The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication scenario where the sender transmits a codeword from some codebook and the receiver obtains multiple noisy reads of the codeword. The common setup assumes the codebook to be the entire space and the problem is to determine the minimum number of distinct reads that is required to reconstruct the transmitted codeword.
Motivated by modern storage devices, we study a variant of the problem where the number of noisy reads $N$ is fixed. Specifically, we design reconstruction codes that reconstruct a codeword from $N$ distinct noisy reads. We focus on channels that introduce single edit error (i.e. a single substitution, insertion, or deletion) and their variants, and design reconstruction codes for all values of $N$. In particular, for the case of a single edit, we show that as the number of noisy reads increases, the number of redundant bits required can be gracefully reduced from $\log n+O(1)$ to $\log \log n+O(1)$, and then to $O(1)$, where $n$ denotes the length of a codeword. We also show that the redundancy of certain reconstruction codes is within one bit of optimality.
This paper considers insertion and deletion channels with the additional assumption that the channel input sequence is implicitly divided into segments such that at most one edit can occur within a segment. No segment markers are available in the received sequence. We propose code constructions for the segmented deletion, segmented insertion, and segmented insertion-deletion channels based on subsets of Varshamov-Tenengolts codes chosen with pre-determined prefixes and/or suffixes. The proposed codes, constructed for any finite alphabet, are zero-error and can be decoded segment-by-segment. We…
Motivated by the sequence reconstruction problem initiated by Levenshtein, reconstruction codes were introduced by Cai \emph{et al}. to combat errors when a fixed number of noisy channels are available. The central problem on this topic is to design codes with sizes as large as possible, such that every codeword can be uniquely reconstructed from any $N$ distinct noisy reads, where $N$ is fixed. In this paper, we study binary reconstruction codes with the constraint that every codeword is balanced, which is a common requirement in the technique of DNA-based storage. For all possible channels w…
A malleable coding scheme considers not only compression efficiency but also the ease of alteration, thus encouraging some form of recycling of an old compressed version in the formation of a new one. Malleability cost is the difficulty of synchronizing compressed versions, and malleable codes are of particular interest when representing information and modifying the representation are both expensive. We examine the trade-off between compression efficiency and malleability cost under a malleability metric defined with respect to a string edit distance. This problem introduces a metric topology…
Constrained lossy source coding and channel coding with side information problems which extend the classic Wyner-Ziv and Gel'fand-Pinsker problems are considered. Inspired by applications in sensor networking and control, we first consider lossy source coding with two-sided partial side information where the quality/availability of the side information can be influenced by a cost-constrained action sequence. A decoder reconstructs a source sequence subject to the distortion constraint, and at the same time, an encoder is additionally required to be able to estimate the decoder's reconstruction…
Consider a pair of correlated Gaussian sources (X1,X2). Two separate encoders observe the two components and communicate compressed versions of their observations to a common decoder. The decoder is interested in reconstructing a linear combination of X1 and X2 to within a mean-square distortion of D. We obtain an inner bound to the optimal rate-distortion region for this problem. A portion of this inner bound is achieved by a scheme that reconstructs the linear function directly rather than reconstructing the individual components X1 and X2 first. This results in a better rate region for cert…
We consider the problem of lossy source coding with side information under a privacy constraint that the reconstruction sequence at a decoder should be kept secret to a certain extent from another terminal such as an eavesdropper, a sender, or a helper. We are interested in how the reconstruction privacy constraint at a particular terminal affects the rate-distortion tradeoff. In this work, we allow the decoder to use a random mapping, and give inner and outer bounds to the rate-distortion-equivocation region for different cases where the side information is available non-causally and causally…
The trace reconstruction problem studies the number of noisy samples needed to recover an unknown string $\boldsymbol{x}\in\{0,1\}^n$ with high probability, where the samples are independently obtained by passing $\boldsymbol{x}$ through a random deletion channel with deletion probability $q$. The problem is receiving significant attention recently due to its applications in DNA sequencing and DNA storage. Yet, there is still an exponential gap between upper and lower bounds for the trace reconstruction problem. In this paper we study the trace reconstruction problem when $\boldsymbol{x}$ is c…
Motivated by DNA-based storage applications, we study the problem of reconstructing a coded sequence from multiple traces. We consider the model where the traces are outputs of independent deletion channels, where each channel deletes each bit of the input codeword \(\mathbf{x} \in \{0,1\}^n\) independently with probability \(p\). We focus on the regime where the deletion probability \(p \to 0\) when \(n\to \infty\). Our main contribution is designing a novel code for trace reconstruction that allows reconstructing a coded sequence efficiently from a constant number of traces. We provide theor…
We present the problem of two-terminal source coding with Common Sum Reconstruction (CSR). Consider two terminals, each with access to one of two correlated sources. Both terminals want to reconstruct the sum of the two sources under some average distortion constraint, and the reconstructions at two terminals must be identical with high probability. In this paper, we develop inner and outer bounds to the achievable rate distortion region of the CSR problem for a doubly symmetric binary source. We employ existing achievability results for Steinberg's common reconstruction and Wyner-Ziv's source…
We study the problem of the reconstruction of a Gaussian field defined in [0,1] using N sensors deployed at regular intervals. The goal is to quantify the total data rate required for the reconstruction of the field with a given mean square distortion. We consider a class of two-stage mechanisms which a) send information to allow the reconstruction of the sensor's samples within sufficient accuracy, and then b) use these reconstructions to estimate the entire field. To implement the first stage, the heavy correlation between the sensor samples suggests the use of distributed coding schemes to …
The broadcast phase (downlink transmission) of the two-way relay network is studied in the source coding and joint source-channel coding settings. The rates needed for reliable communication are characterised for a number of special cases including: small distortions, deterministic distortion measures, and jointly Gaussian sources with quadratic distortion measures. The broadcast problem is also studied with common-reconstruction decoding constraints, and the rates needed for reliable communication are characterised for all discrete memoryless sources and per-letter distortion measures.
The source-coding problem with side information at the decoder is studied subject to a constraint that the encoder---to whom the side information is unavailable---be able to compute the decoder's reconstruction sequence to within some distortion. For discrete memoryless sources and finite single-letter distortion measures, an expression is given for the minimal description rate as a function of the joint law of the source and side information and of the allowed distortions at the encoder and at the decoder. The minimal description rate is also computed for a memoryless Gaussian source with squ…
We consider the problem of synchronizing data in distributed storage networks under an edit model that includes deletions and insertions. We present two modifications of MDS, regenerating and locally repairable codes that allow updates in the parity-check values to be performed with one round of communication at low bit rates and using small storage overhead. Our main contributions are novel protocols for synchronizing both hot and semi-static data and protocols for data deduplication applications, based on intermediary permutation, Vandermonde and Cauchy matrix coding.
University of Washington（华盛顿大学）；Princeton University（普林斯顿大学）；University of California, San Diego（加州大学圣迭戈分校）
In the usual trace reconstruction problem, the goal is to exactly reconstruct an unknown string of length $n$ after it passes through a deletion channel many times independently, producing a set of traces (i.e., random subsequences of the string). We consider the relaxed problem of approximate reconstruction. Here, the goal is to output a string that is close to the original one in edit distance while using much fewer traces than is needed for exact reconstruction. We present several algorithms that can approximately reconstruct strings that belong to certain classes, where the estimate is wit…
