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. Motivated by modern storage devices, we introduced a variant of the problem where the number of noisy reads $N$ is fixed (Kiah et al. 2020). Of significance, for the single-deletion channel, using $\log_2\log_2 n +O(1)$ redundant bits, we designed a reconstruction code of length $n$ that reconstructs codewords from two distinct noisy reads.
In this work, we show that $\log_2\log_2 n -O(1)$ redundant bits are necessary for such reconstruction codes, thereby, demonstrating the optimality of our previous construction. Furthermore, we show that these reconstruction codes can be used in $t$-deletion channels (with $t\ge 2$) to uniquely reconstruct codewords from $n^{t-1}+O\left(n^{t-2}\right)$ distinct noisy reads.
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 channels, a notoriously difficult problem due to its highly combinatorial nature. Although works in theoretical computer science have provided algorithms which guarantee perfect reconstruction with multiple independent observations from the deletion channel, they are only applicable in the large blocklength regime and more restrictively, when the number of observat…
The one-bit deletion and duplication channel is investigated. An input to this channel consists of a block of bits which experiences either a deletion, or a duplication, or remains unchanged. For this channel a capacity expression is obtained in a certain asymptotic regime where the deletion and duplication probabilities tend to zero. As a corollary, we obtain an asymptotic expression for the capacity of the segmented deletion and duplication channel where the input now consists of several blocks and each block independently experiences either a deletion, or a duplication, or remains unchanged…
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 derive an upper bound on the capacity of non-binary deletion channels. Although binary deletion channels have received significant attention over the years, and many upper and lower bounds on their capacity have been derived, such studies for the non-binary case are largely missing. The state of the art is the following: as a trivial upper bound, capacity of an erasure channel with the same input alphabet as the deletion channel can be used, and as a lower bound the results by Diggavi and Grossglauser are available. In this paper, we derive the first non-trivial non-binary deletion channel …
The deletion channel is the simplest point-to-point communication channel that models lack of synchronization. Input bits are deleted independently with probability d, and when they are not deleted, they are not affected by the channel. Despite significant effort, little is known about the capacity of this channel, and even less about optimal coding schemes. In this paper we develop a new systematic approach to this problem, by demonstrating that capacity can be computed in a series expansion for small deletion probability. We compute three leading terms of this expansion, and find an input di…
We consider the class of channels formed from the concatenation of a deletion channel and a finite-state channel. For this class of channels, we show that the operational capacity is equal to the stationary capacity, which can be approached by a sequence of Markov processes with increasing Markovian orders. As a by-product, we show that the polar coding scheme constructed by Tal, Pfister, Fazeli and Vardy achieves the capacity of the deletion channel.
The deletion channel is the simplest point-to-point communication channel that models lack of synchronization. Despite significant effort, little is known about its capacity, and even less about optimal coding schemes. In this paper we intiate a new systematic approach to this problem, by demonstrating that capacity can be computed in a series expansion for small deletion probability. We compute two leading terms of this expansion, and show that capacity is achieved, up to this order, by i.i.d. uniform random distribution of the input. We think that this strategy can be useful in a number of c…
Memoryless channels with deletion errors as defined by a stochastic channel matrix allowing for bit drop outs are considered in which transmitted bits are either independently deleted with probability $d$ or unchanged with probability $1-d$. Such channels are information stable, hence their Shannon capacity exists. However, computation of the channel capacity is formidable, and only some upper and lower bounds on the capacity exist. In this paper, we first show a simple result that the parallel concatenation of two different independent deletion channels with deletion probabilities $d_1$ and $…
Improved Capacity Upper Bounds for the Deletion Channel using a Parallelized Blahut-Arimoto Algorithm
Instituto Superior Técnico, Universidade de Lisboa（里斯本技术学院，里斯本大学）；Instituto de Telecomunicações and Departamento de Matemática, Instituto Superior Técnico, Universidade de Lisboa（电信研究所与数学系，里斯本技术学院，里斯本大学）
We develop several analytical lower bounds on the capacity of binary insertion and deletion channels by considering independent uniformly distributed (i.u.d.) inputs and computing lower bounds on the mutual information between the input and output sequences. For the deletion channel, we consider two different models: independent and identically distributed (i.i.d.) deletion-substitution channel and i.i.d. deletion channel with additive white Gaussian noise (AWGN). These two models are considered to incorporate effects of the channel noise along with the synchronization errors. For the insertio…
This paper presents the first proof of polarization for the deletion channel with a constant deletion rate and a regular hidden-Markov input distribution. A key part of this work involves representing the deletion channel using a trellis and describing the plus and minus polar-decoding operations on that trellis. In particular, the plus and minus operations can be seen as combining adjacent trellis stages to yield a new trellis with half as many stages. Using this viewpoint, we prove a weak polarization theorem for standard polar codes on the deletion channel. To achieve strong polarization, w…
Let $C(d)$ be the capacity of the binary deletion channel with deletion probability $d$. It was proved by Drinea and Mitzenmacher that, for all $d$, $C(d)/(1-d)\geq 0.1185 $. Fertonani and Duman recently showed that $\limsup_{d\to 1}C(d)/(1-d)\leq 0.49$. In this paper, it is proved that $\lim_{d\to 1}C(d)/(1-d)$ exists and is equal to $\inf_{d}C(d)/(1-d)$. This result suggests the conjecture that the curve $C(d)$ my be convex in the interval $d\in [0,1]$. Furthermore, using currently known bounds for $C(d)$, it leads to the upper bound $\lim_{d\to 1}C(d)/(1-d)\leq 0.4143$.
We consider the maximum coding rate achievable by uniformly-random codes for the deletion channel. We prove an upper bound that's within 0.1 of the best known lower bounds for all values of the deletion probability $d,$ and much closer for small and large $d.$ We give simulation results which suggest that our upper bound is within 0.05 of the exact value for all $d$, and within $0.01$ for $d>0.75$. Despite our upper bounds, based on simulations, we conjecture that a positive rate is achievable with uniformly-random codes for all deletion probabilities less than 1. Our results imply impossibili…
We present novel bounds on the capacity of the independent and identically distributed binary deletion channel. Four upper bounds are obtained by providing the transmitter and the receiver with genie-aided information on suitably-defined random processes. Since some of the proposed bounds involve infinite series, we also introduce provable inequalities that lead to more manageable results. For most values of the deletion probability, these bounds improve the existing ones and significantly narrow the gap with the available lower bounds. Exploiting the same auxiliary processes, we also derive, …
We study the application of polar codes in deletion channels by analyzing the cascade of a binary erasure channel (BEC) and a deletion channel. We show how polar codes can be used effectively on a BEC with a single deletion, and propose a list decoding algorithm with a cyclic redundancy check for this case. The decoding complexity is $O(N^2\log N)$, where $N$ is the blocklength of the code. An important contribution is an optimization of the amount of redundancy added to minimize the overall error probability. Our theoretical results are corroborated by numerical simulations which show that th…
This paper presents a coding scheme for an insertion deletion substitution channel. We extend a previous scheme for the deletion channel where polar codes are modified by adding "guard bands" between segments. In the new scheme, each guard band is comprised of a middle segment of '1' symbols, and left and right segments of '0' symbols. Our coding scheme allows for a regular hidden-Markov input distribution, and achieves the information rate between the input and corresponding output of such a distribution. Thus, we prove that our scheme can be used to efficiently achieve the capacity of the ch…
The channel output entropy of a transmitted word is the entropy of the possible channel outputs and similarly, the input entropy of a received word is the entropy of all possible transmitted words. The goal of this work is to study these entropy values for the k-deletion, k-insertion channel, where exactly k symbols are deleted, and inserted in the transmitted word, respectively. If all possible words are transmitted with the same probability then studying the input and output entropies is equivalent. For both the 1-insertion and 1-deletion channels, it is proved that among all words with a fi…
Motivated by the sequence reconstruction problem from traces in DNA-based storage, we consider the problem of designing codes for the deletion channel when multiple observations (or traces) are available to the decoder. We propose simple binary and non-binary codes based on Varshamov-Tenengolts (VT) codes. The proposed codes split the codeword in blocks and employ a VT code in each block. The availability of multiple traces helps the decoder to identify deletion-free copies of a block, and to avoid mis-synchronization while decoding. The encoding complexity of the proposed scheme is linear in …
Memoryless channels with synchronization errors as defined by a stochastic channel matrix allowing for symbol insertions and deletions in addition to random errors are considered. Such channels are information stable, hence their Shannon capacity exists. However, computation of the channel capacity is formidable, and only some upper and lower bounds on the capacity (for some special cases) exist. In this short paper, using a simple methodology, we prove that the channel capacity is a convex function of the stochastic channel matrix. Since the more widely studied model of an independent identic…
Two of the most common models for channels with synchronisation errors are the Binary Deletion Channel with parameter $p$ ($\text{BDC}_p$) -- a channel where every bit of the codeword is deleted i.i.d with probability $p$, and the Poisson Repeat Channel with parameter $λ$ ($\text{PRC}_λ$) -- a channel where every bit of the codeword is repeated $\text{Poisson}(λ)$ times. Previous constructions based on synchronisation strings yielded codes with rates far lower than the capacities of these channels [CS19, GL18], and the only efficient construction to achieve capacity on the BDC at the time of w…
Motivated by the study of deletion channels, this work presents improved bounds on the number of subsequences obtained from a binary sting X of length n under t deletions. It is known that the number of subsequences in this setting strongly depends on the number of runs in the string X; where a run is a maximal sequence of the same character. Our improved bounds are obtained by a structural analysis of the family of r-run strings X, an analysis in which we identify the extremal strings with respect to the number of subsequences. Specifically, for every r, we present r-run strings with the mini…
This work gives an explicit construction of a family of error correcting codes for the binary deletion channel and for the Poisson repeat channel. In the binary deletion channel with parameter $p$ (BDC$_p$) every bit is deleted independently with probability $p$. A lower bound of $(1-p)/9$ is known on the capacity of the BDC$_p$ \cite{mitzenmacher2006simple}, yet no explicit construction is known to achieve this rate. We give an explicit family of codes of rate $(1-p)/16$, for every $p$. This improves upon the work of Guruswami and Li \cite{guruswami2017efficiently} that gave a construction of…
This work studies problems in data reconstruction, an important area with numerous applications. In particular, we examine the reconstruction of binary and non-binary sequences from synchronization (insertion/deletion-correcting) codes. These sequences have been corrupted by a fixed number of symbol insertions (larger than the minimum edit distance of the code), yielding a number of distinct traces to be used for reconstruction. We wish to know the minimum number of traces needed for exact reconstruction. This is a general version of a problem tackled by Levenshtein for uncoded sequences. We i…
The construction of deletion codes for the Levenshtein metric is reduced to the construction of codes over the integers for the Manhattan metric by run length coding. The latter codes are constructed by expurgation of translates of lattices. These lattices, in turn, are obtained from Construction~A applied to binary codes and $\Z_4-$codes. A lower bound on the size of our codes for the Manhattan distance are obtained through generalized theta series of the corresponding lattices.
We consider the zero-error capacity of deletion channels. Specifically, we consider the setting where we choose a codebook ${\cal C}$ consisting of strings of $n$ bits, and our model of the channel corresponds to an adversary who may delete up to $pn$ of these bits for a constant $p$. Our goal is to decode correctly without error regardless of the actions of the adversary. We consider what values of $p$ allow non-zero capacity in this setting. We suggest multiple approaches, one of which makes use of the natural connection between this problem and the problem of finding the expected length of …
In this paper, we consider a class of symmetry groups associated to communication channels, which can informally be viewed as the transformations of the set of inputs that ``commute'' with the action of the channel. These groups were first studied by Polyanskiy in (IEEEToIT 2013). We show the simple result that the input distribution that attains the maximum mutual information for a given channel is a ``fixed point'' of its group. We conjecture (and give empirical evidence) that the channel group of the deletion channel is extremely small (it contains a number of elements constant in the block…
Suppose a binary string x = x_1...x_n is being broadcast repeatedly over a faulty communication channel. Each time, the channel delivers a fixed number m of the digits (m<n) with the lost digits chosen uniformly at random, and the order of the surviving digits preserved. How large does m have to be to reconstruct the message?
This paper studies the problem of reconstructing a word given several of its noisy copies. This setup is motivated by several applications, among them is reconstructing strands in DNA-based storage systems. Under this paradigm, a word is transmitted over some fixed number of identical independent channels and the goal of the decoder is to output the transmitted word or some close approximation. The main focus of this paper is the case of two deletion channels and studying the error probability of the maximum-likelihood (ML) decoder under this setup. First, it is discussed how the ML decoder op…
In the random deletion channel, each bit is deleted independently with probability $p$. For the random deletion channel, the existence of codes of rate $(1-p)/9$, and thus bounded away from $0$ for any $p < 1$, has been known. We give an explicit construction with polynomial time encoding and deletion correction algorithms with rate $c_0 (1-p)$ for an absolute constant $c_0 > 0$.
We propose a new coding scheme, called the delayed coding (DC) scheme, for channels with insertion, deletion, and substitution (IDS) errors. The proposed scheme employs delayed encoding and non-iterative detection and decoding strategies to manage the transmission of multiple codewords in a linear code. In the DC scheme, a channel input sequence consists of subblocks of multiple codewords from the previous to current time instances. At the receiver side, the maximum a posteriori detection applies to the received sequences that contain information of the codeword at the current time instance, w…
We consider a new formulation of a class of synchronization error channels and derive analytical bounds and numerical estimates for the capacity of these channels. For the binary channel with only deletions, we obtain an expression for the symmetric information rate in terms of subsequence weights which reduces to a tight lower bound for small deletion probabilities. We are also able to exactly characterize the Markov-1 rate for the binary channel with only replications. For a channel that introduces deletions as well as replications of input symbols, we design approximating channels that para…
This paper considers a binary channel with deletions and insertions, where each input bit is transformed in one of the following ways: it is deleted with probability d, or an extra bit is added after it with probability i, or it is transmitted unmodified with probability 1-d-i. A computable lower bound on the capacity of this channel is derived. The transformation of the input sequence by the channel may be viewed in terms of runs as follows: some runs of the input sequence get shorter/longer, some runs get deleted, and some new runs are added. It is difficult for the decoder to synchronize th…
Transmit a codeword $x$, that belongs to an $(\ell-1)$-deletion-correcting code of length $n$, over a $t$-deletion channel for some $1\le \ell\le t<n$. Levenshtein, in 2001, proposed the problem of determining $N(n,\ell,t)+1$, the minimum number of distinct channel outputs required to uniquely reconstruct $x$. Prior to this work, $N(n,\ell,t)$ is known only when $\ell\in\{1,2\}$. Here, we provide an asymptotically exact solution for all values of $\ell$ and $t$. Specifically, we show that $N(n,\ell,t)=\binom{2\ell}{\ell}/(t-\ell)! n^{t-\ell} - O(n^{t-\ell-1})$ and in the special instance where…
We consider the problem of reliable communication over non-binary insertion/deletion channels where symbols are randomly deleted from or inserted in the transmitted sequence and all symbols are corrupted by additive white Gaussian noise. To this end, we utilize the inherent redundancy achievable in non-binary symbol sets by first expanding the symbol set and then allocating part of the bits associated with each symbol to watermark symbols. The watermark sequence, known at the receiver, is then used by a forward-backward algorithm to provide soft information for an outer code which decodes the …
Quantum deletions, which are harder to correct than erasure errors, occur in many realistic settings. It is therefore pertinent to develop quantum coding schemes for quantum deletion channels. To date, not much is known about which explicit quantum error correction codes can combat quantum deletions. We note that {\em any} permutation-invariant quantum code that has a distance of $t+1$ can correct $t$ quantum deletions for any positive integer $t$ in both the qubit and the qudit setting. Leveraging on coding properties of permutation-invariant quantum codes under erasure errors, we derive corr…
In the trace reconstruction problem an unknown string ${\bf x}=(x_0,\dots,x_{n-1})\in\{0,1,...,m-1\}^n$ is observed through the deletion channel, which deletes each $x_k$ with a certain probability, yielding a contracted string $\widetilde{\bf X}$. Earlier works have proved that if each $x_k$ is deleted with the same probability $q\in[0,1)$, then $\exp(O(n^{1/3}))$ independent copies of the contracted string $\widetilde{\bf X}$ suffice to reconstruct $\bf x$ with high probability. We extend this upper bound to the setting where the deletion probabilities vary, assuming certain regularity condi…
The deletion channel takes as input a bit string $\mathbf{x} \in \{0,1\}^n$, and deletes each bit independently with probability $q$, yielding a shorter string. The trace reconstruction problem is to recover an unknown string $\mathbf{x}$ from many independent outputs (called "traces") of the deletion channel applied to $\mathbf{x}$. We show that if $\mathbf{x}$ is drawn uniformly at random and $q < 1/2$, then $e^{O(\log^{1/2} n)}$ traces suffice to reconstruct $\mathbf{x}$ with high probability. The previous best bound, established in 2008 by Holenstein-Mitzenmacher-Panigrahy-Wieder, uses $n^…
The insertion-deletion channel takes as input a bit string ${\bf x}\in\{0,1\}^{n}$, and outputs a string where bits have been deleted and inserted independently at random. The trace reconstruction problem is to recover $\bf x$ from many independent outputs (called "traces") of the insertion-deletion channel applied to $\bf x$. We show that if $\bf x$ is chosen uniformly at random, then $\exp(O(\log^{1/3} n))$ traces suffice to reconstruct $\bf x$ with high probability. For the deletion channel with deletion probability $q < 1/2$ the earlier upper bound was $\exp(O(\log^{1/2} n))$. The case of …
We develop a systematic approach, based on convex programming and real analysis, for obtaining upper bounds on the capacity of the binary deletion channel and, more generally, channels with i.i.d. insertions and deletions. Other than the classical deletion channel, we give a special attention to the Poisson-repeat channel introduced by Mitzenmacher and Drinea (IEEE Transactions on Information Theory, 2006). Our framework can be applied to obtain capacity upper bounds for any repetition distribution (the deletion and Poisson-repeat channels corresponding to the special cases of Bernoulli and Po…
