# Chi-Geometry: A Library for Benchmarking Chirality Prediction of GNNs

arXiv: https://arxiv.org/abs/2508.09097 · HTML: https://mlsanity.com/paper/2508.09097/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 34 of its 49 references that are in the map.
- First posted on arXiv 12 Aug 2025.

## Builds on (most cited first, 30 of 34)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning](https://mlsanity.com/paper/1801.07606/) (2018)
- [How Attentive are Graph Attention Networks?](https://mlsanity.com/paper/2105.14491/) (2021)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [Fast Transformer Decoding: One Write-Head is All You Need](https://mlsanity.com/paper/1911.02150/) (2019)
- [E(3)-Equivariant Graph Neural Networks for Data-Efficient and Accurate Interatomic Potentials](https://mlsanity.com/paper/2101.03164/) (2021)
- [CogView: Mastering Text-to-Image Generation via Transformers](https://mlsanity.com/paper/2105.13290/) (2021)
- [On the Bottleneck of Graph Neural Networks and its Practical Implications](https://mlsanity.com/paper/2006.05205/) (2020)
- [SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networks](https://mlsanity.com/paper/2006.10503/) (2020)
- [SchNet: A continuous-filter convolutional neural network for modeling quantum interactions](https://mlsanity.com/paper/1706.08566/) (2017)
- [Directional Message Passing for Molecular Graphs](https://mlsanity.com/paper/2003.03123/) (2020)
- [Understanding over-squashing and bottlenecks on graphs via curvature](https://mlsanity.com/paper/2111.14522/) (2021)
- [MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields](https://mlsanity.com/paper/2206.07697/) (2022)
- [On the Generalization of Equivariance and Convolution in Neural Networks to the Action of Compact Groups](https://mlsanity.com/paper/1802.03690/) (2018)
- [Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs](https://mlsanity.com/paper/2206.11990/) (2022)
- [A Survey on Oversmoothing in Graph Neural Networks](https://mlsanity.com/paper/2303.10993/) (2023)
- [The Reversible Residual Network: Backpropagation Without Storing Activations](https://mlsanity.com/paper/1707.04585/) (2017)
- [EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations](https://mlsanity.com/paper/2306.12059/) (2023)
- [Zoology: Measuring and Improving Recall in Efficient Language Models](https://mlsanity.com/paper/2312.04927/) (2023)
- [The Lipschitz Constant of Self-Attention](https://mlsanity.com/paper/2006.04710/) (2020)
- [Quantizable Transformers: Removing Outliers by Helping Attention Heads Do Nothing](https://mlsanity.com/paper/2306.12929/) (2023)
- [Reducing SO(3) Convolutions to SO(2) for Efficient Equivariant GNNs](https://mlsanity.com/paper/2302.03655/) (2023)
- [Open Materials 2024 (OMat24) Inorganic Materials Dataset and Models](https://mlsanity.com/paper/2410.12771/) (2024)
- [Spherical Channels for Modeling Atomic Interactions](https://mlsanity.com/paper/2206.14331/) (2022)
- [On Vanishing Gradients, Over-Smoothing, and Over-Squashing in GNNs: Bridging Recurrent and Graph Learning](https://mlsanity.com/paper/2502.10818/) (2025)
- [Learning 3D Representations of Molecular Chirality with Invariance to Bond Rotations](https://mlsanity.com/paper/2110.04383/) (2021)
- [Geometry-Complete Perceptron Networks for 3D Molecular Graphs](https://mlsanity.com/paper/2211.02504/) (2022)

## Abstract (arXiv)

We introduce Chi-Geometry - a library that generates graph data for testing and benchmarking GNNs' ability to predict chirality. Chi-Geometry generates synthetic graph samples with (i) user-specified geometric and topological traits to isolate certain types of samples and (ii) randomized node positions and species to minimize extraneous correlations. Each generated graph contains exactly one chiral center labeled either R or S, while all other nodes are labeled N/A (non-chiral). The generated samples are then combined into a cohesive dataset that can be used to assess a GNN's ability to predict chirality as a node classification task. Chi-Geometry allows more interpretable and less confounding benchmarking of GNNs for prediction of chirality in the graph samples which can guide the design of new GNN architectures with improved predictive performance. We illustrate Chi-Geometry's efficacy by using it to generate synthetic datasets for benchmarking various state-of-the-art (SOTA) GNN architectures. The conclusions of these benchmarking results guided our design of two new GNN architectures. The first GNN architecture established all-to-all connections in the graph to accurately predict chirality across all challenging configurations where previously tested SOTA models failed, but at a computational cost (both for training and inference) that grows quadratically with the number of graph nodes. The second GNN architecture avoids all-to-all connections by introducing a virtual node in the original graph structure of the data, which restores the linear scaling of training and inference computational cost with respect to the number of nodes in the graph, while still ensuring competitive accuracy in detecting chirality with respect to SOTA GNN architectures.