Related papers: Space efficient merging of de Bruijn graphs and Wh…
We address the following general question: given a graph class C on which we can solve Maximum Matching in (quasi) linear time, does the same hold true for the class of graphs that can be modularly decomposed into C ? A major difficulty in…
Computing over compressed data combines the space saving of data compression with efficient support for queries directly on the compressed representation. Such data structures are widely applied in text indexing and have been successfully…
Many graph problems can be solved using ordered parallel graph algorithms that achieve significant speedup over their unordered counterparts by reducing redundant work. This paper introduces a new priority-based extension to GraphIt, a…
Recently, Marcus et al. (Bioinformatics 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related species. They devised an $O(n \log g)$…
Many computational problems admit fast algorithms on special inputs, however, the required properties might be quite restrictive. E.g., many graph problems can be solved much faster on interval or cographs, or on graphs of small…
Bipartite graphs are a prevalent modeling tool for real-world networks, capturing interactions between vertices of two different types. Within this framework, bicliques emerge as crucial structures when studying dense subgraphs: they are…
We address the problem of computing the distribution of induced connected subgraphs, aka \emph{graphlets} or \emph{motifs}, in large graphs. The current state-of-the-art algorithms estimate the motif counts via uniform sampling, by…
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…
Recently, Holt and McMillan [Bionformatics 2014, ACM-BCB 2014] have proposed a simple and elegant algorithm to merge the Burrows-Wheeler transforms of a family of strings. In this paper we show that the H&M algorithm can be improved so…
The de Bruijn graph, its sequences, and their various generalizations, have found many applications in information theory, including many new ones in the last decade. In this paper, motivated by a coding problem for emerging memory…
Compact and I/O-efficient data representations play an important role in efficient algorithm design, as memory bandwidth and latency can present a significant performance bottleneck, slowing the computation by orders of magnitude. While…
As two fundamental problems, graph cuts and graph matching have been investigated over decades, resulting in vast literature in these two topics respectively. However the way of jointly applying and solving graph cuts and matching receives…
In this paper, we introduce a graph matching method that can account for constraints of arbitrary order, with arbitrary potential functions. Unlike previous decomposition approaches that rely on the graph structures, we introduce a…
This paper proposes a new algorithm for simultaneous graph matching and clustering. For the first time in the literature, these two problems are solved jointly and synergetically without relying on any training data, which brings advantages…
The reduction of the fragment assembly problem to (variations of) the classical Eulerian trail problem [Pevzner et al., PNAS 2001] has led to remarkable progress in genome assembly. This reduction employs the notion of de Bruijn graph…
We introduce a new concept of a subgraph class called a superbubble for analyzing assembly graphs, and propose an efficient algorithm for detecting it. Most assembly algorithms utilize assembly graphs like the de Bruijn graph or the overlap…
Hypergraphs, increasingly utilised to model complex and diverse relationships in modern networks, have gained significant attention for representing intricate higher-order interactions. Among various challenges, cohesive subgraph discovery…
We describe an efficient method for drawing any n-vertex simple graph G in the hyperbolic plane. Our algorithm produces greedy drawings, which support greedy geometric routing, so that a message M between any pair of vertices may be routed…
Balanced partitioning is often a crucial first step in solving large-scale graph optimization problems, e.g., in some cases, a big graph can be chopped into pieces that fit on one machine to be processed independently before stitching the…
This article introduces new algorithms for the uniform random generation of labelled planar graphs. Its principles rely on Boltzmann samplers, as recently developed by Duchon, Flajolet, Louchard, and Schaeffer. It combines the Boltzmann…