Related papers: Automated DNA Motif Discovery
Large Language models (LLMs) have emerged as powerful tools for addressing challenges across diverse domains. Notably, recent studies have demonstrated that large language models significantly enhance the efficiency of biomolecular analysis…
Complex biological functions are carried out by the interaction of genes and proteins. Uncovering the gene regulation network behind a function is one of the central themes in biology. Typically, it involves extensive experiments of…
The success of many natural language processing (NLP) tasks is bound by the number and quality of annotated data, but there is often a shortage of such training data. In this paper, we ask the question: "Can we combine a neural network (NN)…
Recent advances in next-generation sequencing technologies have facilitated the use of deoxyribonucleic acid (DNA) as a novel covert channels in steganography. There are various methods that exist in other domains to detect hidden messages…
Grammar plays a critical role in natural language processing and text/code generation by enabling the definition of syntax, the creation of parsers, and guiding structured outputs. Although large language models (LLMs) demonstrate…
Background: In addition to known protein-coding genes, large amount of apparently non-coding sequence are conserved between the human and mouse genomes. It seems reasonable to assume that these conserved regions are more likely to contain…
The most common gene regulation mechanism is when a protein binds to a regulatory sequence to change RNA transcription. However, these sequences are short relative to the genome length, so finding them poses a challenging search problem.…
Self-assembly is a process found everywhere in the Nature. In particular, it is known that DNA self-assembly is Turing universal. Thus one can do arbitrary computations or build nano-structures using DNA self-assembly. In order to…
Statistical analysis of bacteria genomes texts has been performed on the basis of 20 complete genomes origin from Genebank. It has been revealed that the word ranked distributions are quite well approximated by logarithmic law. Results…
Regular expressions with backreferences (regex, for short), as supported by most modern libraries for regular expression matching, have an NP-complete matching problem. We define a complexity parameter of regex, called active variable…
Recently, services and business models based on large language models, such as OpenAI Chatgpt, Google BARD, and Microsoft copilot, have been introduced, and the applications utilizing natural language processing with deep learning are…
Designing RNA molecules that interact with specific proteins is a critical challenge in experimental and computational biology. Existing computational approaches require a substantial amount of previously known interacting RNA sequences for…
Transcriptional regulation by transcription factors and post-transcriptional regulation by microRNAs constitute two major modes of regulation of gene expression. While gene expression motifs incorporating solely transcriptional regulation…
Advances in data collecting technologies in genomics have significantly increased the need for tools designed to study the genetic basis of many diseases. Effective statistical methods should excel in both prediction accuracy and biomarker…
Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory…
In modern age, the increasing complexity of computation and communication technology is leading us towards the necessity of new paradigm. As a result, unconventional approach like DNA coding theory is gaining considerable attention. The…
The mainstream of research in genetics, epigenetics and imaging data analysis focuses on statistical association or exploring statistical dependence between variables. Despite their significant progresses in genetic research, understanding…
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,…
The primary aim of automated performance improvement is to reduce the running time of programs while maintaining (or improving on) functionality. In this paper, Genetic Programming is used to find performance improvements in regular…
Statistical analysis of evolutionary-related protein sequences provides insights about their structure, function, and history. We show that Restricted Boltzmann Machines (RBM), designed to learn complex high-dimensional data and their…