adaptive-nthash

https://github.com/siddharthastoic/adaptive-nthash

Science Score: 44.0%

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Low similarity (7.5%) to scientific vocabulary

Last synced: 10 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: SiddharthaStoic
License: mit
Language: C++
Default Branch: main
Size: 13.4 MB

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Watchers: 1
Forks: 0
Open Issues: 0
Releases: 0

Created about 1 year ago · Last pushed about 1 year ago

Metadata Files

Readme License Citation

Adaptive ntHash

This project extends the ntHash library with an adaptive spaced seed hashing mechanism based on local sequence entropy. The implementation dynamically switches between sparse and dense spaced seed patterns during hashing to optimize performance, especially in regions of varying sequence complexity.

Key Features

Adaptive Hashing: Uses entropy thresholds to switch between sparse and dense seed configurations at runtime.
Optimized Rolling Entropy: Efficient entropy computation using a rolling window and fixed-point log₂ lookup.
Faster Than Standard ntHash: Consistently outperforms the standard ntHash across multiple benchmark runs.
Drop-in Integration: Fully compatible with existing ntHash codebase and Meson build system.

Benchmark Results

The plot below shows runtime (in seconds) for 1000 iterations of hashing a 1 million base pair sequence using standard ntHash vs the adaptive version.

Benchmark Comparison

Build Instructions

This project uses the Meson build system.

git clone https://github.com/SiddharthaStoic/adaptive-nthash.git cd adaptive-nthash meson setup build --wipe meson compile -C build meson test -C build

Run Benchmarks

```

Adaptive hash benchmark

./build/adaptive_benchmark.exe

Standard ntHash benchmark

./build/normal_benchmark.exe ```

Contributing

This repository was developed as a high-performance extension to the ntHash project. Contributions are welcome to further optimize, test, or extend the adaptive entropy model.

License

This project is licensed under the MIT License

Owner

Name: Siddhartha
Login: SiddharthaStoic
Kind: user

Twitter: 8BitStoic
Repositories: 1
Profile: https://github.com/SiddharthaStoic

Student Developer at Jyothy Institute of Technology

Citation (CITATION.bib)

@article{10.1093/bioinformatics/btac564,
    author = {Kazemi, Parham and Wong, Johnathan and Nikolić, Vladimir and Mohamadi, Hamid and Warren, René L and Birol, Inanç},
    title = "{ntHash2: recursive spaced seed hashing for nucleotide sequences}",
    journal = {Bioinformatics},
    volume = {38},
    number = {20},
    pages = {4812-4813},
    year = {2022},
    month = {08},
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btac564},
    url = {https://doi.org/10.1093/bioinformatics/btac564},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/38/20/4812/46535020/btac564.pdf},
}

@article{doi:10.1093/bioinformatics/btw397,
author = {Mohamadi, Hamid and Chu, Justin and Vandervalk, Benjamin P. and Birol, Inanc},
title = {ntHash: recursive nucleotide hashing},
journal = {Bioinformatics},
volume = {32},
number = {22},
pages = {3492},
year = {2016},
doi = {10.1093/bioinformatics/btw397},
URL = { + http://dx.doi.org/10.1093/bioinformatics/btw397},
eprint = {/oup/backfile/Content_public/Journal/bioinformatics/32/22/10.1093_bioinformatics_btw397/3/btw397.pdf}
}

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