相关论文: Efficient Construction of a Complete Index for Pan…

Designing efficient optimizers for large language models (LLMs) with low-memory requirements and fast convergence is an important and challenging problem. This paper makes a step towards the systematic design of such optimizers through the…

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 paper we develop a theory describing how the extended Burrows-Wheeler Transform (eBWT) of a collection of DNA fragments tends to cluster together the copies of nucleotides sequenced from a genome G. Our theory accurately predicts…

String kernels are attractive data analysis tools for analyzing string data. Among them, alignment kernels are known for their high prediction accuracies in string classifications when tested in combination with SVM in various applications.…

We propose two suffix array inspired full-text indexes. One, called SA-hash, augments the suffix array with a hash table to speed up pattern searches due to significantly narrowed search interval before the binary search phase. The other,…

Protein quantification and analysis are well-accepted approaches for biomarker discovery but are limited to identification without structural information. High-throughput omics data (i.e., genomics, transcriptomics, and proteomics) have…

We consider an index data structure for similar strings. The generalized suffix tree can be a solution for this. The generalized suffix tree of two strings $A$ and $B$ is a compacted trie representing all suffixes in $A$ and $B$. It has…

We study the problem of indexing and compressing tries using a BWT-based approach. Specifically, we consider a succinct and compressed representation of the XBWT of Ferragina et al.\ [FOCS '05, JACM '09] corresponding to the analogous of…

Recently, Flow Matching models have pushed the boundaries of high-fidelity data generation across a wide range of domains. It typically employs a single large network to learn the entire generative trajectory from noise to data. Despite…

Tensor completion is crucial in many scientific domains with missing data problems. Traditional low-rank tensor models, including CP, Tucker, and Tensor-Train, exploit low-dimensional structures to recover missing data. However, these…

Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…

A parameterized string (p-string) is a string over an alphabet $(\Sigma_{s} \cup \Sigma_{p})$, where $\Sigma_{s}$ and $\Sigma_{p}$ are disjoint alphabets for static symbols (s-symbols) and for parameter symbols (p-symbols), respectively.…

The Burrows-Wheeler Transform (BWT) is a word transformation introduced in 1994 for Data Compression. It has become a fundamental tool for designing self-indexing data structures, with important applications in several area in science and…

Existing methods for bulk loading disk-based multidimensional points involve multiple applications of external sorting. In this paper, we propose techniques that apply linear scan, and are therefore significantly faster. The resulting FMBI…

We present a distributed full-text index for big data applications in a distributed environment. Our index can answer different types of pattern matching queries (existential, counting and enumeration). We perform experiments on inputs up…

The problem of finding factors of a text string which are identical or similar to a given pattern string is a central problem in computer science. A generalised version of this problem consists in implementing an index over the text to…

Matrices of (approximate) low rank are pervasive in data science, appearing in recommender systems, movie preferences, topic models, medical records, and genomics. While there is a vast literature on how to exploit low rank structure in…

Index structures are a building block of query processing and computer science in general. Since the dawn of computer technology there have been index structures. And since then, a myriad of index structures are being invented and published…

In this paper, we resolve a long-standing question in self-stabilization by demonstrating that it is indeed possible to construct a spanning tree in a semi-uniform network using constant memory per node. We introduce a self-stabilizing…

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…