Related papers: New constructions of DNA codes under multiple cons…
Nucleic acid sequence design via codon optimization is a fundamental task with applications across synthetic biology, mRNA therapeutics, and vaccine design. Given a target protein, it is a major open challenge to navigate the…
Recently, DNA storage has surfaced as a promising alternative for data storage, presenting notable benefits in terms of storage capacity, cost-effectiveness in maintenance, and the capability for parallel replication. Mathematically, the…
Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…
Weighted Hamming distance, as a similarity measure between binary codes and binary queries, provides superior accuracy in search tasks than Hamming distance. However, how to efficiently and accurately find $K$ binary codes that have the…
Motivation: Despite significant advances in Third-Generation Sequencing (TGS) technologies, Next-Generation Sequencing (NGS) technologies remain dominant in the current sequencing market. This is due to the lower error rates and richer…
We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…
In this paper, we study achievable rates of concatenated coding schemes over a deoxyribonucleic acid (DNA) storage channel. Our channel model incorporates the main features of DNA-based data storage. First, information is stored on many,…
Huffman coding is well known to be useful in certain decision problems involving minimizing the average number of (freely chosen) queries to determine an unknown random variable. However, in problems where the queries are more constrained,…
The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…
Large language models (LLMs) have notably enhanced the fluency and diversity of machine-generated text. However, this progress also presents a significant challenge in detecting the origin of a given text, and current research on detection…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
The problem of fast items retrieval from a fixed collection is often encountered in most computer science areas, from operating system components to databases and user interfaces. We present an approach based on hash tables that focuses on…
In standard generative deep learning models, such as autoencoders or GANs, the size of the parameter set is proportional to the complexity of the generated data distribution. A significant challenge is to deploy resource-hungry deep…
Code generation maps a program description to executable source code in a programming language. Existing approaches mainly rely on a recurrent neural network (RNN) as the decoder. However, we find that a program contains significantly more…
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 ($q=2$)…
Generative retrieval generates identifiers of relevant documents in an end-to-end manner using a sequence-to-sequence architecture for a given query. The relation between generative retrieval and other retrieval methods, especially those…
In this work, we study the DNA codes from the ring R = Z4 + wZ4, where w^2 = 2+2w with 16 elements. We establish a one to one correspondence between the elements of the ring R and all the DNA codewords of length 2 by defining a…
We introduce a consistent and efficient method to construct self-dual codes over $GF(q)$ with symmetric generator matrices from a self-dual code over $GF(q)$ of smaller length where $q \equiv 1 \pmod 4$. Using this method, we improve the…
We consider the problem of constructing codes that can correct $\delta$ deletions occurring in an arbitrary binary string of length $n$ bits. Varshamov-Tenengolts (VT) codes can correct all possible single deletions $(\delta=1)$ with an…