Related papers: TwoPaCo: An efficient algorithm to build the compa…

The block-cut tree decomposes a connected graph along its cutvertices, displaying its 2-connected components. The Tutte-decomposition extends this idea to 2-separators in 2-connected graphs, yielding a canonical tree-decomposition that…

We propose a simple and natural approximation algorithm for the problem of finding a 2-edge-connected spanning subgraph of minimum total edge cost in a graph. The algorithm maintains a spanning forest starting with an empty edge set. In…

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…

Animals are able to discover the topological map (graph) of surrounding environment, which will be used for navigation. Inspired by this biological phenomenon, researchers have recently proposed to generate graph representation for Markov…

Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…

Recently we create so much data (2.5 quintillion bytes every day) that 90% of the data in the world today has been created in the last two years alone [1]. This data comes from sensors used to gather traffic or climate information, posts to…

Attributed graphs, which contain rich contextual features beyond just network structure, are ubiquitous and have been observed to benefit various network analytics applications. Graph structure optimization, aiming to find the optimal…

Clustering is a fundamental task in machine learning. One of the most successful and broadly used algorithms is DBSCAN, a density-based clustering algorithm. DBSCAN requires $\epsilon$-nearest neighbor graphs of the input dataset, which are…

Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…

The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…

Recent advances in neural recording technology allow simultaneously recording action potentials from hundreds to thousands of neurons in awake, behaving animals. However, characterizing spike patterns in the resulting data, and linking…

Deep generative models, since their inception, have become increasingly more capable of generating novel and perceptually realistic signals (e.g., images and sound waves). With the emergence of deep models for graph structured data, natural…

Since the release of human genome sequences, one of the most important research issues is about indexing the genome sequences, and the suffix tree is most widely adopted for that purpose. The traditional suffix tree construction algorithms…

This paper introduces DEM-Engine, a new submodule of Project Chrono, that is designed to carry out Discrete Element Method (DEM) simulations. Based on spherical primitive shapes, DEM-Engine can simulate polydisperse granular materials and…

The greedy Prefer-same de Bruijn sequence construction was first presented by Eldert et al.[AIEE Transactions 77 (1958)]. As a greedy algorithm, it has one major downside: it requires an exponential amount of space to store the length $2^n$…

Topological data analysis (TDA) detects geometric structure in biological data. However, many TDA algorithms are memory intensive and impractical for massive datasets. Here, we introduce a statistical protocol that reduces TDA's memory…

Contour trees offer an abstract representation of the level set topology in scalar fields and are widely used in topological data analysis and visualization. However, applying contour trees to large-scale scientific datasets remains…

A recent surprising result in the implementation of worst-case-optimal (wco) multijoins in graph databases (specifically, basic graph patterns) is that they can be supported on graph representations that take even less space than a plain…

Analysis of signals defined on complex topologies modeled by graphs is a topic of increasing interest. Signal decomposition plays a crucial role in the representation and processing of such information, in particular, to process graph…

Human-swarm interaction is facilitated by a low-dimensional encoding of the swarm formation, independent of the (possibly large) number of robots. We propose using image moments to encode two-dimensional formations of robots. Each robot…