IEEE journal on selected areas in information theory最新文献

Geno-Weaving: A Framework for Low-Complexity Capacity-Achieving DNA Data Storage 基因编织：低复杂度的DNA数据存储框架

IF 2.2

IEEE journal on selected areas in information theory Pub Date : 2025-09-16 DOI: 10.1109/JSAIT.2025.3610643

Hsin-Po Wang;Venkatesan Guruswami

{"title":"Geno-Weaving: A Framework for Low-Complexity Capacity-Achieving DNA Data Storage","authors":"Hsin-Po Wang;Venkatesan Guruswami","doi":"10.1109/JSAIT.2025.3610643","DOIUrl":"https://doi.org/10.1109/JSAIT.2025.3610643","url":null,"abstract":"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. In this paper, we lay down a capacity-achieving rateless code along each strand to encode its index; we then lay down a capacity-achieving block code at the same position across all strands to protect the data. These codes weave a low-complexity storage scheme that saturates the fundamental upper limit of DNA. This improves upon the previous work of Weinberger and Merhav, which proves said bound and uses high-complexity random codes to saturate the limit. Our scheme also differs from other concatenation-based implementations of DNA data storage in the sense that, instead of decoding the inner codes first and passing the results to the outer code, our decoder alternates between the rateless codes and the block codes.","PeriodicalId":73295,"journal":{"name":"IEEE journal on selected areas in information theory","volume":"6 ","pages":"383-393"},"PeriodicalIF":2.2,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145315409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Tailoring Fault-Tolerance to Quantum Algorithms 裁剪对量子算法的容错

IF 2.2

IEEE journal on selected areas in information theory Pub Date : 2025-08-25 DOI: 10.1109/JSAIT.2025.3602446

Zhuangzhuang Chen;Narayanan Rengaswamy

{"title":"Tailoring Fault-Tolerance to Quantum Algorithms","authors":"Zhuangzhuang Chen;Narayanan Rengaswamy","doi":"10.1109/JSAIT.2025.3602446","DOIUrl":"https://doi.org/10.1109/JSAIT.2025.3602446","url":null,"abstract":"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. Hence, a universal quantum computer can likely gain from compiling such specific algorithms using tailored quantum error correction schemes. In this work, we take the first steps towards such algorithm-tailored quantum fault-tolerance. We consider Trotter circuits in quantum simulation, which is an important application of quantum computing. We develop a solve-and-stitch algorithm to systematically synthesize physical realizations of Clifford Trotter circuits on the well-known <inline-formula> <tex-math>$[![n,n-2,2]!]$ </tex-math></inline-formula> error-detecting code family. Our analysis shows that this family implements Trotter circuits with essentially optimal depth under reasonable assumptions, thereby serving as an illuminating example of tailored quantum error correction. We achieve fault-tolerance for these circuits using flag gadgets, which add minimal overhead. Importantly, the solve-and-stitch algorithm has the potential to scale beyond this specific example, as illustrated by a generalization to the four-qubit logical Clifford Trotter circuit on the <inline-formula> <tex-math>$[![{ 20,4,2 }]!] $ </tex-math></inline-formula> hypergraph product code, thereby providing a principled approach to tailored fault-tolerance in quantum computing.","PeriodicalId":73295,"journal":{"name":"IEEE journal on selected areas in information theory","volume":"6 ","pages":"311-324"},"PeriodicalIF":2.2,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144998382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Codeword Stabilized Codes From m-Uniform Graph States m-一致图状态的码字稳定码

IF 2.2

IEEE journal on selected areas in information theory Pub Date : 2025-08-25 DOI: 10.1109/JSAIT.2025.3602744

Sowrabh Sudevan;Sourin Das;Thamadathil Aswanth;Nupur Patanker;Navin Kashyap

引用次数: 0

Shadow Area and Degrees of Freedom for Free-Space Communication 自由空间通信的阴影面积和自由度

IF 2.2

IEEE journal on selected areas in information theory Pub Date : 2025-08-19 DOI: 10.1109/JSAIT.2025.3600363

Mats Gustafsson

{"title":"Shadow Area and Degrees of Freedom for Free-Space Communication","authors":"Mats Gustafsson","doi":"10.1109/JSAIT.2025.3600363","DOIUrl":"https://doi.org/10.1109/JSAIT.2025.3600363","url":null,"abstract":"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. In the electrically large limit, where the NDoF is high, it is well approximated by the mutual shadow area, measured in units of wavelength squared. This area corresponds to the projected overlap of the regions, integrated over all lines of sight, and captures their effective spatial coupling. The proposed estimate generalizes and unifies several previously established results, including those based on Weyl’s law, shadow area, and the paraxial approximation. We analyze several example configurations to illustrate the accuracy of the estimate and validate it through comparisons with numerical SVD computations of the propagation channel. The results provide both practical tools and physical insight for the design and analysis of high-capacity communication and sensing systems.","PeriodicalId":73295,"journal":{"name":"IEEE journal on selected areas in information theory","volume":"6 ","pages":"325-337"},"PeriodicalIF":2.2,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145110296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Achievable Rates and Error Probability Bounds of Frequency-Based Channels of Unlimited Input Resolution 无限输入分辨率下基于频率信道的可达率和误差概率界限

IF 2.2

IEEE journal on selected areas in information theory Pub Date : 2025-08-18 DOI: 10.1109/JSAIT.2025.3599794

Ran Tamir;Nir Weinberger

引用次数: 0

Achievable Rates of Nanopore-Based DNA Storage 基于纳米孔的DNA存储的可实现速率

IF 2.2

IEEE journal on selected areas in information theory Pub Date : 2025-08-14 DOI: 10.1109/JSAIT.2025.3598756

Brendon McBain;Emanuele Viterbo

{"title":"Achievable Rates of Nanopore-Based DNA Storage","authors":"Brendon McBain;Emanuele Viterbo","doi":"10.1109/JSAIT.2025.3598756","DOIUrl":"https://doi.org/10.1109/JSAIT.2025.3598756","url":null,"abstract":"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. Previously, evaluation of this channel model was limited by the lack of DNA storage datasets with nanopore signals included. This is solved by deriving an achievable rate based on the dynamic time-warping (DTW) algorithm that can be applied to genomic sequencing datasets subject to constraints that make the resulting rate applicable to DNA storage. Using a publicly-available dataset from Oxford Nanopore Technologies (ONT), it is demonstrated that coding over multiple DNA strands of 100 bases in length and decoding with the NNC-Scrappie decoder can achieve rates of at least <inline-formula> <tex-math>$0.64-1.18$ </tex-math></inline-formula> bits per base, depending on the channel quality of the nanopore that is chosen in the sequencing device per channel-use, and 0.96 bits per base on average assuming uniformly chosen nanopores. These rates are pessimistic since they only apply to single reads and do not include calibration of the pore model to specific nanopores.","PeriodicalId":73295,"journal":{"name":"IEEE journal on selected areas in information theory","volume":"6 ","pages":"261-269"},"PeriodicalIF":2.2,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144926889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

On Achievable Rates Over Noisy Nanopore Channels 噪声纳米孔通道上可实现的速率

IF 2.2

IEEE journal on selected areas in information theory Pub Date : 2025-08-14 DOI: 10.1109/JSAIT.2025.3598773

V. Arvind Rameshwar;Nir Weinberger

引用次数: 0

Sequence Reconstruction for the Single-Deletion Single-Substitution Channel 单缺失单替换通道的序列重建

IF 2.2

IEEE journal on selected areas in information theory Pub Date : 2025-08-08 DOI: 10.1109/JSAIT.2025.3597013

Wentu Song;Kui Cai;Tony Q. S. Quek

{"title":"Sequence Reconstruction for the Single-Deletion Single-Substitution Channel","authors":"Wentu Song;Kui Cai;Tony Q. S. Quek","doi":"10.1109/JSAIT.2025.3597013","DOIUrl":"https://doi.org/10.1109/JSAIT.2025.3597013","url":null,"abstract":"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 <inline-formula> <tex-math>$qgeq 2$ </tex-math></inline-formula>. First, we prove that if two q-ary sequences of length n have a Hamming distance <inline-formula> <tex-math>$dgeq 2$ </tex-math></inline-formula>, then the intersection size of their error balls is upper bounded by <inline-formula> <tex-math>$2qn-3q-2-delta _{q,2}$ </tex-math></inline-formula>, where <inline-formula> <tex-math>$delta _{i,j}$ </tex-math></inline-formula> is the Kronecker delta, and this bound is achievable. Next, we prove that if two q-ary sequences have a Hamming distance <inline-formula> <tex-math>$dgeq 3$ </tex-math></inline-formula> and a Levenshtein distance <inline-formula> <tex-math>$d_{text {L}}geq 2$ </tex-math></inline-formula>, then the intersection size of their error balls is upper bounded by <inline-formula> <tex-math>$3q+11$ </tex-math></inline-formula>, and we show that the gap between this bound and the tight bound is at most 2.","PeriodicalId":73295,"journal":{"name":"IEEE journal on selected areas in information theory","volume":"6 ","pages":"232-247"},"PeriodicalIF":2.2,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144914375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Survey of Sequence Reconstruction Problems and Their Applications in DNA-Based Storage 序列重建问题及其在dna存储中的应用综述

IF 2.2

IEEE journal on selected areas in information theory Pub Date : 2025-08-04 DOI: 10.1109/JSAIT.2025.3595457

Yaoyu Yang

引用次数: 0

Input Optimization in the Composite DNA Storage Channel 复合DNA存储通道的输入优化

IF 2.2

IEEE journal on selected areas in information theory Pub Date : 2025-08-01 DOI: 10.1109/JSAIT.2025.3595005

Adir Kobovich;Nir Weinberger

引用次数: 0