相关论文: Multi-strand Reconstruction from Substrings

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 consider the problem of storing and retrieving information from synthetic DNA media. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on their collection of substrings…

DNA strings and their properties are widely studied since last 20 years due to its applications in DNA computing. In this area, one designs a set of DNA strings (called DNA code) which satisfies certain thermodynamic and combinatorial…

In the longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, and we are asked to find a longest string occurring as a fragment of both $S$ and $T$. This is a classical and well-studied…

Dominant sequence models like the Transformer represent structure implicitly through dense attention weights, incurring quadratic complexity. We propose RewriteNets, a novel neural architecture built on an alternative paradigm: explicit,…

This study develops an algorithm to solve a variation of the Shortest Common Superstring (SCS) problem. There are two modifications to the base SCS problem. First, one string in the set S is allowed to have up to K mistakes, defined as not…

In the trace reconstruction problem, one observes the output of passing a binary string $s \in \{0,1\}^n$ through a deletion channel $T$ times and wishes to recover $s$ from the resulting $T$ "traces." Most of the literature has focused on…

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 consider $(n,k,l)$ MDS codes of length $n$, dimension $k$, and subpacketization $l$ over a finite field $\mathbb{F}$. A codeword of such a code consists of $n$ column-vectors of length $l$ over $\mathbb{F}$, with the property that any…

Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…

Convolutional neural network (CNN) and its variants have led to many state-of-art results in various fields. However, a clear theoretical understanding about them is still lacking. Recently, multi-layer convolutional sparse coding (ML-CSC)…

The Shortest Superstring Problem (SSP) consists, for a set of strings S = {s_1,...,s_n}, to find a minimum length string that contains all s_i, 1 <= i <= k, as substrings. This problem is proved to be NP-Complete and APX-hard. Guaranteed…

Synthetic polymer-based storage seems to be a particularly promising candidate that could help to cope with the ever-increasing demand for archival storage requirements. It involves designing molecules of distinct masses to represent the…

In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…

\emph{Population recovery} is the problem of learning an unknown distribution over an unknown set of $n$-bit strings, given access to independent draws from the distribution that have been independently corrupted according to some noise…

Frequent pattern mining is a flagship problem in data mining. In its most basic form, it asks for the set of substrings of a given string $S$ of length $n$ that occur at least $\tau$ times in $S$, for some integer $\tau\in[1,n]$. We…

The repair problem in distributed storage addresses recovery of the data encoded using an erasure code, for instance, a Reed-Solomon (RS) code. We consider the problem of repairing a single node or multiple nodes in RS-coded storage systems…

An elastic-degenerate string is a sequence of $n$ finite sets of strings of total length $N$, introduced to represent a set of related DNA sequences, also known as a pangenome. The ED string matching (EDSM) problem consists in reporting all…

\ac{fl} proposed a distributed \ac{ml} framework where every distributed worker owns a complete copy of global model and their own data. The training is occurred locally, which assures no direct transmission of training data. However, the…

Double-strand breaks (DSBs) in DNA are naturally occurring destructive events in all organisms that may lead to genome instability. Cells employ various repair methods known as non-homologous end joining (NHEJ), microhomology mediated end…