Paper List
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Formation of Artificial Neural Assemblies by Biologically Plausible Inhibition Mechanisms
This work addresses the core limitation of the Assembly Calculus model—its fixed-size, biologically implausible k-WTA selection process—by introducing...
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How to make the most of your masked language model for protein engineering
This paper addresses the critical bottleneck of efficiently sampling high-quality, diverse protein sequences from Masked Language Models (MLMs) for pr...
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Module control in youth symptom networks across COVID-19
This paper addresses the core challenge of distinguishing whether a prolonged societal stressor (COVID-19) fundamentally reorganizes the architecture ...
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JEDI: Jointly Embedded Inference of Neural Dynamics
This paper addresses the core challenge of inferring context-dependent neural dynamics from noisy, high-dimensional recordings using a single unified ...
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ATP Level and Phosphorylation Free Energy Regulate Trigger-Wave Speed and Critical Nucleus Size in Cellular Biochemical Systems
This work addresses the core challenge of quantitatively predicting how the cellular energy state (ATP level and phosphorylation free energy) governs ...
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Packaging Jupyter notebooks as installable desktop apps using LabConstrictor
This paper addresses the core pain point of ensuring Jupyter notebook reproducibility and accessibility across different computing environments, parti...
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SNPgen: Phenotype-Supervised Genotype Representation and Synthetic Data Generation via Latent Diffusion
This paper addresses the core challenge of generating privacy-preserving synthetic genotype data that maintains both statistical fidelity and downstre...
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Continuous Diffusion Transformers for Designing Synthetic Regulatory Elements
This paper addresses the challenge of efficiently generating novel, cell-type-specific regulatory DNA sequences with high predicted activity while min...
Realizing Common Random Numbers: Event-Keyed Hashing for Causally Valid Stochastic Models
Institute for Disease Modeling, Gates Foundation | Department of Epidemiology, University of North Carolina | Institute for Disease Modeling, Gates Foundation
30秒速读
IN SHORT: This paper addresses the critical problem that standard stateful PRNG implementations in agent-based models violate causal validity by making random draws execution-path-dependent, thereby breaking the fundamental assumption of common random numbers needed for valid counterfactual comparisons.
核心创新
- Methodology Identifies and formalizes the fundamental mismatch between scientific causal structure in ABMs and program-level causal structure induced by stateful PRNGs through the lens of Structural Causal Models (SCMs)
- Methodology Introduces the concept of 'execution invariance' as a necessary property for causally valid ABM counterfactuals, requiring that exogenous noise terms remain stable across intervention scenarios
- Methodology Proposes event-keyed random number generation combining counter-based PRNGs (Philox/Threefry) with event identifiers to decouple random draws from simulation execution order
主要结论
- Standard stateful PRNG practices violate the execution invariance required for valid SCM-style interventions, as demonstrated through formal analysis of the structural causal model framework
- Event-keyed hashing with counter-based PRNGs restores the stable event-indexed exogenous structure assumed by SCMs, enabling proper counterfactual comparisons with variance reduction benefits
- The proposed approach allows ABMs to function as valid structural causal models under interventions, maintaining the critical property that interventions change only structural equations while holding exogenous noise terms fixed
摘要: Agent-based models (ABMs) are widely used to estimate causal treatment effects via paired counterfactual simulation. A standard variance reduction technique is common random numbers (CRNs), which couples replicates across intervention scenarios by sharing the same random inputs. In practice, CRNs are implemented by reusing the same base seed, but this relies on a critical assumption: that the same draw index corresponds to the same modeled event across scenarios. Stateful pseudorandom number generators (PRNGs) violate this assumption whenever interventions alter the simulation's execution path, because any change in control flow shifts the draw index used for all downstream events. We argue that this execution-path-dependent draw indexing is not only a variance-reduction nuisance, but represents a fundamental mismatch between the scientific causal structure ABMs are intended to encode and the program-level causal structure induced by stateful PRNG implementations. Formalizing this through the lens of structural causal models (SCMs), we show that standard PRNG practices yield causally incoherent paired counterfactual comparisons even when the mechanistic specification is otherwise sound. We show that a remedy is to combine counter-based random number generators (e.g., Philox/Threefry) with event identifiers. This decouples random number generation from simulation execution order by making random draws explicit functions of the particular modeled event that called them, restoring the stable event-indexed exogenous structure assumed by SCMs.