# PerFlow: Physics-Embedded Rectified Flow for Efficient Reconstruction and Uncertainty Quantification of Spatiotemporal Dynamics

arXiv: https://arxiv.org/abs/2605.03548 · HTML: https://mlsanity.com/paper/2605.03548/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Flow matching, time series and science, one of 14 directions in Diffusion models.
- Builds on 35 of its 44 references that are in the map.
- First posted on arXiv 5 May 2026.

## Placed in

- Diffusion models / [Flow matching, time series and science](https://mlsanity.com/diffusion/flow-matching-time-series-and-science/)

## Builds on (most cited first, 30 of 35)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
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- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Generative Adversarial Networks](https://mlsanity.com/paper/2203.00667/) (2022)
- [Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flow](https://mlsanity.com/paper/2209.03003/) (2022)
- [Fourier Neural Operator for Parametric Partial Differential Equations](https://mlsanity.com/paper/2010.08895/) (2020)
- [Variational Inference with Normalizing Flows](https://mlsanity.com/paper/1505.05770/) (2015)
- [DeepONet: Learning nonlinear operators for identifying differential equations based on the universal approximation theorem of operators](https://mlsanity.com/paper/1910.03193/) (2019)
- [DPM-Solver++: Fast Solver for Guided Sampling of Diffusion Probabilistic Models](https://mlsanity.com/paper/2211.01095/) (2022)
- [Physics-Informed Neural Operator for Learning Partial Differential Equations](https://mlsanity.com/paper/2111.03794/) (2021)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [Transolver: A Fast Transformer Solver for PDEs on General Geometries](https://mlsanity.com/paper/2402.02366/) (2024)
- [Factorized Fourier Neural Operators](https://mlsanity.com/paper/2111.13802/) (2021)
- [U-NO: U-shaped Neural Operators](https://mlsanity.com/paper/2204.11127/) (2022)
- [Neural Operators for Accelerating Scientific Simulations and Design](https://mlsanity.com/paper/2309.15325/) (2023)
- [PDE-Refiner: Achieving Accurate Long Rollouts with Neural PDE Solvers](https://mlsanity.com/paper/2308.05732/) (2023)
- [Scalable Transformer for PDE Surrogate Modeling](https://mlsanity.com/paper/2305.17560/) (2023)
- [DiffusionPDE: Generative PDE-Solving Under Partial Observation](https://mlsanity.com/paper/2406.17763/) (2024)
- [PDE-GCN: Novel Architectures for Graph Neural Networks Motivated by Partial Differential Equations](https://mlsanity.com/paper/2108.01938/) (2021)
- [On conditional diffusion models for PDE simulations](https://mlsanity.com/paper/2410.16415/) (2024)
- [A survey of sparse representation: algorithms and applications](https://mlsanity.com/paper/1602.07017/) (2016)
- [Geom-DeepONet: A Point-cloud-based Deep Operator Network for Field Predictions on 3D Parameterized Geometries](https://mlsanity.com/paper/2403.14788/) (2024)
- [Koopman neural operator as a mesh-free solver of non-linear partial differential equations](https://mlsanity.com/paper/2301.10022/) (2023)
- [Wavelet Diffusion Neural Operator](https://mlsanity.com/paper/2412.04833/) (2024)
- [Generative Latent Neural PDE Solver using Flow Matching](https://mlsanity.com/paper/2503.22600/) (2025)
- [FunDiff: Diffusion Models over Function Spaces for Physics-Informed Generative Modeling](https://mlsanity.com/paper/2506.07902/) (2025)
- [PhyMPGN: Physics-encoded Message Passing Graph Network for spatiotemporal PDE systems](https://mlsanity.com/paper/2410.01337/) (2024)
- [DiffPhyCon: A Generative Approach to Control Complex Physical Systems](https://mlsanity.com/paper/2407.06494/) (2024)

## Abstract (arXiv)

Reconstructing PDE-governed fields from sparse and irregular measurements is challenging due to their ill-posed nature. Deterministic surrogates are trained on dense fields that struggle with limited measurements and uncertainty quantification. Generative models, by learning distributions over spatiotemporal fields, can better handle sparsity and uncertainty. However, existing generative approaches enforce data consistency and PDE constraints simultaneously via sampling-time gradient guidance, resulting in slow and unstable inference. To this end, we propose PerFlow, a Physics-embedded rectified Flow for efficient sparse reconstruction and uncertainty quantification of spatiotemporal dynamics. PerFlow decouples observation conditioning from physics enforcement, performing guidance-free conditioning by feeding observations into rectified-flow dynamics while embedding hard physics via a constraint-preserving projection (e.g., incompressibility or conservation). Theoretically, we establish invariance guarantees to ensure that trajectories remain on the physics-consistent manifold throughout sampling. Experiments on various PDE systems demonstrate competitive reconstruction accuracy with sound physics consistency, while enabling efficient conditional sampling (e.g., 50 steps) and up to 320x faster inference than 2000-step guided diffusion baselines.