Yuchen Ren

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, Zhengyu Zhao, Chenhao Lin et al.

Transferable adversarial examples are known to cause threats in practical, black-box attack scenarios. A notable approach to improving transferability is using integrated gradients (IG), originally developed for model interpretability. In this paper, we find that existing IG-based attacks have limited transferability due to their naive adoption of IG in model interpretability. To address this limitation, we focus on the IG integration path and refine it in three aspects: multiplicity, monotonicity, and diversity, supported by theoretical analyses. We propose the Multiple Monotonic Diversified Integrated Gradients (MuMoDIG) attack, which can generate highly transferable adversarial examples on different CNN and ViT models and defenses. Experiments validate that MuMoDIG outperforms the latest IG-based attack by up to 37.3\% and other state-of-the-art attacks by 8.4\%. In general, our study reveals that migrating established techniques to improve transferability may require non-trivial efforts. Code is available at \url{https://github.com/RYC-98/MuMoDIG}.

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.

Haonan He, Yuchen Ren, Yining Tang et al.

Large language models (LLMs) have shown remarkable capabilities in general domains, but their application to multi-omics biology remains underexplored. To address this gap, we introduce Biology-Instructions, the first large-scale instruction-tuning dataset for multi-omics biological sequences, including DNA, RNA, proteins, and multi-molecules. This dataset bridges LLMs and complex biological sequence-related tasks, enhancing their versatility and reasoning while maintaining conversational fluency. We also highlight significant limitations of current state-of-the-art LLMs on multi-omics tasks without specialized training. To overcome this, we propose ChatMultiOmics, a strong baseline with a novel three-stage training pipeline, demonstrating superior biological understanding through Biology-Instructions. Both resources are publicly available, paving the way for better integration of LLMs in multi-omics analysis. The Biology-Instructions is publicly available at: https://github.com/hhnqqq/Biology-Instructions.

Ming Hu, Chenglong Ma, Wei Li et al. · pku

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a comprehensive, data-centric synthesis that reframes the development of Sci-LLMs as a co-evolution between models and their underlying data substrate. We formulate a unified taxonomy of scientific data and a hierarchical model of scientific knowledge, emphasizing the multimodal, cross-scale, and domain-specific challenges that differentiate scientific corpora from general natural language processing datasets. We systematically review recent Sci-LLMs, from general-purpose foundations to specialized models across diverse scientific disciplines, alongside an extensive analysis of over 270 pre-/post-training datasets, showing why Sci-LLMs pose distinct demands -- heterogeneous, multi-scale, uncertainty-laden corpora that require representations preserving domain invariance and enabling cross-modal reasoning. On evaluation, we examine over 190 benchmark datasets and trace a shift from static exams toward process- and discovery-oriented assessments with advanced evaluation protocols. These data-centric analyses highlight persistent issues in scientific data development and discuss emerging solutions involving semi-automated annotation pipelines and expert validation. Finally, we outline a paradigm shift toward closed-loop systems where autonomous agents based on Sci-LLMs actively experiment, validate, and contribute to a living, evolving knowledge base. Collectively, this work provides a roadmap for building trustworthy, continually evolving artificial intelligence (AI) systems that function as a true partner in accelerating scientific discovery.

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.

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.

Bo Yang, Hengwei Zhang, Jindong Wang et al.

In surrogate ensemble attacks, using more surrogate models yields higher transferability but lower resource efficiency. This practical trade-off between transferability and efficiency has largely limited existing attacks despite many pre-trained models are easily accessible online. In this paper, we argue that such a trade-off is caused by an unnecessary common assumption, i.e., all models should be \textit{identical} across iterations. By lifting this assumption, we can use as many surrogates as we want to unleash transferability without sacrificing efficiency. Concretely, we propose Selective Ensemble Attack (SEA), which dynamically selects diverse models (from easily accessible pre-trained models) across iterations based on our new interpretation of decoupling within-iteration and cross-iteration model diversity. In this way, the number of within-iteration models is fixed for maintaining efficiency, while only cross-iteration model diversity is increased for higher transferability. Experiments on ImageNet demonstrate the superiority of SEA in various scenarios. For example, when dynamically selecting 4 from 20 accessible models, SEA yields 8.5% higher transferability than existing attacks under the same efficiency. The superiority of SEA also generalizes to real-world systems, such as commercial vision APIs and large vision-language models. Overall, SEA opens up the possibility of adaptively balancing transferability and efficiency according to specific resource requirements.

Zhangyin Feng, Yuchen Ren, Xinmiao Yu et al.

Diffusion models developed on top of powerful text-to-image generation models like Stable Diffusion achieve remarkable success in visual story generation. However, the best-performing approach considers historically generated results as flattened memory cells, ignoring the fact that not all preceding images contribute equally to the generation of the characters and scenes at the current stage. To address this, we present a simple method that improves the leading system with adaptive context modeling, which is not only incorporated in the encoder but also adopted as additional guidance in the sampling stage to boost the global consistency of the generated story. We evaluate our model on PororoSV and FlintstonesSV datasets and show that our approach achieves state-of-the-art FID scores on both story visualization and continuation scenarios. We conduct detailed model analysis and show that our model excels at generating semantically consistent images for stories.

Zhaoyang Hai, Xiabi Liu, Yuchen Ren et al.

The field of meta-learning has seen a dramatic rise in interest in recent years. In existing meta-learning approaches, learning tasks for training meta-models are usually collected from public datasets, which brings the difficulty of obtaining a sufficient number of meta-learning tasks with a large amount of training data. In this paper, we propose a meta-learning approach based on randomly generated meta-learning tasks to obtain a parametric loss for classification learning based on big data. The loss is represented by a deep neural network, called meta-loss network (MLN). To train the MLN, we construct a large number of classification learning tasks through randomly generating training data, validation data, and corresponding ground-truth linear classifier. Our approach has two advantages. First, sufficient meta-learning tasks with large number of training data can be obtained easily. Second, the ground-truth classifier is given, so that the difference between the learned classifier and the ground-truth model can be measured to reflect the performance of MLN more precisely than validation accuracy. Based on this difference, we apply the evolutionary strategy algorithm to find out the optimal MLN. The resultant MLN not only leads to satisfactory learning effects on generated linear classifier learning tasks for testing, but also behaves very well on generated nonlinear classifier learning tasks and various public classification tasks. Our MLN stably surpass cross-entropy (CE) and mean square error (MSE) in testing accuracy and generalization ability. These results illustrate the possibility of achieving satisfactory meta-learning effects using generated learning tasks.