相关论文: Computing Maximal Unique Matches with the r-index
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…
We describe a compression-aware method to compute all-vs-all maximal exact matches (MEM) among strings of a repetitive collection $\mathcal{T}$. The key concept in our work is the construction of a fully-balanced grammar $\mathcal{G}$ from…
Mixture-of-Experts (MoE) large language models (LLMs) are among the top-performing architectures. The largest models, often with hundreds of billions of parameters, pose significant memory challenges for deployment. Traditional approaches…
Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being…
It is known that the exact form of the Burrows-Wheeler-Transform (BWT) of a string collection depends, in most implementations, on the input order of the strings in the collection. Reordering strings of an input collection affects the…
MONI (Rossi et al., 2022) can store a pangenomic dataset T in small space and later, given a pattern P, quickly find the maximal exact matches (MEMs) of P with respect to T. In this paper we consider its one-pass version (Boucher et al.,…
Decreasing sequence length is a common way to accelerate transformers, but prior token reduction work often targets classification and reports proxy metrics rather than end-to-end latency. For semantic segmentation, token reduction is…
We study the problem of finding maximal exact matches (MEMs) between a query string $Q$ and a labeled graph $G$. MEMs are an important class of seeds, often used in seed-chain-extend type of practical alignment methods because of their…
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…
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…
Generative information retrieval (GenIR) consolidates retrieval into a single neural model that decodes document identifiers (docids) directly from queries. While this model-as-index paradigm offers architectural simplicity, it is poorly…
Given a weighted bipartite graph $G = (L, R, E, w)$, the maximum weight matching (MWM) problem seeks to find a matching $M \subseteq E$ that maximizes the total weight $\sum_{e \in M} w(e)$. This paper presents a novel algorithm with a time…
The recent introduction of learned indexes has shaken the foundations of the decades-old field of indexing data structures. Combining, or even replacing, classic design elements such as B-tree nodes with machine learning models has proven…
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…
The Boolean product $R = P \cdot Q$ of two $\{ 0, 1\} \; m \times m \; $ matrices is $$R(j,k) = 1 \; \mathrm{\ IF\ for\ some\ } \; t \; \,P(j, t) = Q(t, k) = 1\; \; \mathrm{ELSE\ } \, R(j, k) = 0. $$ The near-optimal design reduces the…
Learned indexes have attracted significant research interest due to their ability to offer better space-time trade-offs compared to traditional B+-tree variants. Among various learned indexes, the PGM-Index based on error-bounded piecewise…
We study the problem of finding a maximum matching in a graph given by an input stream listing its edges in some arbitrary order, where the quantity to be maximized is given by a monotone submodular function on subsets of edges. This…
We present the mixture-of-parents maximum entropy Markov model (MoP-MEMM), a class of directed graphical models extending MEMMs. The MoP-MEMM allows tractable incorporation of long-range dependencies between nodes by restricting the…
Large language models (LLMs) have brought a great breakthrough to the natural language processing (NLP) community, while leading the challenge of handling concurrent customer queries due to their high throughput demands. Data multiplexing…
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the…