Rethinking the BERT-like Pretraining for DNA Sequences. - Chaoqi Liang; Weiqiang Bai; Lifeng Qiao; Yuchen Ren 001; Jianle Sun; Peng Ye 006; Hongliang Yan; Xinzhu Ma; Wangmeng Zuo; Wanli Ouyang (CoRR, 2023)

Model Decides How to Tokenize: Adaptive DNA Sequence Tokenization with MxDNA. - Lifeng Qiao; Peng Ye 006; Yuchen Ren 001; Weiqiang Bai; Chaoqi Liang; Xinzhu Ma; Nanqing Dong; Wanli Ouyang (NeurIPS, 2024)

COMET: Benchmark for Comprehensive Biological Multi-omics Evaluation Tasks and Language Models. - Yuchen Ren 001; Wenwei Han; Qianyuan Zhang; Yining Tang; Weiqiang Bai; Yuchen Cai; Lifeng Qiao; Hao Jiang; Dong Yuan; Tao Chen 003; Siqi Sun; Pan Tan; et al. (CoRR, 2024)

Revisiting Convolution Architecture in the Realm of DNA Foundation Models. - Yu Bo; Weian Mao; Yanjun Shao; Weiqiang Bai; Peng Ye 006; Xinzhu Ma; Junbo Zhao; Hao Chen 041; Chunhua Shen (ICLR, 2025)