use qwt::{QWT256, AccessUnsigned, RankUnsigned, SelectUnsigned};

let data = vec![1u8, 0, 1, 0, 2, 4, 5, 3];

let qwt = QWT256::from(data);

assert_eq!(qwt.get(2), Some(1));
assert_eq!(qwt.get(3), Some(0));
assert_eq!(qwt.get(8), None);

assert_eq!(qwt.rank(1, 2), Some(1));
assert_eq!(qwt.rank(1, 0), Some(0));
assert_eq!(qwt.rank(3, 8), Some(1));
assert_eq!(qwt.rank(1, 9), None);

assert_eq!(qwt.select(1, 1), Some(0));
assert_eq!(qwt.select(0, 2), Some(3));
assert_eq!(qwt.select(4, 0), None);
assert_eq!(qwt.select(1, 3), None);

In the following example, we use QWT to index a sequence over a larger alphabet.

use qwt::{QWT256, AccessUnsigned, RankUnsigned, SelectUnsigned};

let data = vec![1u32, 0, 1, 0, 2, 1000000, 5, 3];
let qwt = QWT256::from(data);

assert_eq!(qwt.get(2), Some(1));
assert_eq!(qwt.get(5), Some(1000000));
assert_eq!(qwt.get(8), None);

For more details, take a look at the documentation.

Serialization and deserialization can be done with bincode as follows.

use std::fs;
use std::path::Path;

use qwt::{QWT256, AccessUnsigned};

let data = vec![1u8, 0, 1, 0, 2, 4, 5, 3];
let qwt = QWT256::from(data);

assert_eq!(qwt.get(2), Some(1));

// serialize
let serialized = bincode::serialize(&qwt).unwrap();

// write on file, if needed
let output_filename = "example.qwt256".to_string();
fs::write(Path::new(&output_filename), serialized).unwrap();

// read from file 
let serialized = fs::read(Path::new(&output_filename)).unwrap();

// deserialize
let qwt = bincode::deserialize::<QWT256<u8>>(&serialized).unwrap();

assert_eq!(qwt.get(2), Some(1));

We can index any sequence over any num::traits::Unsigned integers. As the space usage depends on the largest value in the sequence, it could be worth remapping the values to remove "holes".

Bibliography

  1. Roberto Grossi, Ankur Gupta, and Jeffrey Scott Vitter. High-order entropy-compressed text indexes. In SODA, pages 841–850. ACM/SIAM, 2003.
  2. Francisco Claude, Gonzalo Navarro, and Alberto Ordóñez Pereira. The wavelet matrix: An efficient wavelet tree for large alphabets. Information Systems, 47:15–32, 2015.
  3. Matteo Ceregini, Florian Kurpicz, Rossano Venturini. Faster Wavelet Trees with Quad Vectors. Arxiv, 2023.

Please cite the following paper if you use this code.

@misc{QWT,
  author = {Matteo Ceregini, Florian Kurpicz, Rossano Venturini},
  title = {Faster Wavelet Trees with Quad Vectors},
  publisher = {arXiv},
  year = {2023},
  doi = {10.48550/ARXIV.2302.09239},
  url = {http://arxiv.org/abs/2302.09239}
}

Dependencies

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~68K SLoC