Structure-preserving machine learning embeds physical structure directly into model architectures, yet uncertainty quantification (UQ) for such hard-constrained models remains limited because standard UQ methods may violate the encoded admissibility conditions, require architectural modifications, or impose substantial computational costs. In this work, we propose Structure-Preserving Epistemic Neural Networks (S-PENNs), a general framework for UQ in scientific machine learning models with hard architectural constraints, and instantiate it for GENERIC (General Equation for Non-Equilibrium Reversible-Irreversible Coupling) dynamics. S-PENNs preserve the structural constraints of a pretrained model by attaching lightweight epinets to its constrained components, ensuring that every sampled realization remains physically admissible by construction. When applied to GENERIC dynamics, such a proposed framework yields thermodynamically consistent rollouts that preserve the first and second laws. Furthermore, we combine S-PENNs with split conformal prediction as a post-hoc calibration method to produce prediction intervals with finite-sample marginal coverage guarantees. We validate S-PENNs on three numerical examples: a harmonic oscillator coupled to a heat bath and an idealized chemical motor, both governed by ODEs, and a one-dimensional viscoplastic model governed by PDEs. Across all three examples, S-PENNs produce thermodynamically consistent stochastic realizations and well-calibrated prediction intervals while reducing the computational cost by about one to three orders of magnitude compared to deep ensembles. Although the present study focuses on GENERIC dynamics, S-PENNs can be extended more broadly to scientific machine learning models in computational mechanics with either hard or soft constraints.

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