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In recent years several compressed indexes based on variants of the Burrows-Wheeler transformation have been introduced. Some of these index structures far more complex than a single string, as was originally done with the FM-index…
Branchwidth determines how graphs, and more generally, arbitrary connectivity (basically symmetric and submodular) functions could be decomposed into a tree-like structure by specific cuts. We develop a general framework for designing…
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 network embedding problem that maps nodes in a graph to vectors in Euclidean space can be very useful for addressing several important tasks on a graph. Recently, graph neural networks (GNNs) have been proposed for solving such a…
A reassembling of a simple graph G = (V,E) is an abstraction of a problem arising in earlier studies of network analysis. There are several equivalent definitions of graph reassembling; in this report we use a definition which makes it…
We initiate the study of computational problems on $k$-mers (strings of length $k$) in labeled graphs. As a starting point, we consider the problem of counting the number of distinct $k$-mers found on the walks of a graph. We establish that…
Nowadays, deep learning is widely applied to extract features for similarity computation in person re-identification (re-ID) and have achieved great success. However, due to the non-overlapping between training and testing IDs, the…
In distance query reconstruction, we wish to reconstruct the edge set of a hidden graph by asking as few distance queries as possible to an oracle. Given two vertices $u$ and $v$, the oracle returns the shortest path distance between $u$…
Let $G=(V,E)$ and $H$ be two graphs. Packing problem is to find in $G$ the largest number of independent subgraphs each of which is isomorphic to $H$. Let $U\subset{V}$. If the graph $G-U$ has no subgraph isomorphic to $H$, $U$ is a cover…
The problem of subgraph counting asks for the number of occurrences of a pattern graph $H$ as a subgraph of a host graph $G$ and is known to be computationally challenging: it is $\#W[1]$-hard even when $H$ is restricted to simple…
We revisit the algorithmic problem of reconstructing a graph from homomorphism counts that has first been studied in (B\"oker et al., STACS 2024): given graphs $F_1,\ldots,F_k$ and counts $m_1,\ldots,m_k$, decide if there is a graph $G$…
Disjoint paths problems are among the most prominent problems in combinatorial optimization. The edge- as well as vertex-disjoint paths problem, are NP-complete on directed and undirected graphs. But on undirected graphs, Robertson and…
Trace reconstruction considers the task of recovering an unknown string $x \in \{0,1\}^n$ given a number of independent "traces", i.e., subsequences of $x$ obtained by randomly and independently deleting every symbol of $x$ with some…
The transversal hypergraph problem is the task of enumerating the minimal hitting sets of a hypergraph. It is a long-standing open question whether this can be done in output-polynomial time. For hypergraphs whose solutions have bounded…
In the standard trace reconstruction problem, the goal is to \emph{exactly} reconstruct an unknown source string $\mathsf{x} \in \{0,1\}^n$ from independent "traces", which are copies of $\mathsf{x}$ that have been corrupted by a…
Motivation: Second generation sequencing technology makes it feasible for many researches to obtain enough sequence reads to attempt the de novo assembly of higher eukaryotes (including mammals). De novo assembly not only provides a tool…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
We consider the problem of reconstructing an undirected graph $G$ on $n$ vertices given multiple random noisy subgraphs or "traces". Specifically, a trace is generated by sampling each vertex with probability $p_v$, then taking the…
In recent years, graph neural networks (GNN) have achieved significant developments in a variety of graph analytical tasks. Nevertheless, GNN's superior performance will suffer from serious damage when the collected node features or…
In the trace reconstruction problem our goal is to learn an unknown string $x\in \{0,1\}^n$ given independent traces of $x$. A trace is obtained by independently deleting each bit of $x$ with some probability $\delta$ and concatenating the…