Related papers: Assembling Omnitigs using Hidden-Order de Bruijn G…
We present novel graph kernels for graphs with node and edge labels that have ordered neighborhoods, i.e. when neighbor nodes follow an order. Graphs with ordered neighborhoods are a natural data representation for evolving graphs where…
The nodes of the de Bruijn graph B(d,3) consist of all strings of length 3, taken from an alphabet of size d, with edges between words which are distinct substrings of a word of length 4. We give an inductive characterization of the maximum…
The discovery and analysis of network patterns are central to the scientific enterprise. In the present work, we developed and evaluated a new approach that learns the building blocks of graphs that can be used to understand and generate…
The future of main memory appears to lie in the direction of new technologies that provide strong capacity-to-performance ratios, but have write operations that are much more expensive than reads in terms of latency, bandwidth, and energy.…
The aim of this article is to provide space level maps between configuration spaces of graphs that are predicted by algebraic manipulations of cellular chains. More explicitly, we consider edge contraction and half-edge deletion, and…
The reassembling of a simple connected graph G = (V,E) is an abstraction of a problem arising in earlier studies of network analysis. Its simplest formulation is in two steps: (1) We cut every edge of G into two halves, thus obtaining a…
In this paper we study graph problems in dynamic streaming model, where the input is defined by a sequence of edge insertions and deletions. As many natural problems require $\Omega(n)$ space, where $n$ is the number of vertices, existing…
We consider the problem of finding an edge in a hidden undirected graph $G = (V, E)$ with $n$ vertices, in a model where we only allowed queries that ask whether or not a subset of vertices contains an edge. We study the non-adaptive model…
We generalize the problem of reconstructing strings from their substring compositions first introduced by Acharya et al. in 2015 motivated by polymer-based advanced data storage systems utilizing mass spectrometry. Namely, we see strings as…
The most commonly used method to tackle the graph partitioning problem in practice is the multilevel approach. During a coarsening phase, a multilevel graph partitioning algorithm reduces the graph size by iteratively contracting nodes and…
A flow graph $G=(V,E,s)$ is a directed graph with a distinguished start vertex $s$. The dominator tree $D$ of $G$ is a tree rooted at $s$, such that a vertex $v$ is an ancestor of a vertex $w$ if and only if all paths from $s$ to $w$…
Finding dense substructures in a graph is a fundamental graph mining operation, with applications in bioinformatics, social networks, and visualization to name a few. Yet most standard formulations of this problem (like clique, quasiclique,…
Deep neural networks have enabled researchers to create powerful generalized frameworks, such as transformers, that can be used to solve well-studied problems in various application domains, such as text and image. However, such generalized…
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…
Directed acyclic graphs are the basic representation of the structure underlying Bayesian networks, which represent multivariate probability distributions. In many practical applications, such as the reverse engineering of gene regulatory…
We propose an interpretable graph neural network framework to denoise single or multiple noisy graph signals. The proposed graph unrolling networks expand algorithm unrolling to the graph domain and provide an interpretation of the…
Learning representations of sets of nodes in a graph is crucial for applications ranging from node-role discovery to link prediction and molecule classification. Graph Neural Networks (GNNs) have achieved great success in graph…
Reconstructing components of a genomic mixture from data obtained by means of DNA sequencing is a challenging problem encountered in a variety of applications including single individual haplotyping and studies of viral communities.…
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 $2^n$…
Despite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds), whose order and/or…