Related papers: Capacity-Approaching Constrained Codes with Error …
Synchronization errors, such as insertions and deletions, present a fundamental challenge in DNA-based data storage systems, arising from both synthesis and sequencing noise. These channels are often modeled as…
A range of recent works addresses the problem of compression of sequence of tokens into a shorter sequence of real-valued vectors to be used as inputs instead of token embeddings or key-value cache. These approaches are focused on reduction…
We consider the problem of correcting mass readout errors in information encoded in binary polymer strings. Our work builds on results for string reconstruction problems using composition multisets [Acharya et al., 2015] and the unique…
We propose a new framework for constructing polar codes (i.e., selecting the frozen bit positions) for arbitrary channels, and tailored to a given decoding algorithm, rather than based on the (not necessarily optimal) assumption of…
We call {\it monomer} a B-DNA base-pair and examine, analytically and numerically, electron or hole oscillations in monomer- and dimer-polymers, i.e., periodic sequences with repetition unit made of one or two monomers. We employ a…
This paper extends the foundational work of Dollma \emph{et al}. on codes for ordered composite DNA sequences. We consider the general setting with an alphabet of size $q$ and a resolution parameter $k$, moving beyond the binary ($q=2$)…
We investigate weakly constrained codes, in which specific patterns occur with prescribed frequencies rather than being strictly forbidden as in conventional constrained coding. We propose a capacity-achieving construction of a weakly…
Regenerating codes are efficient methods for distributed storage in storage networks, where node failures are common. They guarantee low cost data reconstruction and repair through accessing only a predefined number of arbitrarily chosen…
In this paper, we leverage polar codes and the well-established channel polarization to design capacity-achieving codes with a certain constraint on the weights of all the columns in the generator matrix (GM) while having a low-complexity…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (rarely accessed data), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…
As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…
Motivated by DNA-based data storage, we investigate a system where digital information is stored in an unordered set of several vectors over a finite alphabet. Each vector begins with a unique index that represents its position in the whole…
The efficient storage of digital data is becoming very challenging over the years due to the exponential increase in the generation of data which can't compete with the existing storage resources. Furthermore, the infrequently accessed data…
Text compression schemes and compact data structures usually combine sophisticated probability models with basic coding methods whose average codeword length closely match the entropy of known distributions. In the frequent case where basic…
Constrained coding plays a key role in optimizing performance and mitigating errors in applications such as storage and communication, where specific constraints on codewords are required. While non-parametric constraints have been…
Insertion-deletion codes (insdel codes for short) are used for correcting synchronization errors in communications, and in other many interesting fields such as DNA storage, date analysis, race-track memory error correction and language…
Identifying palindromes in sequences has been an interesting line of research in combinatorics on words and also in computational biology, after the discovery of the relation of palindromes in the DNA sequence with the HIV virus. Efficient…
The short lifespan of traditional data storage media, coupled with an exponential increase in storage demand, has made long-term archival a fundamental problem in the data storage industry and beyond. Consequently, researchers are looking…
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…