Related papers: A 5' UTR Language Model for Decoding Untranslated …

Understanding how 5' untranslated regions (5'UTRs) regulate mRNA translation is critical for controlling protein expression and designing effective therapeutic mRNAs. While recent deep learning models have shown promise in predicting…

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…

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…

Translation is a crucial step in gene expression. During translation, macromolecules called ribosomes "read" the mRNA strand in a sequential manner and produce a corresponding protein. Translation is known to consume most of the cell's…

Automatic speech recognition (ASR) systems normally consist of an acoustic model (AM) and a language model (LM). The acoustic model estimates the probability distribution of text given the input speech, while the language model calibrates…

Computational biology and bioinformatics provide vast data gold-mines from protein sequences, ideal for Language Models taken from NLP. These LMs reach for new prediction frontiers at low inference costs. Here, we trained two…

Protein language models have shown remarkable success in learning biological information from protein sequences. However, most existing models are limited by either autoencoding or autoregressive pre-training objectives, which makes them…

Instruction fine-tuned language models on a collection of instruction annotated datasets (FLAN) have shown highly effective to improve model performance and generalization to unseen tasks. However, a majority of standard parsing tasks…

With the thriving of pre-trained language model (PLM) widely verified in various of NLP tasks, pioneer efforts attempt to explore the possible cooperation of the general textual information in PLM with the personalized behavioral…

Translation is an important stage in gene expression. During this stage, macro-molecules called ribosomes travel along the mRNA strand linking amino-acids together in a specific order to create a functioning protein. An important question…

Masked language modelling (MLM) as a pretraining objective has been widely adopted in genomic sequence modelling. While pretrained models can successfully serve as encoders for various downstream tasks, the distribution shift between…

This study tackles unsupervised domain adaptation of reading comprehension (UDARC). Reading comprehension (RC) is a task to learn the capability for question answering with textual sources. State-of-the-art models on RC still do not have…

Large language models (LLMs) have demonstrated significant success in natural language processing (NLP) tasks and have shown promising results in other domains such as protein sequence generation. However, there remain salient differences…

Recent advancements in immune sequencing and experimental techniques are generating extensive T cell receptor (TCR) repertoire data, enabling the development of models to predict TCR binding specificity. Despite the computational challenges…

Generative Large Language Models (LLMs) have achieved remarkable advancements in various NLP tasks. However, these advances have not been reflected in the translation task, especially those with moderate model sizes (i.e., 7B or 13B…

Pre-trained language models have recently emerged as a powerful tool for fine-tuning a variety of language tasks. Ideally, when models are pre-trained on large amount of data, they are expected to gain implicit knowledge. In this paper, we…

Current Large Language Models (LLMs) for understanding proteins primarily treats amino acid sequences as a text modality. Meanwhile, Protein Language Models (PLMs), such as ESM-2, have learned massive sequential evolutionary knowledge from…

3' untranslated regions (3' UTRs) contain binding sites for many regulatory elements, and in particular for microRNAs (miRNAs). The importance of miRNA-mediated post-transcriptional regulation has become increasingly clear in the last few…

Large language models (LLMs) have demonstrated remarkable advancements in language understanding and generation. Building on the success of text-based LLMs, recent research has adapted these models to use speech embeddings for prompting,…

Large language models (LLMs) have demonstrated strong performance in general-purpose machine translation, but their effectiveness in complex, domain-sensitive translation tasks remains underexplored. Recent advancements in Large Reasoning…