Ye Peng

Chaoqi Liang, Lifeng Qiao, Peng Ye et al.

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 because of their potential to capture general information about genes. However, existing pre-training methods for DNA sequences largely rely on direct adoptions of BERT pre-training from NLP, lacking a comprehensive understanding and a specifically tailored approach. To address this research gap, we provide the first empirical study with three insightful observations. Based on the empirical study, we notice that overlapping tokenizer can benefit the fine-tuning of downstream tasks but leads to inadequate pre-training with fast convergence. To unleash the pre-training potential, we introduce a novel approach called RandomMask, which gradually increases the task difficulty of BERT-like pre-training by continuously expanding its mask boundary, forcing the model to learn more knowledge. RandomMask is simple but effective, achieving state-of-the-art performance across 6 downstream tasks. RandomMask achieves a staggering 68.16\% in Matthew's correlation coefficient for Epigenetic Mark Prediction, a groundbreaking increase of 19.85\% over the baseline and a remarkable 3.69\% improvement over the previous state-of-the-art result.

Yuchen Ren, Zhiyuan Chen, Lifeng Qiao et al.

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (\textbf{BE}nchm\textbf{A}rk for \textbf{CO}mprehensive R\textbf{N}A Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

Lifeng Qiao, Peng Ye, Yuchen Ren et al.

Foundation models have made significant strides in understanding the genomic language of DNA sequences. However, previous models typically adopt the tokenization methods designed for natural language, which are unsuitable for DNA sequences due to their unique characteristics. In addition, the optimal approach to tokenize DNA remains largely under-explored, and may not be intuitively understood by humans even if discovered. To address these challenges, we introduce MxDNA, a novel framework where the model autonomously learns an effective DNA tokenization strategy through gradient decent. MxDNA employs a sparse Mixture of Convolution Experts coupled with a deformable convolution to model the tokenization process, with the discontinuous, overlapping, and ambiguous nature of meaningful genomic segments explicitly considered. On Nucleotide Transformer Benchmarks and Genomic Benchmarks, MxDNA demonstrates superior performance to existing methods with less pretraining data and time, highlighting its effectiveness. Finally, we show that MxDNA learns unique tokenization strategy distinct to those of previous methods and captures genomic functionalities at a token level during self-supervised pretraining. Our MxDNA aims to provide a new perspective on DNA tokenization, potentially offering broad applications in various domains and yielding profound insights.

Biqing Qi, Fangyuan Li, Zhen Wang et al.

As an effective approach to equip models with multi-task capabilities without additional training, model merging has garnered significant attention. However, existing methods face challenges of redundant parameter conflicts and the excessive storage burden of parameters. In this work, through controlled experiments, we reveal that for task vectors, only those parameters with magnitudes above a certain threshold contribute positively to the task, exhibiting a pulse-like characteristic. We then attempt leveraging this characteristic to binarize the task vectors and reduce storage overhead. Further controlled experiments show that the binarized task vectors incur almost no decrease in fine-tuning and merging performance, and even exhibit stronger performance improvements as the proportion of redundant parameters increases. Based on these insights, we propose Task Switch (T-Switch), which decomposes task vectors into three components: 1) an activation switch instantiated by a binarized mask vector, 2) a polarity switch instantiated by a binarized sign vector, and 3) a scaling knob instantiated by a scalar coefficient. By storing task vectors in a binarized form, T-Switch alleviates parameter conflicts while ensuring efficient task parameter storage. Furthermore, to enable automated switch combination in T-Switch, we further introduce Auto-Switch, which enables training-free switch combination via retrieval from a small query set. Experiments indicate that our methods achieve significant performance improvements over existing baselines, requiring only 1-3% of the storage space of full-precision parameters.