Procela: Epistemic Governance in Mechanistic Simulations Under Structural Uncertainty

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.

Scientific progress emerges from a longitudinal ecosystem in which researchers, institutions, funding agencies, collaboration networks, and the scientific literature co-evolve. As AI becomes increasingly involved throughout the scientific research cycle, understanding these interconnected and evolving processes becomes increasingly important. We introduce SciUtopia, a persistent, closed-loop LLM-agent simulation framework for studying academic research ecosystems. SciUtopia models interconnected scientific processes such as research-direction choice, collaboration, submission, peer review, resubmission, citation, funding, and researcher attrition, while maintaining evolving states across simulated years. Its configurable institutional mechanisms and information channels provide a controlled testbed for matched counterfactual experiments and targeted interventions. Across 61 simulation worlds, SciUtopia simulates over 40,000 researchers from 8,000 institutions, producing around 400,000 publication decisions and 1.2 million LLM-generated peer reviews. Using these longitudinal simulations, we find that rejection-driven resubmission substantially amplifies reviewer burden beyond population growth alone, cautious exploration balances citation impact with career success and long-term topic diversity, and resource inequality can emerge even without detectable cumulative advantage from narrowly winning early funding. Code is available at https://github.com/Ahren09/ScienceUtopia.

The scientific claims drawn from LLM social simulations should be no stronger than the robustness audits that support them. Generative agents bring new expressive power to agent-based modeling, enabling simulations of collective social processes like cooperation, polarization, and norm formation. Yet they also introduce complexity through additional architectural choices, such as agent specification, memory representation, interaction protocols, and environment design. Small perturbations that appear minor to researchers can cascade into macro-level outcomes through repeated interaction, creating a "butterfly effect." Consequently, scientific claims drawn from LLM social simulations may reflect implementation artifacts rather than the social mechanisms being modeled. We support this position with two case studies: a repeated Prisoner's Dilemma and a social media echo chamber simulation. Across multiple models, minor perturbations in persona format and game-instruction framing shift cooperation rates by up to 76 percentage points, while network homophily and hub assignment produce significant and consistent shifts in polarization metrics. We also find that sensitivity is unevenly distributed across both architectural choices and model families: the same perturbation that produces the 76 pp shift in one frontier model only shifts another by 1 pp. Robustness is therefore a property that should be measured per claim and per model, not assumed. To address this validation gap, we introduce TRAILS (Taxonomy for Robustness Audits In LLM Simulations), a robustness-audit taxonomy spanning three levels of simulation design: agent (micro-level), interaction (meso-level), and system (macro-level). We call for robustness to become a first-order validation requirement before LLM social simulations are used to explain mechanisms, evaluate interventions, or inform decisions.