Related papers: Tailoring r-index for metagenomics

Deep learning (DL) techniques have shown unprecedented success when applied to images, waveforms, and text. Generally, when the sample size ($N$) is much bigger than the number of features ($d$), DL often outperforms other machine learning…

Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of…

The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…

Although considerable efforts have been devoted to transformer-based ranking models for document search, the relevance-efficiency tradeoff remains a critical problem for ad-hoc ranking. To overcome this challenge, this paper presents BECR…

Metagenomic disease prediction commonly relies on species abundance tables derived from large, incomplete reference catalogs, constraining resolution and discarding valuable information contained in DNA reads. To overcome these limitations,…

To store and search genomic databases efficiently, researchers have recently started building compressed self-indexes based on grammars. In this paper we show how, given a straight-line program with $r$ rules for a string (S [1..n]) whose…

Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that…

Sample re-weighting strategies provide a promising mechanism to deal with imperfect training data in machine learning, such as noisily labeled or class-imbalanced data. One such strategy involves formulating a bi-level optimization problem…

Order-preserving pattern matching was introduced recently but it has already attracted much attention. Given a reference sequence and a pattern, we want to locate all substrings of the reference sequence whose elements have the same…

With the recent advances in DNA sequencing, it is now possible to have complete genomes of individuals sequenced and assembled. This rich and focused genotype information can be used to do different population-wide studies, now first time…

Dense retrieval systems increasingly need to handle complex queries. In many realistic settings, users express intent through long instructions or task-specific descriptions, while target documents remain relatively simple and static. This…

Estimating the abundances of all $k$-mers in a set of biological sequences is a fundamental and challenging problem with many applications in biological analysis. While several methods have been designed for the exact or approximate…

The classic string indexing problem is to preprocess a string $S$ into a compact data structure that supports efficient subsequent pattern matching queries, that is, given a pattern string $P$, report all occurrences of $P$ within $S$. In…

We consider compact representations of collections of similar strings that support random access queries. The collection of strings is given by a rooted tree where edges are labeled by an edit operation (inserting, deleting, or replacing a…

Data pruning, or instance selection, is an important problem in machine learning especially in terms of nearest neighbour classifier. However, in data pruning which speeds up the prediction phase, there is an issue related to the speed and…

We propose algorithms that, given the input string of length $n$ over integer alphabet of size $\sigma$, construct the Burrows-Wheeler transform (BWT), the permuted longest-common-prefix (PLCP) array, and the LZ77 parsing in…

Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text $T$, pre-process it off-line so that, later, we can quickly count and locate the occurrences of any string (the query pattern) in $T$…

Genome and metagenome comparisons based on large amounts of next-generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads.…

We consider document listing on string collections, that is, finding in which strings a given pattern appears. In particular, we focus on repetitive collections: a collection of size $N$ over alphabet $[1,\sigma]$ is composed of $D$ copies…

We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…