Related papers: Trace reconstruction with varying deletion probabi…
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,…
In the random deletion channel, each bit is deleted independently with probability $p$. For the random deletion channel, the existence of codes of rate $(1-p)/9$, and thus bounded away from $0$ for any $p < 1$, has been known. We give an…
A $k$-deck of a (coloured) graph is a multiset of its induced $k$-vertex subgraphs. Given a graph $G$, when is it possible to reconstruct with high probability a uniformly random colouring of its vertices in $r$ colours from its $k$-deck?…
This paper considers the model problem of reconstructing an object from incomplete frequency samples. Consider a discrete-time signal $f \in \C^N$ and a randomly chosen set of frequencies $\Omega$ of mean size $\tau N$. Is it possible to…
Let $\mathcal{B}(\cdot)$ be an error ball function. A set of $q$-ary sequences of length $n$ is referred to as an \emph{$(n,q,N;\mathcal{B})$-reconstruction code} if each sequence $\boldsymbol{x}$ within this set can be uniquely…
This paper considers a problem that relates to the theories of covering arrays, permutation patterns, Vapnik-Chervonenkis (VC) classes, and probability thresholds. Specifically, we want to find the number of subsets of [n]:={1,2,....,n} we…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for unique string…
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…
We study here the so called subsequence pattern matching also known as hidden pattern matching in which one searches for a given pattern $w$ of length $m$ as a subsequence in a random text of length $n$. The quantity of interest is the…
We introduce the problem of reconstructing a sequence of multidimensional real vectors where some of the data are missing. This problem contains regression and mapping inversion as particular cases where the pattern of missing data is…
We consider the zero-error capacity of deletion channels. Specifically, we consider the setting where we choose a codebook ${\cal C}$ consisting of strings of $n$ bits, and our model of the channel corresponds to an adversary who may delete…
Suppose a graph $G$ is stochastically created by uniformly sampling vertices along a line segment and connecting each pair of vertices with a probability that is a known decreasing function of their distance. We ask if it is possible to…
The network inference problem consists of reconstructing the edge set of a network given traces representing the chronology of infection times as epidemics spread through the network. This problem is a paradigmatic representative of…
We consider rate R = k/n causal linear codes that map a sequence of k-dimensional binary vectors {b_t} to a sequence of n-dimensional binary vectors {c_t}, such that each c_t is a function of {b_1,b_2,...,b_t}. Such a code is called anytime…
In this paper we show a polar coding scheme for the deletion channel with a probability of error that decays roughly like $2^{-\sqrt{\Lambda}}$, where $\Lambda$ is the length of the codeword. That is, the same decay rate as that of seminal…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Motivation: Word-based or `alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input…
We consider the maximum coding rate achievable by uniformly-random codes for the deletion channel. We prove an upper bound that's within 0.1 of the best known lower bounds for all values of the deletion probability $d,$ and much closer for…
This paper studies the problem of reconstructing binary matrices that are only accessible through few evaluations of their discrete X-rays. Such question is prominently motivated by the demand in material science for developing a tool for…
We consider upper bounds on the error probability in channel coding. We derive an improved maximum-likelihood union bound, which takes into account events where the likelihood of the correct codeword is tied with that of some competitors.…