51ÂÜÀò

Synchronization errors, arising from both synthesis and sequencing noise, present a fundamental challenge in DNA-based data storage systems. These errors are often modeled as insertion-deletion-substitution (IDS) channels, for which maximum-likelihood decoding is quite computationally expensive. In this work, we propose a data-driven approach based on neural polar decoders (NPDs) to design decoders with reduced complexity for channels with synchronization errors.

As a potential implementation of data storage using DNA molecules, multiple strands of DNA are stored unordered in a liquid container. When the data are needed, an array of DNA readers will sample the strands with replacement, producing a Poisson-distributed number of noisy reads for each strand. The primary challenge here is to design an algorithm that reconstructs data from these unsorted, repetitive, and noisy reads.

An m-uniform quantum state on n qubits is an entangled state in which every m-qubit subsystem is maximally mixed. Starting with an m-uniform state realized as the graph state associated with an m-regular graph, and a classical n,k,d≥m+1 binary linear code with certain additional properties, we show that pure [n,k,m+1]]2 quantum error-correcting codes (QECCs) can be constructed within the codeword stabilized (CWS) code framework. As illustrations, we construct pure [[22r-1,22r-2r-3,3]]2 and [[(24r-1)2,(24r-1)2-32r-7,5]]2 QECCs.

The standard approach to universal fault-tolerant quantum computing is to develop a general purpose quantum error correction mechanism that can implement a universal set of logical gates fault-tolerantly. Given such a scheme, any quantum algorithm can be realized fault-tolerantly by composing the relevant logical gates from this set. However, we know that quantum computers provide a significant quantum advantage only for specific quantum algorithms.

The number of degrees of freedom (NDoF) in a communication channel fundamentally limits the number of independent spatial modes available for transmitting and receiving information. Although the NDoF can be computed numerically for specific configurations using singular value decomposition (SVD) of the channel operator, this approach provides limited physical insight. In this paper, we introduce a simple analytical estimate for the NDoF between arbitrarily shaped transmitter and receiver regions in free space.

We consider a molecular channel, in which messages are encoded to the frequency of objects in a pool, and whose output during reading time is a noisy version of the input frequencies, as obtained by sampling with replacement from the pool. Motivated by recent DNA storage techniques, we focus on the regime in which the input resolution is unlimited.

This paper studies achievable rates of nanopore-based DNA storage when nanopore signals are decoded using a tractable channel model that does not rely on a basecalling algorithm. Specifically, the noisy nanopore channel (NNC) with the Scrappie pore model generates average output levels via i.i.d. geometric sample duplications corrupted by i.i.d. Gaussian noise (NNC-Scrappie). Simplified message passing algorithms are derived for efficient soft decoding of nanopore signals using NNC-Scrappie.

In this paper, we consider a recent channel model of a nanopore sequencer proposed by McBain, Viterbo, and Saunderson (2024), termed the noisy nanopore channel (NNC). In essence, an NNC is a duplication channel with structured, Markov inputs, that is corrupted by memoryless noise. We first discuss a (tight) lower bound on the capacity of the NNC in the absence of random noise. Next, we present lower and upper bounds on the channel capacity of general noisy nanopore channels.

The central problem in sequence reconstruction is to find the minimum number of distinct channel outputs required to uniquely reconstruct the transmitted sequence. According to Levenshtein’s work in 2001, this number is determined by the size of the maximum intersection between the error balls of any two distinct input sequences of the channel. In this work, we study the sequence reconstruction problem for the q-ary single-deletion single-substitution channel for any fixed integer q≥2.

In DNA sequencing, we often need to infer an unknown sequence from a collection of its corrupted copies. Each copy cannot faithfully tell the truth due to DNA fragmentation, point mutations, and measurement errors. The theoretical guarantee of unique reconstruction is thus of concern. This motivated the study of sequence reconstruction problems three decades ago. Recently, synthetic DNA has been regarded as an ultra-dense data storage medium. Sequence reconstruction is a crucial step in achieving reliable and efficient data readout.