SCALE:Scalable Conditional Atlas-Level Endpoint transport for virtual cell perturbation prediction

Virtual cell models aim to enable in silico experimentation by predicting how cells respond to genetic, chemical, or cytokine perturbations from single-cell measurements. In practice, however, large-scale perturbation prediction remains constrained by three coupled bottlenecks: inefficient training and inference pipelines, unstable modeling in high-dimensional sparse expression space, and evaluation protocols that overemphasize reconstruction-like accuracy while underestimating biological fidelity. In this work we present a specialized large-scale foundation model SCALE for virtual cell perturbation prediction that addresses the above limitations jointly. First, we build a BioNeMo-based training and inference framework that substantially improves data throughput, distributed scalability, and deployment efficiency, yielding 12.51* speedup on pretrain and 1.29* on inference over the prior SOTA pipeline under matched system settings. Second, we formulate perturbation prediction as conditional transport and implement it with a set-aware flow architecture that couples LLaMA-based cellular encoding with endpoint-oriented supervision. This design yields more stable training and stronger recovery of perturbation effects. Third, we evaluate the model on Tahoe-100M using a rigorous cell-level protocol centered on biologically meaningful metrics rather than reconstruction alone. On this benchmark, our model improves PDCorr by 12.02% and DE Overlap by 10.66% over STATE. Together, these results suggest that advancing virtual cells requires not only better generative objectives, but also the co-design of scalable infrastructure, stable transport modeling, and biologically faithful evaluation.

BEYOND DIALOGUE: A Profile-Dialogue Alignment Framework Towards General Role-Playing Language Model

The rapid advancement of large language models (LLMs) has revolutionized role-playing, enabling the development of general role-playing models. However, current role-playing training has two significant issues: (I) Using a predefined role profile to prompt dialogue training for specific scenarios usually leads to inconsistencies and even conflicts between the dialogue and the profile, resulting in training biases. (II) The model learns to imitate the role based solely on the profile, neglecting profile-dialogue alignment at the sentence level. In this work, we propose a simple yet effective framework called BEYOND DIALOGUE, designed to overcome these hurdles. This framework innovatively introduces "beyond dialogue" tasks to align dialogue with profile traits based on each specific scenario, thereby eliminating biases during training. Furthermore, by adopting an innovative prompting mechanism that generates reasoning outcomes for training, the framework allows the model to achieve fine-grained alignment between profile and dialogue at the sentence level. The aforementioned methods are fully automated and low-cost. Additionally, the integration of automated dialogue and objective evaluation methods forms a comprehensive framework, paving the way for general role-playing. Experimental results demonstrate that our model excels in adhering to and reflecting various dimensions of role profiles, outperforming most proprietary general and specialized role-playing baselines. All code and datasets are available at https://github.com/yuyouyu32/BeyondDialogue.