相关论文: Tunneling on Wheeler Graphs

One of the most well-known variants of the Burrows-Wheeler transform (BWT) [Burrows and Wheeler, 1994] is the bijective BWT (BBWT) [Gil and Scott, arXiv 2012], which applies the extended BWT (EBWT) [Mantaci et al., TCS 2007] to the multiset…

A general class of unidirectional transforms is presented that can be computed in a distributed manner along an arbitrary routing tree. Additionally, we provide a set of conditions under which these transforms are invertible. These…

It is known that the exact form of the Burrows-Wheeler-Transform (BWT) of a string collection depends, in most implementations, on the input order of the strings in the collection. Reordering strings of an input collection affects the…

Cartesian tree matching is a form of generalized pattern matching where a substring of the text matches with the pattern if they share the same Cartesian tree. This form of matching finds application for time series of stock prices and can…

In this paper we describe algorithms for computing the BWT and for building (compressed) indexes in external memory. The innovative feature of our algorithms is that they are lightweight in the sense that, for an input of size $n$, they use…

We propose a new technique for creating a space-efficient index for large repetitive text collections, such as pangenomic databases containing sequences of many individuals from the same species. We combine two recent techniques from this…

Given a string $T$ on an alphabet of size $\sigma$, we describe a bidirectional Burrows-Wheeler index that takes $O(|T|\log{\sigma})$ bits of space, and that supports the addition \emph{and removal} of one character, on the left or right…

Motivation: Burrows-Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant sequences such as pangenome data. However, BWT construction…

We propose algorithms that, given the input string of length $n$ over integer alphabet of size $\sigma$, construct the Burrows-Wheeler transform (BWT), the permuted longest-common-prefix (PLCP) array, and the LZ77 parsing in…

Motivated by challenges in pangenomic read alignment, we propose a generalization of Wheeler graphs that we call Wheeler maps. A Wheeler map stores a text $T[1..n]$ and an assignment of tags to the characters of $T$ such that we can…

Compressed suffix arrays (CSAs) index large repetitive collections and are key in many text applications. The r-index and its derivatives combine the run-length Burrows-Wheeler Transform (BWT) with suffix array sampling to achieve space…

The compression of highly repetitive strings (i.e., strings with many repetitions) has been a central research topic in string processing, and quite a few compression methods for these strings have been proposed thus far. Among them, an…

Parameterized strings are a generalization of strings in that their characters are drawn from two different alphabets, where one is considered to be the alphabet of static characters and the other to be the alphabet of parameter characters.…

In this paper, we consider the problem of compressing a trie while supporting the powerful \emph{locate} queries: to return the pre-order identifiers of all nodes reached by a path labeled with a given query pattern. Our result builds on…

When building Burrows-Wheeler Transforms (BWTs) of truly huge datasets, prefix-free parsing (PFP) can use an unreasonable amount of memory. In this paper we show how if a dataset can be broken down into small datasets that are not very…

We survey the different methods used for extending the BWT to collections of strings, following largely [Cenzato and Lipt\'ak, CPM 2022, Bioinformatics 2024]. We analyze the specific aspects and combinatorial properties of the resulting BWT…

Bearing data compression is vital to manage the large volumes of data generated during condition monitoring. In this paper, a novel asymmetrical autoencoder with a lifting wavelet transform (LWT) layer is developed to compress bearing…

The run-length compressed Burrows-Wheeler transform (RLBWT) used in conjunction with the backward search introduced in the FM index is the centerpiece of most compressed indexes working on highly-repetitive data sets like biological…

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 --…

Modern transportation network modeling increasingly involves the integration of diverse methodologies including sensor-based forecasting, reinforcement learning, classical flow optimization, and demand modeling that have traditionally been…