# GALDS: A Graph-Autoencoder-based Latent Dynamics Surrogate model to predict neurite material transport

arXiv: https://arxiv.org/abs/2507.10871 · HTML: https://mlsanity.com/paper/2507.10871/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 21 of its 63 references that are in the map.
- First posted on arXiv 15 Jul 2025.

## Builds on (most cited first, 21 of 21)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Neural Ordinary Differential Equations](https://mlsanity.com/paper/1806.07366/) (2018)
- [Fourier Neural Operator for Parametric Partial Differential Equations](https://mlsanity.com/paper/2010.08895/) (2020)
- [DeepONet: Learning nonlinear operators for identifying differential equations based on the universal approximation theorem of operators](https://mlsanity.com/paper/1910.03193/) (2019)
- [Learning to Simulate Complex Physics with Graph Networks](https://mlsanity.com/paper/2002.09405/) (2020)
- [Learning Mesh-Based Simulation with Graph Networks](https://mlsanity.com/paper/2010.03409/) (2020)
- [Characterizing possible failure modes in physics-informed neural networks](https://mlsanity.com/paper/2109.01050/) (2021)
- [Graph Neural Ordinary Differential Equations](https://mlsanity.com/paper/1911.07532/) (2019)
- [Deep Learning Methods for Reynolds-Averaged Navier-Stokes Simulations of Airfoil Flows](https://mlsanity.com/paper/1810.08217/) (2018)
- [Machine Learning of Linear Differential Equations using Gaussian Processes](https://mlsanity.com/paper/1701.02440/) (2017)
- [Deep UQ: Learning deep neural network surrogate models for high dimensional uncertainty quantification](https://mlsanity.com/paper/1802.00850/) (2018)
- [Fourier-DeepONet: Fourier-enhanced deep operator networks for full waveform inversion with improved accuracy, generalizability, and robustness](https://mlsanity.com/paper/2305.17289/) (2023)
- [Novel DeepONet architecture to predict stresses in elastoplastic structures with variable complex geometries and loads](https://mlsanity.com/paper/2306.03645/) (2023)
- [Phase-Field DeepONet: Physics-informed deep operator neural network for fast simulations of pattern formation governed by gradient flows of free-energy functionals](https://mlsanity.com/paper/2302.13368/) (2023)
- [Multi-scale Time-stepping of Partial Differential Equations with Transformers](https://mlsanity.com/paper/2311.02225/) (2023)
- [Fourier Neural Operator Surrogate Model to Predict 3D Seismic Waves Propagation](https://mlsanity.com/paper/2304.10242/) (2023)
- [Efficient surrogate modeling methods for large-scale Earth system models based on machine learning techniques](https://mlsanity.com/paper/1901.05125/) (2019)
- [Deep learning of material transport in complex neurite networks](https://mlsanity.com/paper/2103.08654/) (2021)
- [On the locality of local neural operator in learning fluid dynamics](https://mlsanity.com/paper/2312.09820/) (2023)
- [Neurodevelopmental disorders modeling using isogeometric analysis, dynamic domain expansion and local refinement](https://mlsanity.com/paper/2407.00810/) (2024)

## Built on by (most cited first, 2 of 2)

- [Latent Dynamics Graph Convolutional Networks for model order reduction of parameterized time-dependent PDEs](https://mlsanity.com/paper/2601.11259/) (2026)
- [MGRD: Compact morphology-gated residual diffusion for variance-aware cross-domain neurite forecasting](https://mlsanity.com/paper/2609.23990/) (2026)

## Abstract (arXiv)

Neurons exhibit intricate geometries within their neurite networks, which play a crucial role in processes such as signaling and nutrient transport. Accurate simulation of material transport in the networks is essential for understanding these biological phenomena but poses significant computational challenges because of the complex tree-like structures involved. Traditional approaches are time-intensive and resource-demanding, yet the inherent properties of neuron trees, which consists primarily of pipes with steady-state parabolic velocity profiles and bifurcations, provide opportunities for computational optimization. To address these challenges, we propose a Graph-Autoencoder-based Latent Dynamics Surrogate (GALDS) model, which is specifically designed to streamline the simulation of material transport in neural trees. GALDS employs a graph autoencoder to encode latent representations of the network's geometry, velocity fields, and concentration profiles. These latent space representations are then assembled into a global graph, which is subsequently used to predict system dynamics in the latent space via a trained graph latent space system dynamic model, inspired by the Neural Ordinary Differential Equations (Neural ODEs) concept. The integration of an autoencoder allows for the use of smaller graph neural network models with reduced training data requirements. Furthermore, the Neural ODE component effectively mitigates the issue of error accumulation commonly encountered in recurrent neural networks. The effectiveness of the GALDS model is demonstrated through results on eight unseen geometries and four abnormal transport examples, where our approach achieves mean relative error of 3% with maximum relative error <8% and demonstrates a 10-fold speed improvement compared to previous surrogate model approaches.