Related papers: Pre-training Protein Language Models with Label-Ag…

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…

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…

Language model (LM) pre-training has resulted in impressive performance and sample efficiency on a variety of language understanding tasks. However, it remains unclear how to best use pre-trained LMs for generation tasks such as abstractive…

Representation learning and \emph{de novo} generation of proteins are pivotal computational biology tasks. Whilst natural language processing (NLP) techniques have proven highly effective for protein sequence modelling, structure modelling…

Deep neural models (e.g. Transformer) naturally learn spurious features, which create a ``shortcut'' between the labels and inputs, thus impairing the generalization and robustness. This paper advances the self-attention mechanism to its…

Masked language modeling, widely used in discriminative language model (e.g., BERT) pretraining, commonly adopts a random masking strategy. However, random masking does not consider the importance of the different words in the sentence…

Many recent models in software engineering introduced deep neural models based on the Transformer architecture or use transformer-based Pre-trained Language Models (PLM) trained on code. Although these models achieve the state of the arts…

Transformer language models (TLMs) are critical for most NLP tasks, but they are difficult to create for low-resource languages because of how much pretraining data they require. In this work, we investigate two techniques for training…

Prevalent supervised learning methods in natural language processing (NLP) are notoriously data-hungry, which demand large amounts of high-quality annotated data. In practice, acquiring such data is a costly endeavor. Recently, the superior…

Transformer-based large language models (LLMs) have achieved strong performance across many natural language processing tasks. Nonetheless, their quadratic computational and memory requirements, particularly in self-attention layers, pose…

Fine-tuning BERT-based models is resource-intensive in memory, computation, and time. While many prior works aim to improve inference efficiency via compression techniques, e.g., pruning, these works do not explicitly address the…

We study the problem of leveraging the syntactic structure of text to enhance pre-trained models such as BERT and RoBERTa. Existing methods utilize syntax of text either in the pre-training stage or in the fine-tuning stage, so that they…

We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based…

One reason pretraining on self-supervised linguistic tasks is effective is that it teaches models features that are helpful for language understanding. However, we want pretrained models to learn not only to represent linguistic features,…

Protein language models (pLMs) have demonstrated success at generating functional proteins across vast sequence spaces but lack the ability to design high-fitness variants on demand. Here, we iteratively guide pLMs toward user-defined…

The introduction of Large Language Models (LLMs), and the vast volume of publicly available medical data, amplified the application of NLP to the medical domain. However, LLMs are pretrained on data that are not explicitly relevant to the…

Over the past six years, molecular transformer models have become key tools in drug discovery. Most existing models are pre-trained on large, unlabeled datasets such as ZINC or ChEMBL. However, the extent to which large-scale pre-training…

Active learning strives to reduce annotation costs by choosing the most critical examples to label. Typically, the active learning strategy is contingent on the classification model. For instance, uncertainty sampling depends on poorly…

Masked language models (MLMs) such as BERT and RoBERTa have revolutionized the field of Natural Language Understanding in the past few years. However, existing pre-trained MLMs often output an anisotropic distribution of token…

Transformer-based language models, more specifically BERT-based architectures have achieved state-of-the-art performance in many downstream tasks. However, for a relatively low-resource language such as Thai, the choices of models are…