Related papers: LoRA-BERT: a Natural Language Processing Model for…

Research on long non-coding RNAs (lncRNAs) has garnered significant attention due to their critical roles in gene regulation and disease mechanisms. However, the complexity and diversity of lncRNA sequences, along with the limited knowledge…

Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs which play a significant role in several biological processes. RNA-seq based transcriptome sequencing has been extensively used for identification of lncRNAs. However, accurate…

Recent years have witnessed a substantial increase in the use of deep learning to solve various natural language processing (NLP) problems. Early deep learning models were constrained by their sequential or unidirectional nature, such that…

Long non-coding RNAs (lncRNAs) are important regulators to modulate gene expression and cell proliferation in the developing human brain. Previous methods mainly use bulk lncRNA and mRNA expression data to study lncRNA regulation. However,…

Long noncoding RNAs (lncRNAs) are a recently discovered class of non-protein coding RNAs which have now increasingly been shown to be involved in a wide variety of biological processes as regulatory molecules. Little is known regarding the…

Encoder-based transformer models are central to biomedical and clinical Natural Language Processing (NLP), as their bidirectional self-attention makes them well-suited for efficiently extracting structured information from unstructured text…

In the last decade, the discovery of noncoding RNA(ncRNA) has exploded. Classifying these ncRNA is critical todetermining their function. This thesis proposes a new methodemploying deep convolutional neural networks (CNNs) to classifyncRNA…

Deep transcriptome sequencing has revealed the existence of many transcripts that lack long or conserved open reading frames and which have been termed long non-coding RNAs (lncRNAs). Despite the existence of several well-characterized…

Transformer models have achieved great success across many NLP problems. However, previous studies in automated ICD coding concluded that these models fail to outperform some of the earlier solutions such as CNN-based models. In this paper…

Transformers-based models, such as BERT, have dramatically improved the performance for various natural language processing tasks. The clinical knowledge enriched model, namely ClinicalBERT, also achieved state-of-the-art results when…

Objective: Clinical knowledge enriched transformer models (e.g., ClinicalBERT) have state-of-the-art results on clinical NLP (natural language processing) tasks. One of the core limitations of these transformer models is the substantial…

BERT, which stands for Bidirectional Encoder Representations from Transformers, is a recently introduced language representation model based upon the transfer learning paradigm. We extend its fine-tuning procedure to address one of its…

Recent innovations in architecture, pre-training, and fine-tuning have led to the remarkable in-context learning and reasoning abilities of large auto-regressive language models such as LLaMA and DeepSeek. In contrast, encoders like BERT…

Recently, Natural Language Processing (NLP) has witnessed an impressive progress in many areas, due to the advent of novel, pretrained contextual representation models. In particular, Devlin et al. (2019) proposed a model, called BERT…

Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained…

Bidirectional Encoder Representations from Transformers (BERT) has shown marvelous improvements across various NLP tasks, and consecutive variants have been proposed to further improve the performance of the pre-trained language models. In…

Text classification algorithms investigate the intricate relationships between words or phrases and attempt to deduce the document's interpretation. In the last few years, these algorithms have progressed tremendously. Transformer…

Developing high-performance entity normalization algorithms that can alleviate the term variation problem is of great interest to the biomedical community. Although deep learning-based methods have been successfully applied to biomedical…

The paper proposes to employ deep convolutional neural networks (CNNs) to classify noncoding RNA (ncRNA) sequences. To this end, we first propose an efficient approach to convert the RNA sequences into images characterizing their…

In the global challenge of understanding and characterizing biodiversity, short species-specific genomic sequences known as DNA barcodes play a critical role, enabling fine-grained comparisons among organisms within the same kingdom of…