Y. Cai

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.

Yuchen Cai, Ding Cao, Rongxi Guo et al.

Large language models(LLM) are pre-trained on extensive corpora to learn facts and human cognition which contain human preferences. However, this process can inadvertently lead to these models acquiring biases and stereotypes prevalent in society. Prior research has typically tackled the issue of bias through a one-dimensional perspective, concentrating either on locating or mitigating it. This limited perspective has created obstacles in facilitating research on bias to synergistically complement and progressively build upon one another. In this study, we integrate the processes of locating and mitigating bias within a unified framework. Initially, we use causal mediation analysis to trace the causal effects of different components' activation within a large language model. Building on this, we propose the LSDM (Least Square Debias Method), a knowledge-editing based method for mitigating gender bias in occupational pronouns, and compare it against two baselines on three gender bias datasets and seven knowledge competency test datasets. The experimental results indicate that the primary contributors to gender bias are the bottom MLP modules acting on the last token of occupational pronouns and the top attention module acting on the final word in the sentence. Furthermore, LSDM mitigates gender bias in the model more effectively than the other baselines, while fully preserving the model's capabilities in all other aspects.

Yuchen Ren, Wenwei Han, Qianyuan Zhang et al.

As key elements within the central dogma, DNA, RNA, and proteins play crucial roles in maintaining life by guaranteeing accurate genetic expression and implementation. Although research on these molecules has profoundly impacted fields like medicine, agriculture, and industry, the diversity of machine learning approaches-from traditional statistical methods to deep learning models and large language models-poses challenges for researchers in choosing the most suitable models for specific tasks, especially for cross-omics and multi-omics tasks due to the lack of comprehensive benchmarks. To address this, we introduce the first comprehensive multi-omics benchmark COMET (Benchmark for Biological COmprehensive Multi-omics Evaluation Tasks and Language Models), designed to evaluate models across single-omics, cross-omics, and multi-omics tasks. First, we curate and develop a diverse collection of downstream tasks and datasets covering key structural and functional aspects in DNA, RNA, and proteins, including tasks that span multiple omics levels. Then, we evaluate existing foundational language models for DNA, RNA, and proteins, as well as the newly proposed multi-omics method, offering valuable insights into their performance in integrating and analyzing data from different biological modalities. This benchmark aims to define critical issues in multi-omics research and guide future directions, ultimately promoting advancements in understanding biological processes through integrated and different omics data analysis.

Ding Cao, Yuchen Cai, Rongxi Guo et al.

Sequential knowledge editing techniques aim to continuously update the knowledge in large language models at a low cost, preventing the models from generating outdated or incorrect information. However, existing sequential editing methods suffer from a significant decline in editing success rates after long-term editing. Through theoretical analysis and experiments, we identify that as the number of edits increases, the model's output increasingly deviates from the desired target, leading to a drop in editing success rates. We refer to this issue as the accumulation of superimposed noise problem. To address this, we identify the factors contributing to this deviation and propose DeltaEdit, a novel method that optimizes update parameters through a dynamic orthogonal constraints strategy, effectively reducing interference between edits to mitigate deviation. Experimental results demonstrate that DeltaEdit significantly outperforms existing methods in edit success rates and the retention of generalization capabilities, ensuring stable and reliable model performance even under extensive sequential editing.