Paper List
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SpikGPT: A High-Accuracy and Interpretable Spiking Attention Framework for Single-Cell Annotation
This paper addresses the core challenge of robust single-cell annotation across heterogeneous datasets with batch effects and the critical need to ide...
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Unlocking hidden biomolecular conformational landscapes in diffusion models at inference time
This paper addresses the core challenge of efficiently and accurately sampling the conformational landscape of biomolecules from diffusion-based struc...
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Personalized optimization of pediatric HD-tDCS for dose consistency and target engagement
This paper addresses the critical limitation of one-size-fits-all HD-tDCS protocols in pediatric populations by developing a personalized optimization...
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Realistic Transition Paths for Large Biomolecular Systems: A Langevin Bridge Approach
This paper addresses the core challenge of generating physically realistic and computationally efficient transition paths between distinct protein con...
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Consistent Synthetic Sequences Unlock Structural Diversity in Fully Atomistic De Novo Protein Design
This paper addresses the core pain point of low sequence-structure alignment in existing synthetic datasets (e.g., AFDB), which severely limits the pe...
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MoRSAIK: Sequence Motif Reactor Simulation, Analysis and Inference Kit in Python
This work addresses the computational bottleneck in simulating prebiotic RNA reactor dynamics by developing a Python package that tracks sequence moti...
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On the Approximation of Phylogenetic Distance Functions by Artificial Neural Networks
This paper addresses the core challenge of developing computationally efficient and scalable neural network architectures that can learn accurate phyl...
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EcoCast: A Spatio-Temporal Model for Continual Biodiversity and Climate Risk Forecasting
This paper addresses the critical bottleneck in conservation: the lack of timely, high-resolution, near-term forecasts of species distribution shifts ...
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.