Related papers: On the Coverage Required for Diploid Genome Assemb…

Consider a point-to-point message-passing network. We are interested in the asynchronous crash-tolerant consensus problem in incomplete networks. We study the feasibility and efficiency of approximate consensus under different restrictions…

Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…

Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…

We address the problem of efficient and unobstructed surveillance or communication in complex environments. On one hand, one wishes to use a minimal number of sensors to cover the environment. On the other hand, it is often important to…

Self-assembly of dilute sequence-defined macromolecules is a complex phenomenon in which the local arrangement of chemical moieties can lead to the formation of long-range structure. The dependence of this structure on the sequence…

Random sequential adsorption algorithm is a popular tool for modelling structure of monolayers built in irreversible adsorption experiments. However, this algorithm becomes very inefficient when the density of molecules in a layer rises.…

We study adaptive greedy algorithms for the problems of stochastic set cover with perfect and imperfect coverages. In stochastic set cover with perfect coverage, we are given a set of items and a ground set B. Evaluating an item reveals its…

As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…

Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…

The coverage depth problem in DNA data storage is about minimizing the expected number of reads until all data is recovered. When they exist, MDS codes offer the best performance in this context. This paper focuses on the scenario where the…

We present a parallelized bijective graph matching algorithm that leverages seeds and is designed to match very large graphs. Our algorithm combines spectral graph embedding with existing state-of-the-art seeded graph matching procedures.…

The problem of reconstructing strings from their substring spectra has a long history and in its most simple incarnation asks for determining under which conditions the spectrum uniquely determines the string. We study the problem of coded…

In the field of parameterized complexity theory, the study of graph width measures has been intimately connected with the development of width-based model checking algorithms for combinatorial properties on graphs. In this work, we…

We address the long-standing problem of how to learn effective pixel-based image diffusion models at scale, introducing a remarkably simple greedy growing method for stable training of large-scale, high-resolution models. without the needs…

The goal of random sequential adsorption (RSA), a time-dependent packing method, is to create a regular or asymmetric covering of an empty space that can fit in the allocated space without overlapping. The density of coverage tends to reach…

We present kleuren, a novel assembly-free method to reconstruct phylogenetic trees using the Colored de Bruijn Graph. kleuren works by constructing the Colored de Bruijn Graph and then traversing it, finding bubble structures in the graph…

A tessellation of a graph is a partition of its vertices into vertex disjoint cliques. A tessellation cover of a graph is a set of tessellations that covers all of its edges. The $t$-tessellability problem aims to decide whether there is a…

Convergent rewriting systems on algebraic structures give methods to solve decision problems, to prove coherence results, and to compute homological invariants. These methods are based on higher-dimensional extensions of the critical…

The simplest possible informational heteropolymer requires only a two-letter alphabet to be able to store information. The evolutionary choice of four monomers in the informational biomolecules RNA/DNA or their progenitors is intriguing,…

Higher-dimensional rewriting is founded on a duality of rewrite systems and cell complexes, connecting computational mathematics to higher categories and homotopy theory: the two sides of a rewrite rule are two halves of the boundary of an…