Related papers: Unlocking Efficiency: Adaptive Masking for Gene Tr…

Molecular property prediction is an increasingly critical task within drug discovery and development. Typically, neural networks can learn molecular properties using graph-based, language-based or feature-based methods. Recent advances in…

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…

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…

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…

When adapting an encoder to a new domain, the standard approach is to continue training with Masked Language Modeling (MLM). We show that temporarily switching to Causal Language Modeling (CLM) followed by a short MLM decay improves…

Masked image modeling has been demonstrated as a powerful pretext task for generating robust representations that can be effectively generalized across multiple downstream tasks. Typically, this approach involves randomly masking patches…

We propose a novel task-agnostic in-domain pre-training method that sits between generic pre-training and fine-tuning. Our approach selectively masks in-domain keywords, i.e., words that provide a compact representation of the target…

Large Language Models (LLMs) employ three popular training approaches: Masked Language Models (MLM), Causal Language Models (CLM), and Sequence-to-Sequence Models (seq2seq). However, each approach has its strengths and limitations, and…

Pre-trained language model (PTM) has been shown to yield powerful text representations for dense passage retrieval task. The Masked Language Modeling (MLM) is a major sub-task of the pre-training process. However, we found that the…

The practice of fine-tuning Pre-trained Language Models (PLMs) from general or domain-specific data to a specific task with limited resources, has gained popularity within the field of natural language processing (NLP). In this work, we…

Masked language modeling (MLM) pre-training models such as BERT corrupt the input by replacing some tokens with [MASK] and then train a model to reconstruct the original tokens. This is an effective technique which has led to good results…

Masked diffusion models (MDMs) have emerged as a promising alternative to autoregressive models (ARMs) for language modeling. However, MDMs are known to learn substantially more slowly than ARMs, which may become problematic when scaling…

Most works on transformers trained with the Masked Language Modeling (MLM) objective use the original BERT model's fixed masking rate of 15%. We propose to instead dynamically schedule the masking rate throughout training. We find that…

Masked Language Modeling (MLM) has proven to be an essential component of Vision-Language (VL) pretraining. To implement MLM, the researcher must make two design choices: the masking strategy, which determines which tokens to mask, and the…

Recent work has shown the importance of adaptation of broad-coverage contextualised embedding models on the domain of the target task of interest. Current self-supervised adaptation methods are simplistic, as the training signal comes from…

We describe our strategy for the 2025 edition of the BabyLM Challenge. Our main contribution is that of an improved form of Masked Language Modeling (MLM), which adapts the probabilities of the tokens masked according to the model's ability…

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…

DNA language models are increasingly used to represent genomic sequence, yet their effectiveness depends critically on how raw nucleotides are converted into model inputs. Unlike natural language, DNA offers no canonical boundaries, making…

Domain adaptation for large neural language models (NLMs) is coupled with massive amounts of unstructured data in the pretraining phase. In this study, however, we show that pretrained NLMs learn in-domain information more effectively and…