Yixuan Dong

Mengran Li, Bo Li, Jiaying Wang et al.

Virtual Cell Modeling (VCM) requires models that not only predict perturbation responses, but also support targeted revision when predictions fail. Current LLM-assisted modeling workflows face a refinement-routing problem: prediction discrepancies are observed through executable implementations, but the relevant revision may involve the modeling assumption, representation design, implementation, or task constraint. Without structured feedback propagation across these levels, iterative refinement may repair code while failing to revise the assumption responsible for the discrepancy. We propose CellScientist, a dual-space hierarchical framework that couples a high-level hypothesis space with a low-level executable implementation space. CellScientist represents modeling decisions as structured states, realizes them as admissible programs under task and interface constraints, and routes execution discrepancies back to targeted hypothesis or implementation updates. This enables a closed Hypothesis -> Implementation -> Hypothesis loop where failures become structured signals for model refinement rather than debugging events. Across morphology and transcriptomic benchmarks, with additional single-cell perturbation evaluations, the final executable models selected by CellScientist improve over reference baselines under fixed split and evaluation protocols, while the workflow produces auditable refinement traces.

Yixuan Dong, Fang-Yi Su, Jung-Hsien Chiang

Data augmentation for domain-specific image classification tasks often struggles to simultaneously address diversity, faithfulness, and label clarity of generated data, leading to suboptimal performance in downstream tasks. While existing generative diffusion model-based methods aim to enhance augmentation, they fail to cohesively tackle these three critical aspects and often overlook intrinsic challenges of diffusion models, such as sensitivity to model characteristics and stochasticity under strong transformations. In this paper, we propose a novel framework that explicitly integrates diversity, faithfulness, and label clarity into the augmentation process. Our approach employs saliency-guided mixing and a fine-tuned diffusion model to preserve foreground semantics, enrich background diversity, and ensure label consistency, while mitigating diffusion model limitations. Extensive experiments across fine-grained, long-tail, few-shot, and background robustness tasks demonstrate our method's superior performance over state-of-the-art approaches.