Related papers: Prefix-free parsing for merging big BWTs
FM-indexes are a crucial data structure in DNA alignment, for example, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer observed in 2007 that word-based indexes often…
The Burrows-Wheeler Transform is a string transformation that plays a fundamental role for the design of self-indexing compressed data structures. Over the years, researchers have successfully extended this transformation outside the…
In this article we extend the elegant in-place Burrows-Wheeler transform (BWT) algorithm proposed by Crochemore et al. (Crochemore et al., 2015). Our extension is twofold: we first show how to compute simultaneously the longest common…
Prefix parsing asks whether an input prefix can be extended to a complete string generated by a given grammar. In the weighted setting, it also provides prefix probabilities, which are central to context-free language modeling,…
Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…
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…
The Burrows-Wheeler Transform (BWT) is an invertible text transformation that permutes symbols of a text according to the lexicographical order of its suffixes. BWT is the main component of popular lossless compression programs (such as…
Memoryless computation is a new technique to compute any function of a set of registers by updating one register at a time while using no memory. Its aim is to emulate how computations are performed in modern cores, since they typically…
We explore whether it is possible to build lighter parsers, that are statistically equivalent to their corresponding standard version, for a wide set of languages showing different structures and morphologies. As testbed, we use the…
Some recent results have introduced external-memory algorithms to compute self-indexes of a set of strings, mainly via computing the Burrows-Wheeler Transform (BWT) of the input strings. The motivations for those results stem from…
The boom of genomic sequencing makes compression of set of sequences inescapable. This underlies the need for multi-string indexing data structures that helps compressing the data. The most prominent example of such data structures is the…
The Burrows-Wheeler Transform (BWT) of a string is an invertible permutation of the string, which can be used for data compression and compact indexes for string pattern matching. Ganguly et al. [SODA, 2017] introduced the parameterized BWT…
Standard Byte-Pair Encoding (BPE) tokenization compresses text by pairing a learned token vocabulary with a detailed merge list. Recent work has shown that this merge list exposes a potential attack surface for extracting information about…
Training data memorization in NLP can both be beneficial (e.g., closed-book QA) and undesirable (personal data extraction). In any case, successful model training requires a non-trivial amount of memorization to store word spellings,…
Conventional mutual information (MI) based feature selection (FS) methods are unable to handle heterogeneous feature subset selection properly because of data format differences or estimation methods of MI between feature subset and class…
Modern Foundation Models (FMs) are typically trained on corpora spanning a wide range of different data modalities, topics and downstream tasks. Utilizing these models can be very computationally expensive and is out of reach for most…
Bayesian clustering accounts for uncertainty but is computationally demanding at scale. Furthermore, real-world datasets often contain missing values, and simple imputation ignores the associated uncertainty, resulting in suboptimal…
Pretrained Foundation Models (PFMs) are regarded as the foundation for various downstream tasks with different data modalities. A PFM (e.g., BERT, ChatGPT, and GPT-4) is trained on large-scale data which provides a reasonable parameter…
Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many…
The fast Fourier transform (FFT) is undoubtedly an essential primitive that has been applied in various fields of science and engineering. In this paper, we present a decomposition method for parallelization of multi-dimensional FFTs with…