6 papers
Biological Reasoning-Informed Regression for Interpretable Regulatory DNA Activity Prediction
Yi Duan, Zhao Yang, Jiwei Zhu +3
DNA cis-regulatory elements (CREs) such as enhancers control gene expression levels. Accurately predicting regulatory activity from DNA sequences is valuable but challenging, as it…
Extending Sequence Length is Not All You Need: Effective Integration of Multimodal Signals for Gene Expression Prediction
Zhao Yang, Yi Duan, Jiwei Zhu +3
Gene expression prediction, which predicts mRNA expression levels from DNA sequences, presents significant challenges. Previous works often focus on extending input sequence length…
D3LM: A Discrete DNA Diffusion Language Model for Bidirectional DNA Understanding and Generation
Zhao Yang, Hengchang Liu, Chuan Cao +1
Early DNA foundation models adopted BERT-style training, achieving good performance on DNA understanding tasks but lacking generative capabilities. Recent autoregressive models ena…
Nature Language Model: Deciphering the Language of Nature for Scientific Discovery
Yingce Xia, Peiran Jin, Shufang Xie +43
Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspire…
Regulatory DNA sequence Design with Reinforcement Learning
Zhao Yang, Bing Su, Chuan Cao +1
Cis-regulatory elements (CREs), such as promoters and enhancers, are relatively short DNA sequences that directly regulate gene expression. The fitness of CREs, measured by their a…
HybriDNA: A Hybrid Transformer-Mamba2 Long-Range DNA Language Model
Mingqian Ma, Guoqing Liu, Chuan Cao +12
Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling…