Related papers: NucEL: Single-Nucleotide ELECTRA-Style Genomic Pre…

Pre-training is crucial for large language models (LLMs), as it is when most representations and capabilities are acquired. However, natural language pre-training has problems: high-quality text is finite, it contains human biases, and it…

Learning high-quality text representations is fundamental to a wide range of NLP tasks. While encoder pretraining has traditionally relied on Masked Language Modeling (MLM), recent evidence suggests that decoder models pretrained with…

Coarse-grained linguistic information, such as named entities or phrases, facilitates adequately representation learning in pre-training. Previous works mainly focus on extending the objective of BERT's Masked Language Modeling (MLM) from…

We introduce a novel continued pre-training method, MELT (MatEriaLs-aware continued pre-Training), specifically designed to efficiently adapt the pre-trained language models (PLMs) for materials science. Unlike previous adaptation…

Long non-coding RNAs (lncRNAs) serve as crucial regulators in numerous biological processes. Although they share sequence similarities with messenger RNAs (mRNAs), lncRNAs perform entirely different roles, providing new avenues for…

The accurate segmentation of lesions in whole-body PET/CT imaging is es-sential for tumor characterization, treatment planning, and response assess-ment, yet current manual workflows are labor-intensive and prone to inter-observer…

Most existing vision-language pre-training methods focus on understanding tasks and use BERT-like objectives (masked language modeling and image-text matching) during pretraining. Although they perform well in many understanding downstream…

Tokens serve as the basic units of representation in DNA language models (DNALMs), yet their design remains underexplored. Unlike natural language, DNA lacks inherent token boundaries or predefined compositional rules, making tokenization a…

Gene enhancers control when and where genes switch on, yet their sequence diversity and tissue specificity make them hard to pinpoint in colorectal cancer. We take a sequence-only route and fine-tune DNABERT-2, a transformer genomic…

Recently, pre-trained language models mostly follow the pre-train-then-fine-tuning paradigm and have achieved great performance on various downstream tasks. However, since the pre-training stage is typically task-agnostic and the…

Neuro-encoded expression programming(NEEP) that aims to offer a novel continuous representation of combinatorial encoding for genetic programming methods is proposed in this paper. Genetic programming with linear representation uses…

Large pretrained language models (LMs) have become the central building block of many NLP applications. Training these models requires ever more computational resources and most of the existing models are trained on English text only. It is…

Large-scale language model pretraining is a very successful form of self-supervised learning in natural language processing, but it is increasingly expensive to perform as the models and pretraining corpora have become larger over time. We…

This paper presents a new Unified pre-trained Language Model (UniLM) that can be fine-tuned for both natural language understanding and generation tasks. The model is pre-trained using three types of language modeling tasks: unidirectional,…

The Transformer architecture deeply changed the natural language processing, outperforming all previous state-of-the-art models. However, well-known Transformer models like BERT, RoBERTa, and GPT-2 require a huge compute budget to create a…

Less than 1% of protein sequences are structurally and functionally annotated. Natural Language Processing (NLP) community has recently embraced self-supervised learning as a powerful approach to learn representations from unlabeled text,…

Large language models (LLMs) have shown strong ability in generating rich representations across domains such as natural language processing and generation, computer vision, and multimodal learning. However, their application in biomedical…

Pretraining DNA language models (DNALMs) on the full human genome is resource-intensive, yet often considered necessary for strong downstream performance. Inspired by recent findings in NLP and long-context modeling, we explore an…

While originally designed for unidirectional generative modeling, decoder-only large language models (LLMs) are increasingly being adapted for bidirectional modeling. However, unidirectional and bidirectional models are typically trained…

Advancements in lithium battery technology heavily rely on the design and engineering of electrolytes. However, current schemes for molecular design and recipe optimization of electrolytes lack an effective computational-experimental closed…