TI$^2$PS: A Topology-Informed Inverse Design Framework for Stochastic Multicellular Pattern Formation

Systematic exploration of Agent-Based Models (ABMs) is challenged by the curse of dimensionality and their inherent stochasticity. We present a multi-stage pipeline integrating the systematic design of experiments with machine learning surrogates. Using a predator-prey case study, our methodology proceeds in two steps. First, an automated model-based screening identifies dominant variables, assesses outcome variability, and segments the parameter space. Second, we train Machine Learning models to map the remaining nonlinear interaction effects. This approach automates the discovery of unstable regions where system outcomes are highly dependent on nonlinear interactions between many variables. Thus, this work provides modelers with a rigorous, hands-off framework for sensitivity analysis and policy testing, even when dealing with high-dimensional stochastic simulators.

Nonconvex multi-well energies in cell-induced phase transitions give rise to fine-scale microstructures, low-regularity transition layers and sharp interfaces, all of which pose numerical challenges for physics-informed learning. Here we introduce biomimetic physics-informed neural networks (Bio-PINNs), which implement a near-to-far curriculum by progressively revealing the computational domain away from the cell boundary and combining this schedule with a deformation-uncertainty proxy that concentrates collocation points near evolving transition layers and tether-forming regions. Across single-cell and multicellular benchmarks, Bio-PINNs recover the densified phase more reliably near cell boundaries and in intercellular gaps, while capturing tether morphology more faithfully than representative ungated and residual-driven adaptive baselines.

Agent-based epidemic models (ABMs) encode behavioral and policy heterogeneity but are too slow for nightly hospital planning. We develop county-ready surrogates that learn directly from exascale ABM trajectories using Universal Differential Equations (UDEs): mechanistic SEIR-family ODEs with a neural-parameterized contact rate $κ_φ(u,t)$ (no additive residual). Our contributions are threefold: we adapt multiple shooting and an observer-based prediction-error method (PEM) to stabilize identification of neural-augmented epidemiological dynamics across intervention-driven regime shifts; we enforce positivity and mass conservation and show the learned contact-rate parameterization yields a well-posed vector field; and we quantify accuracy, calibration, and compute against ABM ensembles and UDE baselines. On a representative ExaEpi scenario, PEM-UDE reduces mean MSE by 77% relative to single-shooting UDE (3.00 vs. 13.14) and by 20% relative to MS-UDE (3.75). Reliability improves in parallel: empirical coverage of ABM $10$-$90$% and $25$-$75$% bands rises from 0.68/0.43 (UDE) and 0.79/0.55 (MS-UDE) to 0.86/0.61 with PEM-UDE and 0.94/0.69 with MS+PEM-UDE, indicating calibrated uncertainty rather than overconfident fits. Inference runs in seconds on commodity CPUs (20-35 s per $\sim$90-day forecast), enabling nightly ''what-if'' sweeps on a laptop. Relative to a $\sim$100 CPU-hour ABM reference run, this yields $\sim10^{4}\times$ lower wall-clock per scenario. This closes the realism-cadence gap, supports threshold-aware decision-making (e.g., maintaining ICU occupancy $<75$%), preserves mechanistic interpretability, and enables calibrated, risk-aware scenario planning on standard institutional hardware. Beyond epidemics, the ABM$\to$UDE recipe provides a portable path to distill agent-based simulators into fast, trustworthy surrogates for other scientific domains.