相关论文: PFP Data Structures

The suffix tree is a very important data structure in string processing, but it suffers from a huge space consumption. In large-scale applications, compressed suffix trees (CSTs) are therefore used instead. A CST consists of three…

In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…

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…

We deal with the problem of maintaining the suffix tree indexing structure for a fully-online collection of multiple strings, where a new character can be prepended to any string in the collection at any time. The only previously known…

In this paper, we present a new data structure called the packed compact trie (packed c-trie) which stores a set $S$ of $k$ strings of total length $n$ in $n \log\sigma + O(k \log n)$ bits of space and supports fast pattern matching queries…

Much research has been devoted to optimizing algorithms of the Lempel-Ziv (LZ) 77 family, both in terms of speed and memory requirements. Binary search trees and suffix trees (ST) are data structures that have been often used for this…

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,…

Machine learning models perform well across domains such as diagnostics, weather forecasting, NLP, and autonomous driving, but their limited uncertainty handling restricts use in safety-critical settings. Traditional neural networks often…

Recently, Conte et al. generalized the longest-common prefix (LCP) array from strings to Wheeler DFAs, and they showed that it can be used to efficiently determine matching statistics on a Wheeler DFA [DCC 2023]. However, storing the LCP…

Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have…

The Burrows-Wheeler Transform (BWT) has been an essential tool in text compression and indexing. First introduced in 1994, it went on to provide the backbone for the first encoding of the classic suffix tree data structure in space close to…

First-principles density functional theory (DFT) with plane wave (PW) basis set is the most widely used method in quantum mechanical material simulations due to its advantages in accuracy and universality. However, a perceived drawback of…

Discrete Fourier transforms~(DFTs) over finite fields have widespread applications in error correction coding. Hence, reducing the computational complexities of DFTs is of great significance, especially for long DFTs as increasingly longer…

In this paper, we propose a novel neural network structure, namely \emph{feedforward sequential memory networks (FSMN)}, to model long-term dependency in time series without using recurrent feedback. The proposed FSMN is a standard…

Given a dynamic set $K$ of $k$ strings of total length $n$ whose characters are drawn from an alphabet of size $\sigma$, a keyword dictionary is a data structure built on $K$ that provides locate, prefix search, and update operations on…

Given a time series vector, how can we efficiently compute a specified part of Fourier coefficients? Fast Fourier transform (FFT) is a widely used algorithm that computes the discrete Fourier transform in many machine learning applications.…

Prefix circuits are fundamental components in digital adders, widely used in digital systems due to their efficiency in calculating carry signals. Synthesizing prefix circuits with minimized area and delay is crucial for enhancing the…

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…

Mixed-precision quantization is a promising approach for compressing large language models under tight memory budgets. However, existing mixed-precision methods typically suffer from one of two limitations: they either rely on expensive…

We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given…