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

Factorization machine (FM) variants are widely used in recommendation systems that operate under strict throughput and latency requirements, such as online advertising systems. FMs are known both due to their ability to model pairwise…

In recent years, the focus of bioinformatics research has moved from individual sequences to collections of sequences. Given the fundamental role of the Burrows-Wheeler Transform (BWT) in string processing, a number of dedicated tools have…

In this work, we present a literature review for full-text and keyword indexes as well as our contributions (which are mostly practice-oriented). The first contribution is the FM-bloated index, which is a modification of the well-known…

Genomic and metagenomic fields, generating huge sets of short genomic sequences, brought their own share of high performance problems. To extract relevant pieces of information from the huge data sets generated by current sequencing…

We deal with the problem of maintaining the suffix tree indexing structure for a fully-online collection of multiple strings, where a new character can be prepended to any string in the collection at any time. The only previously known…

The Burrows-Wheeler Transform (BWT) has been an essential tool in text compression and indexing. First introduced in 1994, it went on to provide the backbone for the first encoding of the classic suffix tree data structure in space close to…

Genome sequence analysis, which examines the DNA sequences of organisms, drives advances in many critical medical and biotechnological fields. Given its importance and the exponentially growing volumes of genomic sequence data, there are…

In this paper, we propose several improvements on the block-coordinate Frank-Wolfe (BCFW) algorithm from Lacoste-Julien et al. (2013) recently used to optimize the structured support vector machine (SSVM) objective in the context of…

The Fenwick tree is a classical implicit data structure that stores an array in such a way that modifying an element, accessing an element, computing a prefix sum and performing a predecessor search on prefix sums all take logarithmic time.…

Genomics is the critical key to enabling precision medicine, ensuring global food security and enforcing wildlife conservation. The massive genomic data produced by various genome sequencing technologies presents a significant challenge for…

In this paper we propose a flexible and lightweight technique for merging compressed indices based on variants of Burrows-Wheeler transform (BWT), thus addressing the need for algorithms that compute compressed indices over large…

String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…

We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating $k$-mers…

Semiparametric accelerated failure time (AFT) models directly relate the predicted failure times to covariates and are a useful alternative to models that work on the hazard function or the survival function. For case-cohort data, much less…

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…

Given a string $T$ on an alphabet of size $\sigma$, we describe a bidirectional Burrows-Wheeler index that takes $O(|T|\log{\sigma})$ bits of space, and that supports the addition \emph{and removal} of one character, on the left or right…

In this paper, a new and novel data structure is proposed to dynamically insert and delete segments. Unlike the standard segment trees[3], the proposed data structure permits insertion of a segment with interval range beyond the interval…

Support Vector Machines (SVMs) are an important tool for performing classification on scattered data, where one usually has to deal with many data points in high-dimensional spaces. We propose solving SVMs in primal form using feature maps…

The $r$-index represented a breakthrough in compressed indexing of repetitive text collections, outperforming its alternatives by orders of magnitude in query time. Its space usage, $O(r)$ where $r$ is the number of runs in the…

De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…