Related papers: Structure-Aware Masking for Protein Representation…

Proteins are fundamental to biology, executing diverse functions through complex physicochemical interactions, and they hold transformative potential across medicine, materials science, and environmental applications. Protein Language…

Masked Language Modeling (MLM) is widely used to pretrain language models. The standard random masking strategy in MLM causes the pre-trained language models (PLMs) to be biased toward high-frequency tokens. Representation learning of rare…

Prompt tuning and adapter tuning have shown great potential in transferring pre-trained vision-language models (VLMs) to various downstream tasks. In this work, we design a new type of tuning method, termed as regularized mask tuning, which…

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 demonstrated exceptional performance across various tasks, with pre-training stage serving as the cornerstone of their capabilities. However, the conventional fixed-length data composition strategy for…

A possible explanation for the impressive performance of masked language model (MLM) pre-training is that such models have learned to represent the syntactic structures prevalent in classical NLP pipelines. In this paper, we propose a…

Protein language models (PLMs) have shown promise in improving the understanding of protein sequences, contributing to advances in areas such as function prediction and protein engineering. However, training these models from scratch…

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…

Modern Protein Language Models (PLMs) apply transformer-based model architectures from natural language processing to biological sequences, predicting a variety of protein functions and properties. However, protein language has key…

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…

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its…

Masked language modeling has become a standard pretraining objective for training encoder-based language models. In this approach, certain tokens in the input are masked, and the model learns to predict them using the surrounding context.…

Masked Language Model (MLM) framework has been widely adopted for self-supervised language pre-training. In this paper, we argue that randomly sampled masks in MLM would lead to undesirably large gradient variance. Thus, we theoretically…

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.…

Decomposing complex tasks into a sequence of simpler subtasks can improve learning efficiency for an autonomous agent. Reinforcement learning (RL) can be used to optimize agent policies to complete subtasks, but requires well-defined…

A Restricted Boltzmann Machine (RBM) is an unsupervised machine-learning bipartite graphical model that jointly learns a probability distribution over data and extracts their relevant statistical features. As such, RBM were recently…

Representation learning for proteins has primarily focused on the global understanding of protein sequences regardless of their length. However, shorter proteins (known as peptides) take on distinct structures and functions compared to…

The pre-training of masked language models (MLMs) consumes massive computation to achieve good results on downstream NLP tasks, resulting in a large carbon footprint. In the vanilla MLM, the virtual tokens, [MASK]s, act as placeholders and…

Causal Language Modeling (CLM) and Masked Language Modeling (MLM) are two mainstream learning paradigms based on Transformer networks, specifically the Decoder-only and Encoder-only architectures. The strengths of each paradigm in…

Deep neural-network-based language models (LMs) are increasingly applied to large-scale protein sequence data to predict protein function. However, being largely black-box models and thus challenging to interpret, current protein LM…