相关论文: Simulating the DNA String Graph in Succinct Space

The minimizers sampling mechanism is a popular mechanism for string sampling introduced independently by Schleimer et al. [SIGMOD 2003] and by Roberts et al. [Bioinf. 2004]. Given two positive integers $w$ and $k$, it selects the…

Layout is a fundamental component of any graphic design. Creating large varieties of plausible document layouts can be a tedious task, requiring numerous constraints to be satisfied, including local ones relating different semantic elements…

Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…

Standard full-shape clustering analyses in Fourier space rely on a fixed power spectrum template, defined at the fiducial cosmology used to convert redshifts into distances, and compress the cosmological information into the…

The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…

A new, very general, robust procedure for combining estimators in metric spaces is introduced GROS. The method is reminiscent of the well-known median of means, as described in \cite{devroye2016sub}. Initially, the sample is divided into…

In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…

De Brujin graphs are widely used in bioinformatics for processing next-generation sequencing data. Due to a very large size of NGS datasets, it is essential to represent de Bruijn graphs compactly, and several approaches to this problem…

Mini-batch training of Graph Neural Networks (GNNs) is fundamentally different from training on i.i.d. data: sampling a subgraph alters the topology and introduces boundary effects, leading prior work to develop structure-aware samplers…

In real life, it is always an urge to reach our goal in minimum effort i.e., it should have a minimum constrained path. The path may be shortest route in practical life, either physical or electronic medium. The scenario is to represents…

Genome rearrangements can be modeled as $k$-breaks, which break a genome at k positions and glue the resulting fragments in a new order. In particular, reversals, translocations, fusions, and fissions are modeled as $2$-breaks, and…

Short-read DNA sequencing instruments can yield over 1e+12 bases per run, typically composed of reads 150 bases long. Despite this high throughput, de novo assembly algorithms have difficulty reconstructing contiguous genome sequences using…

The Burrows-Wheeler-Transform (BWT), a reversible string transformation, is one of the fundamental components of many current data structures in string processing. It is central in data compression, as well as in efficient query algorithms…

The problem of estimating the structure of a graph from observed data is of growing interest in the context of high-throughput genomic data, and single-cell RNA sequencing in particular. These, however, are challenging applications, since…

We study the NP-hard problem of approximating a Minimum Routing Cost Spanning Tree in the message passing model with limited bandwidth (CONGEST model). In this problem one tries to find a spanning tree of a graph $G$ over $n$ nodes that…

As a possible implementation of data storage using DNA, multiple strands of DNA are stored in a liquid container so that, in the future, they can be read by an array of DNA readers in parallel. These readers will sample the strands with…

Double-strand DNA breaks (DSBs) are a form of DNA damage that can cause abnormal chromosomal rearrangements. Recent technologies based on high-throughput experiments have obvious high costs and technical challenges.Therefore, we design a…

Data represented as strings abounds in biology, linguistics, document mining, web search and many other fields. Such data often have a hierarchical structure, either because they were artificially designed and composed in a hierarchical…

Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…

Summarizing graphs w.r.t. structural features is important to reduce the graph's size and make tasks like indexing, querying, and visualization feasible. Our generic parallel BRS algorithm efficiently summarizes large graphs w.r.t. a custom…