Related papers: Tailoring r-index for metagenomics
Ensembles are popular methods for solving practical supervised learning problems. They reduce the risk of having underperforming models in production-grade software. Although critical, methods for learning heterogeneous regression ensembles…
The natural world is abundant with concepts expressed via visual, acoustic, tactile, and linguistic modalities. Much of the existing progress in multimodal learning, however, focuses primarily on problems where the same set of modalities…
Peer review is the quality assessment of a manuscript by one or more peer experts. Papers are submitted by the authors to scientific venues, and these papers must be reviewed by peers or other authors. The meta-reviewers then gather the…
Summary: We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the…
A classic data structure problem is to preprocess a string T of length $n$ so that, given a query $q$, we can quickly find all substrings of T with Hamming distance at most $k$ from the query string. Variants of this problem have seen…
High-throughput DNA sequencers are becoming indispensable in our understanding of diseases at molecular level, in marker-assisted selection in agriculture and in microbial genetics research. These sequencing instruments produce enormous…
Indexing highly repetitive strings (i.e., strings with many repetitions) for fast queries has become a central research topic in string processing, because it has a wide variety of applications in bioinformatics and natural language…
Low-rank matrix estimation is a fundamental problem in statistics and machine learning with applications across biomedical sciences, including genetics, medical imaging, drug discovery, and electronic health record data analysis. In the…
In pattern matching on strings, a locate query asks for an enumeration of all the occurrences of a given pattern in a given text. The r-index [Gagie et al., 2018] is a recently presented compressed self index that stores the text and…
Distant supervision provides a means to create a large number of weakly labeled data at low cost for relation classification. However, the resulting labeled instances are very noisy, containing data with wrong labels. Many approaches have…
Sequencing errors and biases in metagenomic datasets affect coverage-based assemblies and are often ignored during analysis. Here, we analyze read connectivity in metagenomes and identify the presence of problematic and likely a-biological…
Deep sequencing has enabled the investigation of a wide range of environmental microbial ecosystems, but the high memory requirements for {\em de novo} assembly of short-read shotgun sequencing data from these complex populations are an…
Detecting all the strings that occur in a text more frequently or less frequently than expected according to an IID or a Markov model is a basic problem in string mining, yet current algorithms are based on data structures that are either…
Neural document ranking approaches, specifically transformer models, have achieved impressive gains in ranking performance. However, query processing using such over-parameterized models is both resource and time intensive. In this paper,…
This paper demonstrates the utility of organized numerical representations of genes in research involving flat string gene formats (i.e., FASTA/FASTQ5). FASTA/FASTQ files have several current limitations, such as their large file sizes,…
Datasets may contain observations with multiple labels. If the labels are not mutually exclusive, and if the labels vary greatly in frequency, obtaining a sample that includes sufficient observations with scarcer labels to make inferences…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in…
A 'degenerate string' is a sequence of subsets of some alphabet; it represents any string obtainable by selecting one character from each set from left to right. Recently, Alanko et al. generalized the rank-select problem to degenerate…
Given a static reference string $R$ and a source string $S$, a relative compression of $S$ with respect to $R$ is an encoding of $S$ as a sequence of references to substrings of $R$. Relative compression schemes are a classic model of…