Scalable Multi-GPU Simulation of 3D Multicellular Growth with RNN-Based Workload Balancing

Detailed multicellular growth simulations based on subcellular element models (SEMs) can capture complex tissue development, but their element-level interactions impose substantial computational cost. This work presents a scalable multi-GPU framework for 3D multicellular growth simulation that combines GPU acceleration, spatial binning, domain decomposition, and workload-aware partitioning. Cell movement, growth, and division continuously reshape the spatial workload distribution, causing initially balanced partitions to become inefficient over time. To address this, we introduce an RNN-based load-balancing controller that observes recent per-rank execution times and partition states and learns residual corrections to a reactive boundary-adjustment rule. The controller is trained offline in a differentiable surrogate of the load-balancing loop with randomized workload dynamics, requiring no measured execution traces for training. We evaluate the framework in terms of single-GPU acceleration, multi-GPU computation scaling, controller-level load-balancing behavior, and end-to-end simulation performance, with comparisons against static partitioning, reactive load balancing, and conventional time-series prediction baselines. A representative embryonic epidermal development use case further demonstrates the type of spatially and temporally evolving workload targeted by the framework. In our evaluation, GPU acceleration with spatial binning accelerates the interaction computation by roughly three orders of magnitude over a serial CPU baseline. RNN-guided load balancing reduces the mean global imbalance from 11.3% under static partitioning to 3.5%, lowers end-to-end runtime by 9.0% relative to static partitioning, and reduces slice migration by 7.7x compared with the reactive baseline, showing that history-aware control can improve workload balance while avoiding unnecessary repartitioning.

GeoQ: Geometry-Aware Conditional Quantile Error Estimation for Scientific Surrogate Models

Neural-network surrogate models are increasingly used to accelerate scientific simulations, but their deployment in extrapolative and autoregressive settings requires input-dependent estimates of prediction error. In this work, we introduce GeoQ (Geometry-Aware Conditional Quantile Error Estimation), a non-intrusive calibration framework for estimating surrogate error at individual query points. GeoQ represents the error at a query point as an anchor-averaged calibration error plus a learned nonnegative correction. This correction is modeled as an upper conditional quantile of the anchor-relative error increment, using geometry-based features that encode representation-space displacement and local support density. A cross-fitting procedure generates approximately out-of-sample calibration tuples, while a feature-space k-nearest-neighbor support score identifies regions \textcolor{black}{where the learned error model is supported by calibration data}. We evaluate GeoQ on scalar regression, chaotic dynamics, medium-range weather forecasting, and Richtmyer-Meshkov instability prediction. The results demonstrate that geometry-aware conditional quantile modeling provides a practical and non-intrusive approach for validity-aware error estimation in scientific surrogate models.

PHREEQC-MCQ-200: A Diagnostic Benchmark for Tool-Augmented Scientific Simulator Agents

Large language model agents are increasingly connected to scientific software, yet it remains unclear when tool access makes scientific computation more reliable rather than merely more complex. We introduce PHREEQC-MCQ-200, a benchmark for evaluating tool-augmented agents on deterministic aqueous-geochemistry simulations. The benchmark contains 200 multiple-choice questions derived from 21 validated PHREEQC scenarios, requiring agents to construct simulator inputs, execute PHREEQC, inspect structured outputs, and commit to final answers. Across multiple frontier and mid-tier model families, simulator access substantially improves aggregate accuracy, confirming that grounded execution is necessary for many scientific-computation tasks. However, the gains are not monotonic: tool-augmented agents also lose items they answered correctly without tools, revealing regressions that average accuracy alone hides. We further show that output-access protocol matters. A table-of-contents interface can reduce token cost while preserving or improving accuracy for stronger models, but it degrades performance for mid-tier models that cannot reliably navigate structured simulator outputs. PHREEQC-MCQ-200 therefore frames scientific tool use as an end-to-end diagnostic problem rather than a simple tool-calling capability. We argue that evaluations of scientific agents should report not only accuracy, but also item-level retention, output-access sensitivity, trajectory failures, and where the computation chain breaks.

Quantifying the Impact of Lossy Compression on Neural Generative Surrogate Modeling

Neural networks are used as generative surrogate models for scientific discovery, which are trainable approximations of scientific simulations. These models enable users to replace time-consuming numerical simulations with learned alternatives, providing quick solutions. However, high-fidelity generative surrogate models require massive training datasets, which can create storage and I/O challenges. Lossy compression is a promising way to reduce this burden, but compression errors may affect the model quality in subtle ways, making it challenging to quantify their impact. In this work, we examine how lossy compression of training data impacts the quality of generative surrogate models. We begin by characterizing the uncertainty inherent in training neural networks, showing that identical training configurations can produce different models. By exploiting this variability, we propose a method to estimate how much compression-induced error a surrogate model can tolerate without affecting its accuracy. Evaluation of two application simulations demonstrates that our approach significantly reduces memory/storage requirements and speeds up training while producing high-quality surrogate models. These results show that lossy compression saves data storage up to 23.7x and 39x with negligible impact on the quality of the surrogate model. Meanwhile, reducing the size of the training data set also enhances the data loading speed and reduces the training time by up to 3x.

SIGA: Self-Evolving Coding-Agent Adapters for Scientific Simulation

Advanced scientific simulators expose specialized input languages that turn simulation goals into executable configurations, but learning them can cost domain scientists hours to days. We study simulator setup as a problem of agent-tool interface grounding: what minimal simulator-specific adaptations are needed for an off-the-shelf coding agent to operate real scientific software? Our intuition is that coding agents already know how to navigate files, edit code, run commands, and repair outputs, but they lack the simulator's executable contract: its vocabulary, structural constraints, validation rules, and termination conditions. We introduce SIGA, a Simulator-Interface Grounding Adapter that supplies this contract through retrieval, procedural memory, in-trajectory validation, and validation-enforced termination. We primarily evaluate SIGA on GEOS, an open-source multiphysics simulator used in subsurface science. SIGA produces a complete GEOS deck in about five minutes with TreeSim above 0.90, matching an extended-budget human expert who took about three hours, a roughly 36x wall-clock speedup. On a harder held-out set, grounding raises TreeSim from 0.720 to 0.789, a roughly 10% relative gain over the bare agent, and can reduce the across-seed standard deviation by 16x. Self-evolution further improves SIGA by rewriting adapter contents from prior trajectories, yielding the highest held-out GEOS mean and matching or outperforming the strongest hand-designed configuration. Transfers to OpenFOAM and LAMMPS show that the dominant mechanism shifts by interface: validation matters most when structural completeness is the bottleneck, while memory and retrieval matter most when domain correctness is the bottleneck. These results suggest that lightweight, self-improvable grounding layers can turn general coding agents into practical operators of scientific software.

Simulate, Reason, Decide: Scientific Reasoning with LLMs for Simulation-Driven Decision Making

Scientific simulators are increasingly being integrated into LLM-driven systems for high-stakes simulation-driven decision-making. However, existing frameworks primarily use LLMs to generate, calibrate, or execute simulators, treating them as black-box interfaces rather than as structured mechanistic systems that can be reasoned about. As a result, current approaches lack the ability to identify, represent, and reason about the assumptions and mechanisms underlying simulator behavior, limiting transparency, auditability, and decision justification. We introduce MechSim, a mechanism-grounded neuro-symbolic reasoning framework for executable scientific simulators. Unlike prior neuro-symbolic approaches that primarily reason over static symbolic structures, MechSim enables LLM agents to reason about the mechanisms, assumptions, and execution behavior of scientific simulators. Our framework represents simulators through a shared structured schema capturing assumptions, variables, mechanism dependencies, and execution traces. On top of this representation, LLM agents operate as constrained reasoning engines that generate structured, evidence-grounded explanations linking simulator outcomes to their underlying mechanisms. We evaluate our approach across multiple high-stakes domains and show that it improves mechanism-level explanation quality, simulator analysis, and downstream decision-making reliability.