Related papers: Mutually Uncorrelated Primers for DNA-Based Data S…
The utility of DNA sequence substrings (k-mers) in alignment-free phylogenetic classification, including that of bacteria and viruses, is increasingly recognized. However, its biological basis eludes many twenty-first century practitioners.…
The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors…
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…
High-quality training datasets are crucial for the development of effective protein design models, but existing synthetic datasets often include unfavorable sequence-structure pairs, impairing generative model performance. We leverage…
IoT devices are powered by microcontroller units (MCUs) which are extremely resource-scarce: a typical MCU may have an underpowered processor and around 64 KB of memory and persistent storage, which is orders of magnitude fewer…
The power consumption of digital-to-analog converters (DACs) constitutes a significant proportion of the total power consumption in a massive multiuser multiple-input multiple-output (MU-MIMO) base station (BS). Using 1-bit DACs can…
With the growing complexity and dynamics of the mobile communication networks, accurately predicting key system parameters, such as channel state information (CSI), user location, and network traffic, has become essential for a wide range…
In a DNA sequence, we have the celebrated Watson-Crick complement $\overline{T}=A$, $\overline{A}=T$, $\overline{C}=G$, and $\overline{G}=C$. Given an integer $m\ge 2$, a secondary structure in a DNA sequence refers to the existence of two…
This paper presents a general technique for optimally transforming any dynamic data structure that operates on atomic and indivisible keys by constant-time comparisons, into a data structure that handles unbounded-length keys whose…
DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes \cite{Cengellenmis} and…
Memory consistency models define the order in which accesses to shared memory in a concurrent system may be observed to occur. Such models are a necessity since program order is not a reliable indicator of execution order, due to…
Fully decentralized Muon is difficult because its nonlinear matrix-sign operator does not commute with linear gossip averaging. This makes decentralized Muon a structural design problem: in designing the algorithm, one must distinguish…
Emerging high-throughput technologies have led to a deluge of putative non-coding RNA (ncRNA) sequences identified in a wide variety of organisms. Systematic characterization of these transcripts will be a tremendous challenge. Homology…
While achieving a compression ratio of 2.0 bits/base, the new algorithm codes non-N bases in fixed length. It dramatically reduces the time of coding and decoding than previous DNA compression algorithms and some universal compression…
In the framework of write-once memory (WOM) codes, it is important to distinguish between codes that can be decoded directly and those that require that the decoder knows the current generation to successfully decode the state of the…
Frequent sequence mining methods often make use of constraints to control which subsequences should be mined. A variety of such subsequence constraints has been studied in the literature, including length, gap, span, regular-expression, and…
In order to control the process of data mining and focus on the things of interest to us, many kinds of constraints have been added into the algorithms of data mining. However, discovering the correlated alarms in the alarm database needs…
Linear dimensionality reduction techniques are powerful tools for image analysis as they allow the identification of important features in a data set. In particular, nonnegative matrix factorization (NMF) has become very popular as it is…
Protein similarity searches are a routine job for molecular biologists where a query sequence of amino acids needs to be compared and ranked against an ever-growing database of proteins. All available algorithms in this field can be grouped…
Mutually unbiased bases (MUBs) are highly symmetric bases on complex Hilbert spaces, and the corresponding rank-1 projective measurements are ubiquitous in quantum information theory. In this work, we study a recently introduced…