相关论文: Incorporating indel channels into average-case ana…
Given a sequence of integers, we want to find a longest increasing subsequence of the sequence. It is known that this problem can be solved in $O(n \log n)$ time and space. Our goal in this paper is to reduce the space consumption while…
The coded trace reconstruction problem asks to construct a code $C\subset \{0,1\}^n$ such that any $x\in C$ is recoverable from independent outputs ("traces") of $x$ from a binary deletion channel (BDC). We present binary codes of rate…
An orientable sequence of order $n$ is a cyclic binary sequence such that each length-$n$ substring appears at most once \emph{in either direction}. Maximal length orientable sequences are known only for $n\leq 7$, and a trivial upper bound…
The sequence reconstruction problem involves a model where a sequence is transmitted over several identical channels. This model investigates the minimum number of channels required for the unique reconstruction of the transmitted sequence.…
In the particular case we have insertions/deletions at the tail of a given set S of $n$ one-dimensional elements, we present a simpler and more concrete algorithm than that presented in [Anderson, 2007] achieving the same (but also…
Recent advances in DNA sequencing technology and DNA storage systems have rekindled the interest in deletion channels. Multiple recent works have looked at variants of sequence reconstruction over a single and over multiple deletion…
A new converse bound is presented for the two-user multiple-access channel under the average probability of error constraint. This bound shows that for most channels of interest, the second-order coding rate -- that is, the difference…
We study the Stochastic Shortest Path (SSP) problem with a linear mixture transition kernel, where an agent repeatedly interacts with a stochastic environment and seeks to reach certain goal state while minimizing the cumulative cost.…
Information spreads across social and technological networks, but often the network structures are hidden from us and we only observe the traces left by the diffusion processes, called cascades. Can we recover the hidden network structures…
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…
Various optimality properties of universal sequence predictors based on Bayes-mixtures in general, and Solomonoff's prediction scheme in particular, will be studied. The probability of observing $x_t$ at time $t$, given past observations…
Channels with synchronization errors, exhibiting deletion and insertion errors, find practical applications in DNA storage, data reconstruction, and various other domains. Presence of insertions and deletions render the channel with memory,…
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…
Mean-based reconstruction is a fundamental, natural approach to worst-case trace reconstruction over channels with synchronization errors. It is known that $\exp(O(n^{1/3}))$ traces are necessary and sufficient for mean-based worst-case…
Given access to the vertex set $V$ of a connected graph $G=(V,E)$ and an oracle that given two vertices $u,v\in V$, returns the shortest path distance between $u$ and $v$, how many queries are needed to reconstruct $E$? Firstly, we show…
The problem of reconstructing a sequence from the set of its length-$k$ substrings has received considerable attention due to its various applications in genomics. We study an uncoded version of this problem where multiple random sources…
We give a greedy learning algorithm for reconstructing an evolutionary tree based on a certain harmonic average on triplets of terminal taxa. After the pairwise distances between terminal taxa are estimated from sequence data, the algorithm…
Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider…
When nodes can repeatedly update their behavior (as in agent-based models from computational social science or repeated-game play settings) the problem of optimal network seeding becomes very complex. For a popular spreading-phenomena model…
Recently we presented the first algorithm for maintaining the set of nodes reachable from a source node in a directed graph that is modified by edge deletions with $o(mn)$ total update time, where $m$ is the number of edges and $n$ is the…