相关论文: Burrows-Wheeler transform for terabases
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…
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…
The Lempel-Ziv factorization (LZ77) and the Run-Length encoded Burrows-Wheeler Transform (RLBWT) are two important tools in text compression and indexing, being their sizes $z$ and $r$ closely related to the amount of text…
Recent developments in transfer learning have boosted the advancements in natural language processing tasks. The performance is, however, dependent on high-quality, manually annotated training data. Especially in the biomedical domain, it…
The FM-index is a well-known compressed full-text index, based on the Burrows-Wheeler transform (BWT). During a pattern search, the BWT sequence is accessed at "random" locations, which is cache-unfriendly. In this paper, we are interested…
Enumerating characteristic substrings (e.g., maximal repeats, minimal unique substrings, and minimal absent words) in a given string has been an important research topic because there are a wide variety of applications in various areas such…
Detecting all the strings that occur in a text more frequently or less frequently than expected according to an IID or a Markov model is a basic problem in string mining, yet current algorithms are based on data structures that are either…
A bit catastrophe, loosely defined, is when a change in just one character of a string causes a significant change in the size of the compressed string. We study this phenomenon for the Burrows-Wheeler Transform (BWT), a string transform at…
Summary: Longer sequencing reads, with at least 200 bases per template are now common. While traditional aligners have adopted new strategies to improve the mapping of longer reads, aligners specific to bisulfite-sequencing were optimized…
Recent years have seen a surge in data-driven surrogates for dynamical systems that can be orders of magnitude faster than numerical solvers. However, many machine learning-based models such as neural operators exhibit spectral bias,…
Transformer-based models, exemplified by GPT-3, ChatGPT, and GPT-4, have recently garnered considerable attention in both academia and industry due to their promising performance in general language tasks. Nevertheless, these models…
DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while…
In this paper we study the number $r_{bwt}$ of equal-letter runs produced by the Burrows-Wheeler transform ($BWT$) when it is applied to purely morphic finite words, which are words generated by iterating prolongable morphisms. Such a…
The move structure represents permutations with long contiguously permuted intervals in compressed space with optimal query time. They have become an important feature of compressed text indexes using space proportional to the number of…
Variation graphs, which represent genetic variation within a population, are replacing sequences as reference genomes. Path indexes are one of the most important tools for working with variation graphs. They generalize text indexes to…
The Positional Burrows-Wheeler Transform (PBWT) is a fundamental data structure for the efficient representation and analysis of large-scale haplotype panels. For a panel of $h$ sequences $\{S_1, \dots, S_h\}$ over $m$ sites, a key…
The field of succinct data structures has flourished over the last 16 years. Starting from the compressed suffix array (CSA) by Grossi and Vitter (STOC 2000) and the FM-index by Ferragina and Manzini (FOCS 2000), a number of generalizations…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
Data subset selection aims to find a smaller yet informative subset of a large dataset that can approximate the full-dataset training, addressing challenges associated with training neural networks on large-scale datasets. However, existing…
Transformers have emerged as the cornerstone of state-of-the-art natural language processing models, showcasing exceptional performance across a wide range of AI applications. However, the memory demands posed by the self-attention…