相关论文: Teaching the Burrows-Wheeler Transform via the Pos…

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…

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…

A weight based dynamic compression method has recently been proposed, which is especially suitable for the encoding of files with locally skewed distributions. Its main idea is to assign larger weights to closer to be encoded symbols by…

The k-spectrum of a string is the set of all distinct substrings of length k occurring in the string. K-spectra have many applications in bioinformatics including pseudoalignment and genome assembly. The Spectral Burrows-Wheeler Transform…

In recent years, pangenomes received increasing attention from the scientific community for their ability to incorporate population variation information and alleviate reference genome bias. Maximal Exact Matches (MEMs) and Maximal Unique…

Modern retrieval system often requires recomputing the representation of every piece of data in the gallery when updating to a better representation model. This process is known as backfilling and can be especially costly in the real world…

Inverted indexes are vital in providing fast key-word-based search. For every term in the document collection, a list of identifiers of documents in which the term appears is stored, along with auxiliary information such as term frequency,…

Transformers are arguably the main workhorse in recent Natural Language Processing research. By definition a Transformer is invariant with respect to reordering of the input. However, language is inherently sequential and word order is…

We propose a new model for learning bilingual word representations from non-parallel document-aligned data. Following the recent advances in word representation learning, our model learns dense real-valued word vectors, that is, bilingual…

Recently, Cenzato et al.\ proposed a new text index, called the \emph{suffixient array}, which is a subset of the suffix array and supports locating a single pattern occurrence or finding its maximal exact matches (MEMs), assuming random…

Recently, Holt and McMillan [Bionformatics 2014, ACM-BCB 2014] have proposed a simple and elegant algorithm to merge the Burrows-Wheeler transforms of a family of strings. In this paper we show that the H&M algorithm can be improved so…

Many image understanding tasks involve identifying what is present and where it appears. However, tasks that address where, such as object discovery, detection, and segmentation, are often considerably more complex than image…

We present a new scalable, lightweight algorithm to incrementally construct the BWT and FM-index of large string sets such as those produced by Next Generation Sequencing. The algorithm is designed for massive parallelism and can…

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…

The suffix array is an efficient data structure for in-memory pattern search. Suffix arrays can also be used for external-memory pattern search, via two-level structures that use an internal index to identify the correct block of suffix…

We propose a new class of linear Transformers called FourierLearner-Transformers (FLTs), which incorporate a wide range of relative positional encoding mechanisms (RPEs). These include regular RPE techniques applied for sequential data, as…

Vision Transformers (ViTs) and Swin Transformers (Swin) are currently state-of-the-art in computational pathology. However, domain experts are still reluctant to use these models due to their lack of interpretability. This is not…

This review article was first published in 2008 as chapter 11 in the book "Fast Fourier Transforms," edited by C. S. Burrus, for the Connexions project at Rice University, which is sadly no longer online. It gives a high-level overview of…

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 suffix tree is arguably the most fundamental data structure on strings: introduced by Weiner (SWAT 1973) and McCreight (JACM 1976), it allows solving a myriad of computational problems on strings in linear time. Motivated by its large…