Related papers: BIOptimus: Pre-training an Optimal Biomedical Lang…
This study evaluated the effect of BioBERT in medical text processing for the task of medical named entity recognition. Through comparative experiments with models such as BERT, ClinicalBERT, SciBERT, and BlueBERT, the results showed that…
In recent years, pre-trained language models (PLMs) achieve the best performance on a wide range of natural language processing (NLP) tasks. While the first models were trained on general domain data, specialized ones have emerged to more…
Language models (LMs) have demonstrated remarkable capabilities in NLP, yet adapting them efficiently and robustly to specific tasks remains challenging. As their scale and complexity grow, fine-tuning LMs on labelled data often…
In recent years, there has been substantial progress in using pretrained Language Models (LMs) on a range of tasks aimed at improving the understanding of biomedical texts. Nonetheless, existing biomedical LLMs show limited comprehension of…
Protein language models (pLMs) have recently gained significant attention for their ability to uncover relationships between sequence, structure, and function from evolutionary statistics, thereby accelerating therapeutic drug discovery.…
Large language models (LLMs) are widely applied in various natural language processing tasks such as question answering and machine translation. However, due to the lack of labeled data and the difficulty of manual annotation for…
Pre-trained multilingual language models such as mBERT have shown immense gains for several natural language processing (NLP) tasks, especially in the zero-shot cross-lingual setting. Most, if not all, of these pre-trained models rely on…
Language models pre-trained on biomedical corpora, such as BioBERT, have recently shown promising results on downstream biomedical tasks. Many existing pre-trained models, on the other hand, are resource-intensive and computationally heavy…
Lately, instruction-based techniques have made significant strides in improving performance in few-shot learning scenarios. They achieve this by bridging the gap between pre-trained language models and fine-tuning for specific downstream…
Pre-training a language model and then fine-tuning it for downstream tasks has demonstrated state-of-the-art results for various NLP tasks. Pre-training is usually independent of the downstream task, and previous works have shown that this…
For protein sequence datasets, unlabeled data has greatly outpaced labeled data due to the high cost of wet-lab characterization. Recent deep-learning approaches to protein prediction have shown that pre-training on unlabeled data can yield…
Large Language Models (LLMs) have shown impressive abilities in data annotation, opening the way for new approaches to solve classic NLP problems. In this paper, we show how to use LLMs to create NuNER, a compact language representation…
We present MatSci-NLP, a natural language benchmark for evaluating the performance of natural language processing (NLP) models on materials science text. We construct the benchmark from publicly available materials science text data to…
Fine-tuning pre-trained language models has recently become a common practice in building NLP models for various tasks, especially few-shot tasks. We argue that under the few-shot setting, formulating fine-tuning closer to the pre-training…
Language model pre-training has proven to be useful in many language understanding tasks. In this paper, we investigate whether it is still helpful to add the self-training method in the pre-training step and the fine-tuning step. Towards…
Gene transformer models such as Nucleotide Transformer, DNABert, and LOGO are trained to learn optimal gene sequence representations by using the Masked Language Modeling (MLM) training objective over the complete Human Reference Genome.…
Recently, prompt tuning \cite{lester2021power} has gradually become a new paradigm for NLP, which only depends on the representation of the words by freezing the parameters of pre-trained language models (PLMs) to obtain remarkable…
Masked language modeling (MLM), a self-supervised pretraining objective, is widely used in natural language processing for learning text representations. MLM trains a model to predict a random sample of input tokens that have been replaced…
Pretrained language models have served as important backbones for natural language processing. Recently, in-domain pretraining has been shown to benefit various domain-specific downstream tasks. In the biomedical domain, natural language…
Language Models (LMs) such as BERT, have been shown to perform well on the task of identifying Named Entities (NE) in text. A BERT LM is typically used as a classifier to classify individual tokens in the input text, or to classify spans of…