Nuclear quantification requires locating and typing nuclei, beyond generating a count. Inspired by Jev's structured decisions in place of free-form generation, we introduce NuJEV for nuclear perception in Qwen3-VL-2B. We jointly train visual LoRA and a parallel head to predict nuclear presence, centers, and types. One image encoding feeds both the nuclear head and original language decoder. The decoder interprets region and type requests, with counts computed from the predicted nuclei. On 2,732 PanNuke test images, NuJEV achieves a five-query mean absolute error ($\mathrm{MAE}_5$) of 1.844 overall and 5.268 on dense images, with localization/typed F1 of 0.816/0.682. A matched encoder ablation shows 41.0\% lower dense error with visual adaptation. For language requests, NuJEV reduces request MAE by 76.2\% relative to direct generation. Our code will be released as open source.
Mechanism-AI coupled dynamical systems are increasingly used to study complex biological systems. However, uncertainty associated with noisy, sparse, and partially observed data limits their reliability. This paper presents a systematic mathematical formulation for treating these uncertainties from the perspective of optimal transport and information geometry. We formulate the uncertainty quantification problem as the minimization of an energy functional on a probability density space equipped with a Riemannian metric, with the loss evaluated through a differential equation, and give a unified description of the gradient flows of the energy functional under specific metrics, such as the Wasserstein and Fisher-Rao metrics. Furthermore, we present corresponding numerical methods for solving these gradient flows using abstract adjoint sensitivity analysis. The formulation connects a range of Bayesian inference methods for dynamical systems; numerical experiments compare posterior approximation and predictive uncertainty under a common computational budget. Moreover, it also provides a geometric perspective on dynamical modeling and the study of heterogeneity evolution.