Related papers: Faster Maximal Exact Matches with Lazy LCP Evaluat…
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.,…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…
Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in…
Finding maximal exact matches (MEMs) between strings is an important task in bioinformatics, but it is becoming increasingly challenging as geneticists switch to pangenomic references. Fortunately, we are usually interested only in the…
In recent years, pangenomes received increasing attention from the scientific community for their ability to incorporate population variation information and alleviate reference genome bias. Maximal Exact Matches (MEMs) and Maximal Unique…
For taxonomic classification, we are asked to index the genomes in a phylogenetic tree such that later, given a DNA read, we can quickly choose a small subtree likely to contain the genome from which that read was drawn. Although popular…
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…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
We present MELODI, a novel memory architecture designed to efficiently process long documents using short context windows. The key principle behind MELODI is to represent short-term and long-term memory as a hierarchical compression scheme…
Near-duplicate text alignment is the task of identifying, among the texts in a corpus, all the subsequences (substrings) that are similar to a given query. Traditional approaches rely on seeding-extension-filtering heuristics, which lack…
Suppose we are asked to index a text $T [0..n - 1]$ such that, given a pattern $P [0..m - 1]$, we can quickly report the maximal substrings of $P$ that each occur in $T$ at least $k$ times. We first show how we can add $O (r \log n)$ bits…
Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic database. Bannai et al. gave an efficient solution for this…
Complex Event Processing (CEP) is an emerging field with important applications in many areas. CEP systems collect events arriving from input data streams and use them to infer more complex events according to predefined patterns. The…
The Muon optimizer has recently offered a promising alternative to AdamW for large language model training, leveraging matrix orthogonalization to produce geometry-aware updates. However, like all first-order methods, Muon can become…
Efficient approximation lies at the heart of large-scale machine learning problems. In this paper, we propose a novel, robust maximum entropy algorithm, which is capable of dealing with hundreds of moments and allows for computationally…
Alignment-based conformance checking is the state-of-the-art approach for comparing observed process executions with normative process models. The standard exact solution relies on an A*-based heuristic search, which can exhibit exponential…
Entity matching is a fundamental task in data cleaning and data integration. With the rapid adoption of large language models (LLMs), recent studies have explored zero-shot and few-shot prompting to improve entity matching accuracy.…
Latent class model (LCM), which is a finite mixture of different categorical distributions, is one of the most widely used models in statistics and machine learning fields. Because of its non-continuous nature and the flexibility in shape,…
Cardinality estimation is a key component of database query optimization. Recent studies have demonstrated that learned cardinality estimation techniques can surpass traditional methods in accuracy. However, a significant barrier to their…
In this paper, a fully compressed pattern matching problem is studied. The compression is represented by straight-line programs (SLPs), i.e. a context-free grammars generating exactly one string; the term fully means that both the pattern…