Cheng Tan

Xiangxiang Zhang, Caijun Jia, Siyuan Li et al.

Solving complex geometric problems inherently requires interleaved reasoning: a tight alternation between constructing diagrams and performing logical deductions. Although recent Multimodal Large Language Models (MLLMs) have demonstrated strong capabilities in visual generation and plotting, we identify a counter-intuitive and underexplored phenomenon. Naively applying Supervised Fine-Tuning (SFT) on interleaved plot-solution data leads to a substantial degradation in reasoning performance compared to text-only baselines. We argue that this failure stems from a fundamental limitation of SFT, which primarily induces distributional alignment: the model learns to reproduce the surface format of interleaved plotting but fails to internalize the causal dependency between the generated plot and reasoning steps. To overcome this limitation, we propose Faire (Functional alignment for interleaved reasoning), a reinforcement learning framework that enforces three casual constraints to move beyond superficial imitation toward functional alignment. Extensive experiments show that Faire induces a qualitative shift in model behavior in which the plotting is effectively internalized, yielding competitive performance on challenging geometric reasoning benchmarks.

Wenxuan Huang, Mingyu Tsoi, Yanhao Huang et al.

Single-cell perturbation studies face dual heterogeneity bottlenecks: (i) semantic heterogeneity--identical biological concepts encoded under incompatible metadata schemas across datasets; and (ii) statistical heterogeneity--distribution shifts from biological variation demanding dataset-specific inductive biases. We propose HarmonyCell, an end-to-end agent framework resolving each challenge through a dedicated mechanism: an LLM-driven Semantic Unifier autonomously maps disparate metadata into a canonical interface without manual intervention; and an adaptive Monte Carlo Tree Search engine operates over a hierarchical action space to synthesize architectures with optimal statistical inductive biases for distribution shifts. Evaluated across diverse perturbation tasks under both semantic and distribution shifts, HarmonyCell achieves a 95% valid execution rate on heterogeneous input datasets (versus 0% for general agents) while matching or even exceeding expert-designed baselines in rigorous out-of-distribution evaluations. This dual-track orchestration enables scalable automatic virtual cell modeling without dataset-specific engineering.