相关论文: Incorporating indel channels into average-case ana…

Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…

A seed in a word is a relaxed version of a period in which the occurrences of the repeating subword may overlap. We show a linear-time algorithm computing a linear-size representation of all the seeds of a word (the number of seeds might be…

In the beautifully simple-to-state problem of trace reconstruction, the goal is to reconstruct an unknown binary string $x$ given random "traces" of $x$ where each trace is generated by deleting each coordinate of $x$ independently with…

We show that the edit distance between two run-length encoded strings of compressed lengths $m$ and $n$ respectively, can be computed in $\mathcal{O}(mn\log(mn))$ time. This improves the previous record by a factor of…

Quantum communication enables the implementation of tasks that are unachievable with classical resources. However, losses on the communication channel preclude the direct long-distance transmission of quantum information in many relevant…

We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem…

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…

We revisit the classic combinatorial pattern matching problem of finding a longest common subsequence (LCS). For strings $x$ and $y$ of length $n$, a textbook algorithm solves LCS in time $O(n^2)$, but although much effort has been spent,…

In this paper, we derive an expression for the expected number of runs in a trace of a binary sequence $x \in \{0,1\}^n$ obtained by passing $x$ through a deletion channel that independently deletes each bit with probability $q$. We use…

The linear complexity of a sequence $s$ is one of the measures of its predictability. It represents the smallest degree of a linear recursion which the sequence satisfies. There are several algorithms to find the linear complexity of a…

An added edge to a graph is called an inset edge. Predicting k inset edges which minimize the average distance of a graph is known to be NP-Hard. When k = 1 the complexity of the problem is polynomial. In this paper, we further find the…

This work studies problems in data reconstruction, an important area with numerous applications. In particular, we examine the reconstruction of binary and non-binary sequences from synchronization (insertion/deletion-correcting) codes.…

The reliance of organisations on computer networks is enabled by network programmability, which is typically achieved through Service Function Chaining. These chains virtualise network functions, link them, and programmatically embed them…

Since the introduction of retroactive data structures at SODA 2004, a major unsolved problem has been to bound the gap between the best partially retroactive data structure (where changes can be made to the past, but only the present can be…

We show an $\widetilde{O}(m^{1.5} \epsilon^{-1})$ time algorithm that on a graph with $m$ edges and $n$ vertices outputs its spanning tree count up to a multiplicative $(1+\epsilon)$ factor with high probability, improving on the previous…

In the \emph{$k$-Diameter-Optimally Augmenting Tree Problem} we are given a tree $T$ of $n$ vertices as input. The tree is embedded in an unknown \emph{metric} space and we have unlimited access to an oracle that, given two distinct…

An indel refers to a single insertion or deletion, while an edit refers to a single insertion, deletion or substitution. In this paper, we investigate codes that combat either a single indel or a single edit and provide linear-time…

One of the primary sequencing methods gaining prominence in DNA storage is nanopore sequencing, attributed to various factors. In this work, we consider a simplified model of the sequencer, characterized as a channel. This channel takes a…

An addition chain for $n$ is defined to be a sequence $(a_0,a_1,\ldots,a_r)$ such that $a_0=1$, $a_r=n$, and, for any $1\le k\le r$, there exist $0\le i, j<k$ such that $a_k = a_i + a_j$; the number $r$ is called the length of the addition…

We study the distribution of maximal-chain lengths between two elements of a causal set and its relationship with the embeddability of the causal set in a region of flat spacetime. We start with causal sets obtained from uniformly…