Related papers: Composite repetition-aware data structures
Motivated by studies of data retrieval in polymer-based storage systems, we consider the problem of reconstructing a multiset of binary strings that have the same length and the same weight from the compositions of their prefixes and…
The Positional Burrows--Wheeler Transform (PBWT) is a data structure designed for efficiently representing and querying large collections of sequences, such as haplotype panels in genomics. Forward and backward stepping operations --…
The Burrows-Wheeler Transform (BWT) serves as the basis for many important sequence indexes. On very large datasets (e.g. genomic databases), classical BWT construction algorithms are often infeasible because they usually need to have the…
Detecting and measuring repetitiveness of strings is a problem that has been extensively studied in data compression and text indexing. However, when the data are structured in a non-linear way, like in the context of two-dimensional…
Methods that generate networks sharing a given degree distribution and global clustering can induce changes in structural properties other than that controlled for. Diversity in structural properties, in turn, can affect the outcomes of…
Data augmentation is widely used for training a neural network given little labeled data. A common practice of augmentation training is applying a composition of multiple transformations sequentially to the data. Existing augmentation…
The research on indexing repetitive string collections has focused on the same search problems used for regular string collections, though they can make little sense in this scenario. For example, the basic pattern matching query "list all…
In this paper we examine a number of methods for probing and understanding the large-scale structure of networks that evolve over time. We focus in particular on citation networks, networks of references between documents such as papers,…
Reproducibility must validate architectural robustness, not just numerical accuracy. We evaluate ColBERT-v2 and ConstBERT across five dimensions, finding that while ConstBERT reproduces within 0.05% MRR@10 on MS-MARCO, both models show a…
Patterns are fundamental to human cognition, enabling the recognition of structure and regularity across diverse domains. In this work, we focus on structural repeats, patterns that arise from the repetition of hierarchical relations within…
The last decades have not only been characterized by an explosive growth of data, but also an increasing appreciation of data as a valuable resource. Their value comes with the ability to extract meaningful patterns that are of economic,…
We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…
The advent of modern data collection and processing techniques has seen the size, scale, and complexity of data grow exponentially. A seminal step in leveraging these rich datasets for downstream inference is understanding the…
The wavelet tree (Grossi et al. [SODA, 2003]) and wavelet matrix (Claude et al. [Inf. Syst., 2015]) are compact data structures with many applications such as text indexing or computational geometry. By continuing the recent research of…
While short read aligners, which predominantly use the FM-index, are able to easily index one or a few human genomes, they do not scale well to indexing databases containing thousands of genomes. To understand why, it helps to examine the…
This paper presents a general technique for optimally transforming any dynamic data structure that operates on atomic and indivisible keys by constant-time comparisons, into a data structure that handles unbounded-length keys whose…
The Binary Search Tree (BST) is average in computer science which supports a compact data structure in memory and oneself even conducts a row of quick algorithms, by which people often apply it in dynamical circumstance. Besides these…
In the last decades, the necessity to process massive amounts of textual data fueled the development of compressed text indexes: data structures efficiently answering queries on a given text while occupying space proportional to the…
A string $w$ is said to be a minimal absent word (MAW) for a string $S$ if $w$ does not occur in $S$ and any proper substring of $w$ occurs in $S$. We focus on non-trivial MAWs which are of length at least 2. Finding such non-trivial MAWs…
Recent large language models have been trained on vast datasets, but also often on repeated data, either intentionally for the purpose of upweighting higher quality data, or unintentionally because data deduplication is not perfect and the…