Efficient terabyte-scale text compression via stable local consistency and parallel grammar processing
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| Format: | Preprint |
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2024
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| _version_ | 1866917935474278400 |
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| author | Diaz-Dominguez, Diego |
| author_facet | Diaz-Dominguez, Diego |
| contents | We present a highly parallelizable text compression algorithm that scales efficiently to terabyte-sized datasets. Our method builds on locally consistent grammars, a lightweight form of compression, combined with simple recompression techniques to achieve further space reductions. Locally consistent grammar algorithms are particularly suitable for scaling, as they need minimal satellite information to compact the text. We introduce a novel concept to enable parallelisation, stable local consistency. A grammar algorithm ALG is stable, if for any pattern $P$ occurring in a collection $\mathcal{T}=\{T_1, T_2, \ldots, T_k\}$, the instances $ALG(T_1), ALG(T_2), \ldots, ALG(T_k)$ independently produce cores for $P$ with the same topology. In a locally consistent grammar, the core of $P$ is a subset of nodes and edges in $\mathcal{T}$'s parse tree that remains the same in all the occurrences of $P$. This feature is important to achieve compression, but it only holds if ALG synchronises the parsing of the strings, for instance, by defining a common set of nonterminal symbols for them. Stability removes the need for synchronisation during the parsing phase. Consequently, we can run $ALG(T_1), ALG(T_2), \ldots, ALG(T_k)$ fully in parallel and then merge the resulting grammars into a single compressed output equivalent to $ALG(\mathcal{T})$. We implemented our ideas and tested them on massive datasets. Our results showed that our method could process a diverse collection of bacterial genomes (7.9 TB) in around nine hours, requiring 16 threads and 0.43 bits/symbol of working memory, producing a compressed representation 85 times smaller than the original input. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2411_12439 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Efficient terabyte-scale text compression via stable local consistency and parallel grammar processing Diaz-Dominguez, Diego Data Structures and Algorithms We present a highly parallelizable text compression algorithm that scales efficiently to terabyte-sized datasets. Our method builds on locally consistent grammars, a lightweight form of compression, combined with simple recompression techniques to achieve further space reductions. Locally consistent grammar algorithms are particularly suitable for scaling, as they need minimal satellite information to compact the text. We introduce a novel concept to enable parallelisation, stable local consistency. A grammar algorithm ALG is stable, if for any pattern $P$ occurring in a collection $\mathcal{T}=\{T_1, T_2, \ldots, T_k\}$, the instances $ALG(T_1), ALG(T_2), \ldots, ALG(T_k)$ independently produce cores for $P$ with the same topology. In a locally consistent grammar, the core of $P$ is a subset of nodes and edges in $\mathcal{T}$'s parse tree that remains the same in all the occurrences of $P$. This feature is important to achieve compression, but it only holds if ALG synchronises the parsing of the strings, for instance, by defining a common set of nonterminal symbols for them. Stability removes the need for synchronisation during the parsing phase. Consequently, we can run $ALG(T_1), ALG(T_2), \ldots, ALG(T_k)$ fully in parallel and then merge the resulting grammars into a single compressed output equivalent to $ALG(\mathcal{T})$. We implemented our ideas and tested them on massive datasets. Our results showed that our method could process a diverse collection of bacterial genomes (7.9 TB) in around nine hours, requiring 16 threads and 0.43 bits/symbol of working memory, producing a compressed representation 85 times smaller than the original input. |
| title | Efficient terabyte-scale text compression via stable local consistency and parallel grammar processing |
| topic | Data Structures and Algorithms |
| url | https://arxiv.org/abs/2411.12439 |