Related papers: Fundamental Limits of Multiple Sequence Reconstruc…
Network reconstruction is the first step towards understanding, diagnosing and controlling the dynamics of complex networked systems. It allows us to infer properties of the interaction matrix, which characterizes how nodes in a system…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
\emph{Population recovery} is the problem of learning an unknown distribution over an unknown set of $n$-bit strings, given access to independent draws from the distribution that have been independently corrupted according to some noise…
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…
Recovery sets for vectors and subspaces are important in the construction of distributed storage system codes. These concepts are also interesting in their own right. In this paper, we consider the following very basic recovery question:…
We study the maximum multiplicity $\mathcal{M}(k,n)$ of a simple transposition $s_k=(k \: k+1)$ in a reduced word for the longest permutation $w_0=n \: n-1 \: \cdots \: 2 \: 1$, a problem closely related to much previous work on sorting…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
Reconstructing weighted networks from partial information is necessary in many important circumstances, e.g. for a correct estimation of systemic risk. It has been shown that, in order to achieve an accurate reconstruction, it is crucial to…
The problem of storing large amounts of information safely for a long period of time has become essential. One of the most promising new data storage mediums are the polymer-based data storage systems, like the DNA-storage system. These…
The reconstruction problem for permutations on $n$ elements from their erroneous patterns which are distorted by transpositions is presented in this paper. It is shown that for any $n \geq 3$ an unknown permutation is uniquely…
An early paper by Rashmi et. al. presented the construction of an $(n,k,d=n-1)$ MBR regenerating code featuring the inherent double replication of all code symbols and repair-by-transfer (RBT), both of which are important in practice. We…
We explore the mathematical and numerical aspects of reconstructing a potential energy profile of a molecular bond from its rupture time distribution. While reliable reconstruction of gross attributes, such as the height and the width of an…
Maximal repetition of a string is the maximal length of a repeated substring. This paper investigates maximal repetition of strings drawn from stochastic processes. Strengthening previous results, two new bounds for the almost sure growth…
Frequent pattern mining is a flagship problem in data mining. In its most basic form, it asks for the set of substrings of a given string $S$ of length $n$ that occur at least $\tau$ times in $S$, for some integer $\tau\in[1,n]$. We…
Reconstructing training data from trained neural networks is an active area of research with significant implications for privacy and explainability. Recent advances have demonstrated the feasibility of this process for several data types.…
In this paper we study the structure of specific linear codes called DNA codes. The first attempts on studying such codes have been proposed over four element rings which are naturally matched with DNA four letters. Later, double (pair) DNA…
The $k$-colouring reconfiguration problem asks whether, for a given graph $G$, two proper $k$-colourings $\alpha$ and $\beta$ of $G$, and a positive integer $\ell$, there exists a sequence of at most $\ell+1$ proper $k$-colourings of $G$…
We study the tandem duplication distance between binary sequences and their roots. In other words, the quantity of interest is the number of tandem duplication operations of the form $\seq x = \seq a \seq b \seq c \to \seq y = \seq a \seq b…
A (tandem) duplication of length $ k $ is an insertion of an exact copy of a substring of length $ k $ next to its original position. This and related types of impairments are of relevance in modeling communication in the presence of…
This work is motivated by the problem of error correction in bit-shift channels with the so-called $ (d,k) $ input constraints (where successive $ 1 $'s are required to be separated by at least $ d $ and at most $ k $ zeros, $ 0 \leq d < k…