Related papers: Fundamental Limits of Multiple Sequence Reconstruc…
We describe a method that will reconstruct an unrooted binary phylogenetic level-1 network on n taxa from the set of all quartets containing a certain fixed taxon, in O(n^3) time. We also present a more general method which can handle more…
We construct a family of linear maximally recoverable codes with locality $r$ and dimension $r+1.$ For codes of length $n$ with $r\approx n^\alpha, 0\le\alpha\le 1$ the code alphabet is of the order $n^{1+3\alpha},$ which improves upon the…
Motivated by DNA-based storage applications, we study the problem of reconstructing a coded sequence from multiple traces. We consider the model where the traces are outputs of independent deletion channels, where each channel deletes each…
In a reconfiguration problem, we are given two feasible solutions of a combinatorial problem and our goal is to determine whether it is possible to reconfigure one into the other, with the steps dictated by specific reconfiguration rules.…
We study a problem of reconstruction of connected graphs where the input gives all subsets of size k that induce a connected subgraph. Originally introduced by Bastide et al. (WG 2023) for triples ($k=3$), this problem received…
Frequent pattern mining is widely used to find ``important'' or ``interesting'' patterns in data. While it is not easy to mathematically define such patterns, maximal frequent patterns are promising candidates, as frequency is a natural…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…
Reconstructing continuous signals from a small number of discrete samples is a fundamental problem across science and engineering. In practice, we are often interested in signals with 'simple' Fourier structure, such as bandlimited,…
We introduce a new model of indeterminacy in graphs: instead of specifying all the edges of the graph, the input contains all triples of vertices that form a connected subgraph. In general, different (labelled) graphs may have the same set…
The {\em shortest common superstring} and the {\em shortest common supersequence} are two well studied problems having a wide range of applications. In this paper we consider both problems with resource constraints, denoted as the…
We analyze the fixed-angle high-energy ($\alpha' \to \infty$) structure of $n$-point tree-level string amplitudes from complementary perspectives: locally via saddle-point expansions, algebraically via difference equations and their…
We study the following question: Given are two $k$-colorings $\alpha$ and $\beta$ of a graph $G$ on $n$ vertices, and integer $\ell$. The question is whether $\alpha$ can be modified into $\beta$, by recoloring vertices one at a time, while…
In this paper, we propose {\em distributed network compression via memory}. We consider two spatially separated sources with correlated unknown source parameters. We wish to study the universal compression of a sequence of length $n$ from…
In this paper we consider the reconstruction problem on the tree for the hardcore model. We determine new bounds for the non-reconstruction regime on the k-regular tree showing non-reconstruction when lambda < (ln 2-o(1))ln^2(k)/(2 lnln(k))…
In this paper, we consider a broadcasting process in which information is propagated from a given root node on a noisy tree network, and answer the question that whether the symbols at the nth level of the tree contain non-vanishing…
Consider a finite set of sources, each producing i.i.d. observations that follow a unique probability distribution on a finite alphabet. We study the problem of matching a finite set of observed sequences to the set of sources under the…
The sequence reconstruction problem was proposed by Levenshtein in 2001. In this model, a sequence from a code is transmitted over several channels, and the decoder receives the distinct outputs from each channel. The main problem is 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 the trace reconstruction problem, an unknown bit string $x \in \{0,1\}^n$ is observed through the deletion channel, which deletes each bit of $x$ with some constant probability $q$, yielding a contracted string $\widetilde{x}$. How many…