Related papers: Reconstructing Sets of Strings from Their k-way Pr…
Tree trace reconstruction aims to learn the binary node labels of a tree, given independent samples of the tree passed through an appropriately defined deletion channel. In recent work, Davies, R\'acz, and Rashtchian used combinatorial…
We study an issue commonly seen with graph data analysis: many real-world complex systems involving high-order interactions are best encoded by hypergraphs; however, their datasets often end up being published or studied only in the form of…
The notion of degree-constrained spanning hierarchies, also called k-trails, was recently introduced in the context of network routing problems. They describe graphs that are homomorphic images of connected graphs of degree at most k. First…
String matching is the problem of deciding whether a given $n$-bit string contains a given $k$-bit pattern. We study the complexity of this problem in three settings. Communication complexity. For small $k$, we provide near-optimal upper…
Motivated by applications in polymer-based data storage, we study the problem of reconstructing a string from part of its composition multiset. We give a full description of the structure of the strings that cannot be uniquely reconstructed…
Data processing has to deal with many practical difficulties. Data is often corrupted by artifacts or noise and acquiring data can be expensive and difficult. Thus, the given data is often incomplete and inaccurate. To overcome these…
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…
This paper deals with developing techniques for the reconstruction of high-dimensional datasets given each bivariate projection, as would be found in a matrix scatterplot. A graph-based solution is introduced, involving clique-finding,…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
The problem of reconstructing a sequence from the set of its length-$k$ substrings has received considerable attention due to its various applications in genomics. We study an uncoded version of this problem where multiple random sources…
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 investigate the structure and reconstruction complexity of Manacher arrays. First, we establish a combinatorial lower bound, proving that the number of rooted tandem repeat trees with $n+1$ genes exceeds the number of distinct Manacher…
We introduce in a general setting a dynamic programming method for solving reconfiguration problems. Our method is based on contracted solution graphs, which are obtained from solution graphs by performing an appropriate series of edge…
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…
Graph reconstruction can efficiently detect the underlying topology of massive networks such as the Internet. Given a query oracle and a set of nodes, the goal is to obtain the edge set by performing as few queries as possible. An algorithm…
Hypertree decompositions of hypergraphs are a generalization of tree decompositions of graphs. The corresponding hypertree-width is a measure for the cyclicity and therefore tractability of the encoded computation problem. Many NP-hard…
Most of the fastest-growing string collections today are repetitive, that is, most of the constituent documents are similar to many others. As these collections keep growing, a key approach to handling them is to exploit their…
We present a series of almost settled inapproximability results for three fundamental problems. The first in our series is the subexponential-time inapproximability of the maximum independent set problem, a question studied in the area of…
It is known that problems like Vertex Cover, Feedback Vertex Set and Odd Cycle Transversal are polynomial time solvable in the class of chordal graphs. We consider these problems in a graph that has at most $k$ vertices whose deletion…
Combinatorial optimization lies at the core of many real-world problems. Especially since the rise of graph neural networks (GNNs), the deep learning community has been developing solvers that derive solutions to NP-hard problems by…