Related papers: When is String Reconstruction using de Bruijn Grap…
We consider the problem of sampling from the uniform distribution on the set of Eulerian orientations of subgraphs of the triangular lattice. Although it is known that this can be achieved in polynomial time for any graph, the algorithm…
Quantum compilation requires the development of new algorithms that optimise the cost of implementing quantum computations on physical hardware. Often this gives rise to problems which are asymptotically hard to solve classically, and for…
Since its first use by Euler on the problem of the seven bridges of K\"onigsberg, graph theory has shown excellent abilities in solving and unveiling the properties of multiple discrete optimization problems. The study of the structure of…
Bayesian structure learning is the NP-hard problem of discovering a Bayesian network that optimally represents a given set of training data. In this paper we study the computational worst-case complexity of exact Bayesian structure learning…
Decomposing an Eulerian graph into a minimum respectively maximum number of edge disjoint cycles is an NP-complete problem. We prove that an Eulerian graph decomposes into a unique number of cycles if and only if it does not contain two…
We introduce the notion of de Bruijn entropy of an Eulerian quiver and show how the corresponding relative entropy can be applied to practical string similarity problems. This approach explicitly links the combinatorial and…
In the \emph{trace reconstruction problem}, an unknown source string $x \in \{0,1\}^n$ is sent through a probabilistic \emph{deletion channel} which independently deletes each bit with probability $\delta$ and concatenates the surviving…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
We study a problem of reconstruction of connected graphs where the input gives all subsets of size k that induce a connected subgraph. Originally introduced by Bastide et al. (WG 2023) for triples ($k=3$), this problem received…
In the Graph Reconstruction (GR) problem, the goal is to recover a hidden graph by utilizing some oracle that provides limited access to the structure of the graph. The interest is in characterizing how strong different oracles are when the…
The Subgraph Isomorphism problem is of considerable importance in computer science. We examine the problem when the pattern graph H is of bounded treewidth, as occurs in a variety of applications. This problem has a well-known algorithm via…
We introduce De Bruijn Graph Neural Networks (DBGNNs), a novel time-aware graph neural network architecture for time-resolved data on dynamic graphs. Our approach accounts for temporal-topological patterns that unfold in the causal topology…
Key to successfully deal with complex contemporary datasets is the development of tractable models that account for the irregular structure of the information at hand. This paper provides a comprehensive and unifying view of several…
De Brujin graphs are widely used in bioinformatics for processing next-generation sequencing data. Due to a very large size of NGS datasets, it is essential to represent de Bruijn graphs compactly, and several approaches to this problem…
Let $G$ be a graph, and $H$ be a finite subgraph of $G$. We say that $H$ is a (semi) $S$-Eulerian subgraph if there exists a closed (open) trail $T$ in $G$ such that each edge of $H$ appears in $T$. We show that the problem of determining…
Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs -- a set of strings that are promised to appear in any genome that could have generated the…
Trace reconstruction is the problem of learning an unknown string $x$ from independent traces of $x$, where traces are generated by independently deleting each bit of $x$ with some deletion probability $q$. In this paper, we initiate the…
We study the problem of selecting the best sampling set for bandlimited reconstruction of signals on graphs. A frequency domain representation for graph signals can be defined using the eigenvectors and eigenvalues of variation operators…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
We study the two inference problems of detecting and recovering an isolated community of \emph{general} structure planted in a random graph. The detection problem is formalized as a hypothesis testing problem, where under the null…