arXiv subjects

Enno Adler

Publications and source records attributed to Enno Adler.

4 recordsLinked to original sources

arXiv2025

Compressing Hypergraphs using Suffix Sorting

Hypergraphs model complex, non-binary relationships like co-authorships, social group memberships, and recommendations. Like traditional graphs, hypergraphs can grow large, posing challenges for storage, transmission, and query performance. We propose HyperCSA, a novel compression method for hypergraphs that maintains support for standard queries over the succinct representation. HyperCSA achieves compression ratios of 26% to 79% of the original file size on real-world hypergraphs - outperforming existing methods on all large hypergraphs in our experiments. Additionally, HyperCSA scales to larger datasets than existing approaches. Furthermore, for common real-world hypergraphs, HyperCSA evaluates neighbor queries 6 to 40 times faster than both standard data structures and other hypergraph compression approaches.

cs.DS↗

arXiv2025

IBB: Fast Burrows-Wheeler Transform Construction for Length-Diverse DNA Data

The Burrows-Wheeler transform (BWT) is integral to the FM-index, which is used extensively in text compression, indexing, pattern search, and bioinformatic problems as de novo assembly and read alignment. Thus, efficient construction of the BWT in terms of time and memory usage is key to these applications. We present a novel external algorithm called Improved-Bucket Burrows-Wheeler transform (IBB) for constructing the BWT of DNA datasets with highly diverse sequence lengths. IBB uses a right-aligned approach to efficiently handle sequences of varying lengths, a tree-based data structure to manage relative insert positions and ranks, and fine buckets to reduce the necessary amount of input and output to external memory. Our experiments demonstrate that IBB is 10% to 40% faster than the best existing state-of-the-art BWT construction algorithms on most datasets while maintaining competitive memory consumption.

cs.DS↗

arXiv2024

String Partition for Building Long Burrows-Wheeler Transforms

Constructing the Burrows-Wheeler transform (BWT) for long strings poses significant challenges regarding construction time and memory usage. We use a prefix of the suffix array to partition a long string into shorter substrings, thereby enabling the use of multi-string BWT construction algorithms to process these partitions fast. We provide an implementation, partDNA, for DNA sequences. Through comparison with state-of-the-art BWT construction algorithms, we show that partDNA with IBB offers a novel trade-off for construction time and memory usage for BWT construction on real genome datasets. Beyond this, the proposed partitioning strategy is applicable to strings of any alphabet.

cs.DS↗

arXiv2023

ITR: Grammar-based Graph Compression Supporting Fast Triple Queries

Neighborhood queries and triple queries are the most common queries on graphs; thus, it is desirable to answer them efficiently on compressed data structures. We present a compression scheme called Incidence-Type-RePair (ITR) for graphs with labeled nodes and labeled edges based on RePair and apply the scheme to network, version, and RDF graphs. We show that ITR performs neighborhood queries and triple queries within only a few milliseconds and thereby outperforms existing RePair-based solutions on graphs while providing a compression size comparable to existing graph compressors.

cs.DB↗