# Spinverse: Differentiable Physics for Permeability-Aware Microstructure Reconstruction from Diffusion MRI

arXiv: https://arxiv.org/abs/2603.04638 · HTML: https://mlsanity.com/paper/2603.04638/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 9 of its 24 references that are in the map.
- First posted on arXiv 4 Mar 2026.

## Builds on (most cited first, 9 of 9)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [FiLM: Visual Reasoning with a General Conditioning Layer](https://mlsanity.com/paper/1709.07871/) (2017)
- [Decoupled Weight Decay Regularization](https://mlsanity.com/paper/1711.05101/) (2017)
- [A Point Set Generation Network for 3D Object Reconstruction from a Single Image](https://mlsanity.com/paper/1612.00603/) (2016)
- [Representation Learning on Graphs with Jumping Knowledge Networks](https://mlsanity.com/paper/1806.03536/) (2018)
- [How Attentive are Graph Attention Networks?](https://mlsanity.com/paper/2105.14491/) (2021)
- [DMesh++: An Efficient Differentiable Mesh for Complex Shapes](https://mlsanity.com/paper/2412.16776/) (2024)
- [ReMiDi: Reconstruction of Microstructure Using a Differentiable Diffusion MRI Simulator](https://mlsanity.com/paper/2502.01988/) (2025)

## Abstract (arXiv)

Diffusion MRI (dMRI) is sensitive to microstructural barriers, yet most existing methods either assume impermeable boundaries or estimate voxel-level parameters without recovering explicit interfaces. We present Spinverse, a permeability-aware reconstruction method that inverts dMRI measurements through a fully differentiable Bloch-Torrey simulator. Spinverse represents tissue on a fixed tetrahedral grid and treats each interior face permeability as a learnable parameter; low-permeability faces act as diffusion barriers, so microstructural boundaries whose topology is not fixed a priori (up to the resolution of the ambient mesh) emerge without changing mesh connectivity or vertex positions. Given a target signal, we optimize face permeabilities by backpropagating a signal-matching loss through the PDE forward model, and recover an interface by thresholding the learned permeability field. To mitigate the ill-posedness of permeability inversion, we use mesh-based geometric priors; to avoid local minima, we use a staged multi-sequence optimization curriculum. Across a collection of synthetic voxel meshes, Spinverse reconstructs diverse geometries and demonstrates that sequence scheduling and regularization are critical to avoid outline-only solutions while improving both boundary accuracy and structural validity.