Related papers: Sequence Reconstruction for the Single-Deletion Si…
We consider $t$-Lee-error-correcting codes of length $n$ over the residue ring $\mathbb{Z}_m := \mathbb{Z}/m\mathbb{Z}$ and determine upper and lower bounds on the number of $t$-Lee-error-correcting codes. We use two different methods,…
In distance query reconstruction, we wish to reconstruct the edge set of a hidden graph by asking as few distance queries as possible to an oracle. Given two vertices $u$ and $v$, the oracle returns the shortest path distance between $u$…
We address the inverse problem of reconstructing both the structure and dynamics of a network from mean-field measurements, which are linear combinations of node states. This setting arises in applications where only a few aggregated…
We consider the `one-shot frame synchronization problem' where a decoder wants to locate a sync pattern at the output of a channel on the basis of sequential observations. We assume that the sync pattern of length N starts being emitted at…
Codes correcting bursts of deletions and localized deletions have garnered significant research interest in recent years. One of the primary objectives is to construct codes with minimal redundancy. Currently, the best known constructions…
We introduce a new analysis technique to derive a single-letter upper bound on the mismatch capacity of a stationary, single-user, memoryless channel with a decoding metric $q$. Our bound is obtained by considering a multicast transmission…
The rapid development of DNA storage has brought the deletion and insertion channel, once again, to the front line of research. When the number of deletions is equal to the number of insertions, the Fixed Length Levenshtein (FLL) metric is…
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…
Constrained lossy source coding and channel coding with side information problems which extend the classic Wyner-Ziv and Gel'fand-Pinsker problems are considered. Inspired by applications in sensor networking and control, we first consider…
We develop several lower bounds on the capacity of binary input symmetric output channels with synchronization errors which also suffer from other types of impairments such as substitutions, erasures, additive white Gaussian noise (AWGN)…
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…
The problem of channel code design for the $M$-ary input AWGN channel with additive $Q$-ary interference where the sequence of i.i.d. interference symbols is known causally at the encoder is considered. The code design criterion at high SNR…
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…
For a given $n$, what is the smallest number $k$ such that every sequence of length $n$ is determined by the multiset of all its $k$-subsequences? This is called the $k$-deck problem for sequence reconstruction, and has been generalized to…
A recolouring sequence, between $k$-colourings $\alpha$ and $\beta$ of a graph $G$, transforms $\alpha$ into $\beta$ by recolouring one vertex at a time, such that after each recolouring step we again have a proper $k$-colouring of $G$. The…
We study the broadcasting problem when the underlying tree is a random recursive tree. The root of the tree has a random bit value assigned. Every other vertex has the same bit value as its parent with probability $1-q$ and the opposite…
The deletion channel is the simplest point-to-point communication channel that models lack of synchronization. Input bits are deleted independently with probability d, and when they are not deleted, they are not affected by the channel.…
Consider two remote nodes having binary sequences $X$ and $Y$, respectively. $Y$ is an edited version of ${X}$, where the editing involves random deletions, insertions, and substitutions, possibly in bursts. The goal is for the node with…
In this paper, we construct systematic $q$-ary two-deletion correcting codes and burst-deletion correcting codes, where $q\geq 2$ is an even integer. For two-deletion codes, our construction has redundancy $5\log n+O(\log q\log\log n)$ and…
We study the problem of aligning multiple sequences with the goal of finding an alignment that either maximizes the number of aligned symbols (the longest common subsequence (LCS)), or minimizes the number of unaligned symbols (the…