Related papers: When is String Reconstruction using de Bruijn Grap…
The deletion channel takes as input a bit string $\mathbf{x} \in \{0,1\}^n$, and deletes each bit independently with probability $q$, yielding a shorter string. The trace reconstruction problem is to recover an unknown string $\mathbf{x}$…
This work addresses the challenge of using a deep learning model to prune graphs and the ability of this method to integrate explainability into spatio-temporal problems through a new approach. Instead of applying explainability to the…
Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is…
The problem of finding the degeneracy of a graph is a subproblem of the k-core decomposition problem. In this paper, we present a (1 + epsilon)-approximate solution to the degeneracy problem which runs in O(n log n) time, sublinear in the…
We study the parameterized complexity of the Cograph Deletion problem, which asks whether one can delete at most $k$ edges from a graph to make it $P_4$-free. This is a well-known graph modification problem with applications in computation…
Some recent results have introduced external-memory algorithms to compute self-indexes of a set of strings, mainly via computing the Burrows-Wheeler Transform (BWT) of the input strings. The motivations for those results stem from…
We consider the problem of identifying the densest k-node subgraph in a given graph. We write this problem as an instance of rank-constrained cardinality minimization and then relax using the nuclear and 11 norms. Although the original…
The Subgraph Isomorphism problem asks, given a host graph G on n vertices and a pattern graph P on k vertices, whether G contains a subgraph isomorphic to P. The restriction of this problem to planar graphs has often been considered. After…
The Path Contraction and Cycle Contraction problems take as input an undirected graph $G$ with $n$ vertices, $m$ edges and an integer $k$ and determine whether one can obtain a path or a cycle, respectively, by performing at most $k$ edge…
We study the problem of matching a string in a labeled graph. Previous research has shown that unless the Orthogonal Vectors Hypothesis (OVH) is false, one cannot solve this problem in strongly sub-quadratic time, nor index the graph in…
Reconstructing continuous signals from a small number of discrete samples is a fundamental problem across science and engineering. In practice, we are often interested in signals with 'simple' Fourier structure, such as bandlimited,…
Understanding spatial correlation is vital in many fields including epidemiology and social science. Lee, Meeks and Pettersson (Stat. Comput. 2021) recently demonstrated that improved inference for areal unit count data can be achieved by…
Problems of the following kind have been the focus of much recent research in the realm of parameterized complexity: Given an input graph (digraph) on $n$ vertices and a positive integer parameter $k$, find if there exist $k$ edges (arcs)…
An undirected graph is Eulerian if it is connected and all its vertices are of even degree. Similarly, a directed graph is Eulerian, if for each vertex its in-degree is equal to its out-degree. It is well known that Eulerian graphs can be…
We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree…
Sequence assembly from short reads is an important problem in biology. It is known that solving the sequence assembly problem exactly on a bi-directed de Bruijn graph or a string graph is intractable. However finding a Shortest Double…
How to obtain a graph from data samples is an important problem in graph signal processing. One way to formulate this graph learning problem is based on Gaussian maximum likelihood estimation, possibly under particular topology constraints.…
The basic inverse problem in spectral graph theory consists in determining the graph given its eigenvalue spectrum. In this paper, we are interested in a network of technological agents whose graph is unknown, communicating by means of a…
We study the trace reconstruction problem for spider graphs. Let $n$ be the number of nodes of a spider and $d$ be the length of each leg, and suppose that we are given independent traces of the spider from a deletion channel in which each…
This paper studies reconstruction of strings based upon their substrings spectrum. Under this paradigm, it is assumed that all substrings of some fixed length are received and the goal is to reconstruct the string. While many existing works…