Related papers: GeneMask: Fast Pretraining of Gene Sequences to En…

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.…

With the success of large-scale pre-training in language tasks, there is an increasing trend of applying it to the domain of life sciences. In particular, pre-training methods based on DNA sequences have received increasing attention…

Tokenization sits at the boundary between high-throughput genomic input and GPU compute, posing challenges in both algorithm design and system throughput. Overlapping k-mer tokenization can introduce information leakage under masked…

Pre-training large language models on genomic sequences is a powerful approach for learning biologically meaningful representations. Masked language modeling (MLM) methods, such as DNABERT and Nucleotide Transformer (NT), achieve strong…

There are already many DNA large language models, but most of them still follow traditional uses, such as extracting sequence features for classification tasks. More innovative applications of large language models, such as prompt…

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…

Masked language modeling (MLM) is one of the key sub-tasks in vision-language pretraining. In the cross-modal setting, tokens in the sentence are masked at random, and the model predicts the masked tokens given the image and the text. In…

Language models, especially transformer-based ones, have achieved colossal success in NLP. To be precise, studies like BERT for NLU and works like GPT-3 for NLG are very important. If we consider DNA sequences as a text written with an…

Masked language modeling is widely used for pretraining large language models for natural language understanding (NLU). However, random masking is suboptimal, allocating an equal masking rate for all tokens. In this paper, we propose…

Understanding protein sequences is vital and urgent for biology, healthcare, and medicine. Labeling approaches are expensive yet time-consuming, while the amount of unlabeled data is increasing quite faster than that of the labeled data due…

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…

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…

Existing language models (LMs) predict tokens with a softmax over a finite vocabulary, which can make it difficult to predict rare tokens or phrases. We introduce NPM, the first nonparametric masked language model that replaces this softmax…

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…

Transferring knowledge from one domain to another is of practical importance for many tasks in natural language processing, especially when the amount of available data in the target domain is limited. In this work, we propose a novel…

Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that…

In the genome biology research, regulatory genome modeling is an important topic for many regulatory downstream tasks, such as promoter classification, transaction factor binding sites prediction. The core problem is to model how regulatory…

While encoder-only models such as BERT and ModernBERT are ubiquitous in real-world NLP applications, their conventional reliance on task-specific classification heads can limit their applicability compared to decoder-based large language…

Modeling genomic sequences faces two unsolved challenges: the information density varies widely across different regions, while there is no clearly defined minimum vocabulary unit. Relying on either four primitive bases or independently…

A fine-grained data recipe is crucial for pre-training large language models, as it can significantly enhance training efficiency and model performance. One important ingredient in the recipe is to select samples based on scores produced by…