相关论文: R-enum: Enumeration of Characteristic Substrings i…

Enumerating the minimal hitting sets of a hypergraph is a problem which arises in many data management applications that include constraint mining, discovering unique column combinations, and enumerating database repairs. Previously, Eiter…

In the deletion channel, an important problem is to determine the number of subsequences derived from a string $U$ of length $n$ when subjected to $t$ deletions. It is well-known that the number of subsequences in the setting exhibits a…

This paper proposes a novel Recurrent Neural Network (RNN) language model that takes advantage of character information. We focus on character n-grams based on research in the field of word embedding construction (Wieting et al. 2016). Our…

We study the impact that string reversal can have on several repetitiveness measures. First, we exhibit an infinite family of strings where the number, $r$, of runs in the run-length encoding of the Burrows--Wheeler transform (BWT) can…

Recurrent Neural Networks (RNNs) are a class of machine learning algorithms used for applications with time-series and sequential data. Recently, there has been a strong interest in executing RNNs on embedded devices. However, difficulties…

A string $w$ is called a minimal absent word (MAW) for a string $S$ if $w$ does not occur as a substring in $S$ and all proper substrings of $w$ occur in $S$. MAWs are well-studied combinatorial string objects that have potential…

Global sentence information is crucial for sequence labeling tasks, where each word in a sentence must be assigned a label. While BiLSTM models are widely used, they often fail to capture sufficient global context for inner words. Previous…

Text compression schemes and compact data structures usually combine sophisticated probability models with basic coding methods whose average codeword length closely match the entropy of known distributions. In the frequent case where basic…

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…

A longest repeat query on a string, motivated by its applications in many subfields including computational biology, asks for the longest repetitive substring(s) covering a particular string position (point query). In this paper, we extend…

Prompting has shown impressive success in enabling large pretrained language models (LMs) to perform diverse NLP tasks, especially when only few downstream data are available. Automatically finding the optimal prompt for each task, however,…

Exact string matching has been a fundamental problem in computer science for decades because of many practical applications. Some are related to common procedures, such as searching in files and text editors, or, more recently, to more…

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…

Recurrent neural network (RNN) and connectionist temporal classification (CTC) have showed successes in many sequence labeling tasks with the strong ability of dealing with the problems where the alignment between the inputs and the target…

Computing the {\em matching statistics} of a string $P[1..m]$ with respect to a text $T[1..n]$ is a fundamental problem which has application to genome sequence comparison. In this paper, we study the problem of computing the matching…

We describe an algorithm to find maximal exact matches (MEMs) among HiFi reads with homopolymer errors. The main novelty in our work is that we resort to run-length compression to help deal with errors. Our method receives as input a…

In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…

Recurrent Neural Network (RNN) and one of its specific architectures, Long Short-Term Memory (LSTM), have been widely used for sequence labeling. In this paper, we first enhance LSTM-based sequence labeling to explicitly model label…

We give a near-optimal quantum algorithm for the longest common substring (LCS) problem between two run-length encoded (RLE) strings, with the assumption that the prefix-sums of the run-lengths are given. Our algorithm costs…

This paper performs the analysis necessary to bound the running time of known, efficient algorithms for generating all longest common subsequences. That is, we bound the running time as a function of input size for algorithms with time…