相关论文: Memory Efficient De Bruijn Graph Construction

Motivation: Data volumes generated by next-generation sequencing technolo- gies is now a major concern, both for storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as…

We present shared-memory parallel methods for Maximal Clique Enumeration (MCE) from a graph. MCE is a fundamental and well-studied graph analytics task, and is a widely used primitive for identifying dense structures in a graph. Due to its…

We present TeraPart, a memory-efficient multilevel graph partitioning method that is designed to scale to extremely large graphs. In balanced graph partitioning, the goal is to divide the vertices into $k$ blocks with balanced size while…

Minimum Spanning Trees are a well-studied subset of graph problems. While classical algorithms have existed to solve these problems for decades, new variations and application areas are constantly being discovered. When dealing with large…

Binary neural networks (BNNs) have been widely adopted to reduce the computational cost and memory storage on edge-computing devices by using one-bit representation for activations and weights. However, as neural networks become…

We present fast algorithms for approximate shortest paths in the massively parallel computation (MPC) model. We provide randomized algorithms that take $poly(\log{\log{n}})$ rounds in the near-linear memory MPC model. Our results are for…

We consider the massively parallel computation (MPC) model, which is a theoretical abstraction of large-scale parallel processing models such as MapReduce. In this model, assuming the widely believed 1-vs-2-cycles conjecture, solving many…

We propose a new algorithm for merging succinct representations of de Bruijn graphs introduced in [Bowe et al. WABI 2012]. Our algorithm is based on the lightweight BWT merging approach by Holt and McMillan [Bionformatics 2014, ACM-BCB…

This paper presents an explicit construction for an $((n,k,d=n-1), (\alpha,\beta))$ regenerating code over a field $\mathbb{F}_Q$ operating at the Minimum Storage Regeneration (MSR) point. The MSR code can be constructed to have rate $k/n$…

k-nearest neighbor graph is a key data structure in many disciplines such as manifold learning, machine learning and information retrieval, etc. NN-Descent was proposed as an effective solution for the graph construction problem. However,…

In the decremental $(1+\epsilon)$-approximate Single-Source Shortest Path (SSSP) problem, we are given a graph $G=(V,E)$ with $n = |V|, m = |E|$, undergoing edge deletions, and a distinguished source $s \in V$, and we are asked to process…

Graph kernels are conventional methods for computing graph similarities. However, the existing R-convolution graph kernels cannot resolve both of the two challenges: 1) Comparing graphs at multiple different scales, and 2) Considering the…

Over the past decade, there has been increasing interest in distributed/parallel algorithms for processing large-scale graphs. By now, we have quite fast algorithms -- usually sublogarithmic-time and often $poly(\log\log n)$-time, or even…

Transforming an input sequence into its constituent k-mers is a fundamental operation in computational genomics. To reduce storage costs associated with k-mer datasets, we introduce and formally analyze MCTR, a novel two-stage algorithm for…

Given a graph G and the desired size k in bits, how can we summarize G within k bits, while minimizing the information loss? Large-scale graphs have become omnipresent, posing considerable computational challenges. Analyzing such large…

The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which…

Motivation: Working with a large number of genomes simultaneously is of great interest in genetic population and comparative genomics research. Bubbles discovery in multi-genomes coloured de bruijn graph for de novo genome assembly is a…

Max-k-Cut and correlation clustering are fundamental graph partitioning problems. For a graph with G=(V,E) with n vertices, the methods with the best approximation guarantees for Max-k-Cut and the Max-Agree variant of correlation clustering…

The sparse representation of graphs has shown great potential for accelerating the computation of graph applications (e.g., Social Networks, Knowledge Graphs) on traditional computing architectures (CPU, GPU, or TPU). But the exploration of…

(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…