Related papers: Coding for Trace Reconstruction over Multiple Chan…
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…
An important problem of reconstruction of diffusion network and transmission probabilities from the data has attracted a considerable attention in the past several years. A number of recent papers introduced efficient algorithms for the…
The errors occurring in DNA-based storage are correlated in nature, which is a direct consequence of the synthesis and sequencing processes. In this paper, we consider the memory-$k$ nanopore channel model recently introduced by Hamoum et…
In this paper we study the decoding capabilities of convolutional codes over the erasure channel. Of special interest will be maximum distance profile (MDP) convolutional codes. These are codes which have a maximum possible column distance…
This paper investigates the error probability of several decoding methods for a source code with decoder side information, where the decoding methods are: 1) symbol-wise maximum a posteriori decoding, 2) successive-cancellation decoding,…
We consider the problem of reconstructing an undirected graph $G$ on $n$ vertices given multiple random noisy subgraphs or "traces". Specifically, a trace is generated by sampling each vertex with probability $p_v$, then taking the…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
In this paper, we derive analytic expressions for the success probability of decoding (Partial) Unit Memory codes in memoryless channels. An applications of this result is that these codes outperform individual block codes in certain…
This paper studies an almost-lossless source-channel coding scheme in which source messages are assigned to different classes and encoded with a channel code that depends on the class index. The code performance is analyzed by means of…
This paper studies reconstruction of strings based upon their substrings spectrum. Under this paradigm, it is assumed that all substrings of some fixed length are received and the goal is to reconstruct the string. While many existing works…
We develop upper bounds on code size for an independent and identically distributed deletion and insertion channels for a given code length and target frame error probability. The bounds are obtained as a variation of a general converse…
Diversity coding is a network restoration technique which offers near-hitless restoration, while other state-of-the art techniques are significantly slower. Furthermore, the extra spare capacity requirement of diversity coding is…
Search is a key service within constraint programming systems, and it demands the restoration of previously accessed states during the exploration of a search tree. Restoration proceeds either bottom-up within the tree to roll back…
This chapter develops a theoretical analysis of the convex programming method for recovering a structured signal from independent random linear measurements. This technique delivers bounds for the sampling complexity that are similar with…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
A code construction and repair scheme for optimal functional regeneration of multiple node failures is presented, which is based on stitching together short MDS codes on carefully chosen sets of points lying on a linearized polynomial. The…
Segmental structure is a common pattern in many types of sequences such as phrases in human languages. In this paper, we present a probabilistic model for sequences via their segmentations. The probability of a segmented sequence is…
Relay drones in delay-tolerant applications are dispatched to remote locations in order to gather data transmitted by a source node. Collected data are stored on the drones and delivered to one or multiple bases. This paper considers two…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
DNA data storage offers a high-density, long-term alternative to traditional storage systems, addressing the exponential growth of digital data. Composite DNA extends this paradigm by leveraging mixtures of nucleotides to increase storage…