Results 21 to 30 of about 247,683 (30)

Unsupervised Learning in Genome Informatics [PDF]

arXiv, 2015
With different genomes available, unsupervised learning algorithms are essential in learning genome-wide biological insights. Especially, the functional characterization of different genomes is essential for us to understand lives. In this book chapter, we review the state-of-the-art unsupervised learning algorithms for genome informatics from DNA to ...
arxiv  

Fluent but Culturally Distant: Can Regional Training Teach Cultural Understanding? [PDF]

arXiv
Large language models (LLMs) are used around the world but exhibit Western cultural tendencies. To address this cultural misalignment, many countries have begun developing "regional" LLMs tailored to local communities. Yet it remains unclear whether these models merely speak the language of their users or also reflect their cultural values and ...
arxiv  

Dynamic Past and Future for Neural Machine Translation [PDF]

arXiv, 2019
Previous studies have shown that neural machine translation (NMT) models can benefit from explicitly modeling translated (Past) and untranslated (Future) to groups of translated and untranslated contents through parts-to-wholes assignment. The assignment is learned through a novel variant of routing-by-agreement mechanism (Sabour et al., 2017), namely {
arxiv  

Joint Design of 5' Untranslated Region and Coding Sequence of mRNA [PDF]

arXiv
Messenger RNA (mRNA) vaccines and therapeutics are emerging as powerful tools against a variety of diseases, including infectious diseases and cancer. The design of mRNA molecules, particularly the untranslated region (UTR) and coding sequence (CDS) is crucial for optimizing translation efficiency and stability.
arxiv  

Encoding folding paths of RNA switches [PDF]

arXiv, 2006
RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions. Yet, the underlying mechanisms and coding requirements for efficient co-transcriptional folding remain unclear.
arxiv  

Identifying statistical dependence in genomic sequences via mutual information estimates [PDF]

arXiv, 2007
Questions of understanding and quantifying the representation and amount of information in organisms have become a central part of biological research, as they potentially hold the key to fundamental advances. In this paper, we demonstrate the use of information-theoretic tools for the task of identifying segments of biomolecules (DNA or RNA) that are ...
arxiv  

Helix-mRNA: A Hybrid Foundation Model For Full Sequence mRNA Therapeutics [PDF]

arXiv
mRNA-based vaccines have become a major focus in the pharmaceutical industry. The coding sequence as well as the Untranslated Regions (UTRs) of an mRNA can strongly influence translation efficiency, stability, degradation, and other factors that collectively determine a vaccine's effectiveness.
arxiv  

Using Simulations and kinetic network models to reveal the dynamics and functions of Riboswitches [PDF]

Methods in Enzymology (2015) 553, 235-258, 2014
Riboswitches, RNA elements found in the untranslated region, regulate gene expression by binding to target metaboloites with exquisite specificity. Binding of metabolites to the conserved aptamer domain allosterically alters the conformation in the downstream expression platform.
arxiv  

mRNA2vec: mRNA Embedding with Language Model in the 5'UTR-CDS for mRNA Design [PDF]

arXiv
Messenger RNA (mRNA)-based vaccines are accelerating the discovery of new drugs and revolutionizing the pharmaceutical industry. However, selecting particular mRNA sequences for vaccines and therapeutics from extensive mRNA libraries is costly. Effective mRNA therapeutics require carefully designed sequences with optimized expression levels and ...
arxiv  

Latent Diffusion Models for Controllable RNA Sequence Generation [PDF]

arXiv
This work presents RNAdiffusion, a latent diffusion model for generating and optimizing discrete RNA sequences of variable lengths. RNA is a key intermediary between DNA and protein, exhibiting high sequence diversity and complex three-dimensional structures to support a wide range of functions.
arxiv