Lifeng Qiao

Luozhijie Jin, Zijie Qiu, Jie Liu et al.

Denoising-based generative models, particularly diffusion and flow matching algorithms, have achieved remarkable success. However, aligning their output distributions with complex downstream objectives, such as human preferences, compositional accuracy, or data compressibility, remains challenging. While reinforcement learning (RL) fine-tuning methods, inspired by advances in RL from human feedback (RLHF) for large language models, have been adapted to these generative frameworks, current RL approaches are suboptimal for diffusion models and offer limited flexibility in controlling alignment strength after fine-tuning. In this work, we reinterpret RL fine-tuning for diffusion models through the lens of stochastic differential equations and implicit reward conditioning. We introduce Reinforcement Learning Guidance (RLG), an inference-time method that adapts Classifier-Free Guidance (CFG) by combining the outputs of the base and RL fine-tuned models via a geometric average. Our theoretical analysis shows that RLG's guidance scale is mathematically equivalent to adjusting the KL-regularization coefficient in standard RL objectives, enabling dynamic control over the alignment-quality trade-off without further training. Extensive experiments demonstrate that RLG consistently improves the performance of RL fine-tuned models across various architectures, RL algorithms, and downstream tasks, including human preferences, compositional control, compressibility, and text rendering. Furthermore, RLG supports both interpolation and extrapolation, thereby offering unprecedented flexibility in controlling generative alignment. Our approach provides a practical and theoretically sound solution for enhancing and controlling diffusion model alignment at inference. The source code for RLG is publicly available at the Github: https://github.com/jinluo12345/Reinforcement-learning-guidance.

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 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.