Related papers: Polynomial-time trace reconstruction in the low de…
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…
We consider the problem of correcting mass readout errors in information encoded in binary polymer strings. Our work builds on results for string reconstruction problems using composition multisets [Acharya et al., 2015] and the unique…
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…
The reduction of the fragment assembly problem to (variations of) the classical Eulerian trail problem [Pevzner et al., PNAS 2001] has led to remarkable progress in genome assembly. This reduction employs the notion of de Bruijn graph…
The problem of reconstructing strings from substring information has found many applications due to its importance in genomic data sequencing and DNA- and polymer-based data storage. One practically important and challenging paradigm…
In this paper, we investigate the problem of recovering source information from an incomplete set of network coded data. We first study the theoretical performance of such systems under maximum a posteriori (MAP) decoding and derive the…
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…
In this paper, we consider the Levenshtein's sequence reconstruction problem in the case where the transmitted codeword is chosen from $\{0,1\}^n$ and the channel can delete up to $t$ symbols from the transmitted codeword. We determine the…
In this paper, we address the problem of sampling from a set and reconstructing a set stored as a Bloom filter. To the best of our knowledge our work is the first to address this question. We introduce a novel hierarchical data structure…
We revisit the classical problem of Fourier-sparse signal reconstruction -- a variant of the \emph{Set Query} problem -- which asks to efficiently reconstruct (a subset of) a $d$-dimensional Fourier-sparse signal ($\|\hat{x}(t)\|_0 \leq…
The study of Markov processes and broadcasting on trees has deep connections to a variety of areas including statistical physics, graphical models, phylogenetic reconstruction, Markov Chain Monte Carlo, and community detection in random…
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…
We show that the problem of constructing tree-structured descriptions of data layouts that are optimal with respect to space or other criteria from given sequences of displacements, can be solved in polynomial time. The problem is relevant…
One of the difficulties of neural machine translation (NMT) is the recall and appropriate translation of low-frequency words or phrases. In this paper, we propose a simple, fast, and effective method for recalling previously seen…
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…
Motivated by the sequence reconstruction problem from traces in DNA-based storage, we consider the problem of designing codes for the deletion channel when multiple observations (or traces) are available to the decoder. We propose simple…
We study the classical problem of recovering a multidimensional source signal from observations of nonlinear mixtures of this signal. We show that this recovery is possible (up to a permutation and monotone scaling of the source's original…
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…
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…
We consider the phase retrieval problem of reconstructing a $n$-dimensional real or complex signal $\mathbf{X}^{\star}$ from $m$ (possibly noisy) observations $Y_\mu = | \sum_{i=1}^n \Phi_{\mu i} X^{\star}_i/\sqrt{n}|$, for a large class of…