# Self-Supervised Discovery of Neural Circuits in Spatially Patterned Neural Responses with Graph Neural Networks

arXiv: https://arxiv.org/abs/2509.17174 · HTML: https://mlsanity.com/paper/2509.17174/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 10 of its 49 references that are in the map.
- First posted on arXiv 21 Sep 2025.

## Builds on (most cited first, 10 of 10)

- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift](https://mlsanity.com/paper/1502.03167/) (2015)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Learning to Simulate Complex Physics with Graph Networks](https://mlsanity.com/paper/2002.09405/) (2020)
- [Neural Relational Inference for Interacting Systems](https://mlsanity.com/paper/1802.04687/) (2018)
- [Graph Neural Networks for Molecules](https://mlsanity.com/paper/2209.05582/) (2022)
- [A new method for parameter estimation in probabilistic models: Minimum probability flow](https://mlsanity.com/paper/2007.09240/) (2020)
- [Reconstruction of recurrent synaptic connectivity of thousands of neurons from simulated spiking activity](https://mlsanity.com/paper/1502.04993/) (2015)

## Abstract (arXiv)

Inferring synaptic connectivity from neural population activity is a fundamental challenge in computational neuroscience, complicated by partial observability and mismatches between inference models and true circuit dynamics. In this study, we propose a graph-based neural inference model that simultaneously predicts neural activity and infers latent connectivity by modeling neurons as interacting nodes in a graph. The architecture features two distinct modules: one for learning structural connectivity and another for predicting future spiking activity via a graph neural network (GNN). Our model accommodates unobserved neurons through auxiliary nodes, allowing for inference in partially observed circuits. We evaluate this approach using synthetic data generated from ring attractor network models and real spike recordings from head direction cells in mice. Across a wide range of conditions, including varying recurrent connectivity, external inputs, and incomplete observations, our model reliably resolves spurious correlations and recovers accurate weight profiles. When applied to real data, the inferred connectivity aligns with theoretical predictions of continuous attractor models. These results highlight the potential of GNN-based models to infer latent neural circuitry through self-supervised structure learning, while leveraging the spike prediction task to flexibly link connectivity and dynamics across both simulated and biological neural systems.