# SE(3)-Invariant Multiparameter Persistent Homology for Chiral-Sensitive Molecular Property Prediction

arXiv: https://arxiv.org/abs/2312.07633 · HTML: https://mlsanity.com/paper/2312.07633/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 38 of its 70 references that are in the map.
- First posted on arXiv 12 Dec 2023.

## Builds on (most cited first, 30 of 38)

- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Optuna: A Next-generation Hyperparameter Optimization Framework](https://mlsanity.com/paper/1907.10902/) (2019)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds](https://mlsanity.com/paper/1802.08219/) (2018)
- [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)
- [Measuring and Relieving the Over-smoothing Problem for Graph Neural Networks from the Topological View](https://mlsanity.com/paper/1909.03211/) (2019)
- [Analyzing Learned Molecular Representations for Property Prediction](https://mlsanity.com/paper/1904.01561/) (2019)
- [GemNet: Universal Directional Graph Neural Networks for Molecules](https://mlsanity.com/paper/2106.08903/) (2021)
- [Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules](https://mlsanity.com/paper/2011.14115/) (2020)
- [Molecular Graph Convolutions: Moving Beyond Fingerprints](https://mlsanity.com/paper/1603.00856/) (2016)
- [Persistence Images: A Stable Vector Representation of Persistent Homology](https://mlsanity.com/paper/1507.06217/) (2015)
- [Hierarchical Generation of Molecular Graphs using Structural Motifs](https://mlsanity.com/paper/2002.03230/) (2020)
- [Learning Gradient Fields for Molecular Conformation Generation](https://mlsanity.com/paper/2105.03902/) (2021)
- [A Survey on Graph Kernels](https://mlsanity.com/paper/1903.11835/) (2019)
- [3D Infomax improves GNNs for Molecular Property Prediction](https://mlsanity.com/paper/2110.04126/) (2021)
- [GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles](https://mlsanity.com/paper/2106.07802/) (2021)
- [Learning Neural Generative Dynamics for Molecular Conformation Generation](https://mlsanity.com/paper/2102.10240/) (2021)
- [Molecular Property Prediction: A Multilevel Quantum Interactions Modeling Perspective](https://mlsanity.com/paper/1906.11081/) (2019)
- [Learning to Extend Molecular Scaffolds with Structural Motifs](https://mlsanity.com/paper/2103.03864/) (2021)
- [Uncertainty in Gradient Boosting via Ensembles](https://mlsanity.com/paper/2006.10562/) (2020)
- [Covariant Compositional Networks For Learning Graphs](https://mlsanity.com/paper/1801.02144/) (2018)
- [PotentialNet for Molecular Property Prediction](https://mlsanity.com/paper/1803.04465/) (2018)

## Built on by (most cited first, 1 of 1)

- [Lipschitz Bounds for Persistent Laplacian Eigenvalues under One-Simplex Insertions](https://mlsanity.com/paper/2506.21352/) (2025)

## Abstract (arXiv)

In this study, we present a novel computational method for generating molecular fingerprints using multiparameter persistent homology (MPPH). This technique holds considerable significance for drug discovery and materials science, where precise molecular property prediction is vital. By integrating SE(3)-invariance with Vietoris-Rips persistent homology, we effectively capture the three-dimensional representations of molecular chirality. This non-superimposable mirror image property directly influences the molecular interactions, serving as an essential factor in molecular property prediction. We explore the underlying topologies and patterns in molecular structures by applying Vietoris-Rips persistent homology across varying scales and parameters such as atomic weight, partial charge, bond type, and chirality. Our method's efficacy can be improved by incorporating additional parameters such as aromaticity, orbital hybridization, bond polarity, conjugated systems, as well as bond and torsion angles. Additionally, we leverage Stochastic Gradient Langevin Boosting in a Bayesian ensemble of GBDTs to obtain aleatoric and epistemic uncertainty estimates for gradient boosting models. With these uncertainty estimates, we prioritize high-uncertainty samples for active learning and model fine-tuning, benefiting scenarios where data labeling is costly or time consuming. Compared to conventional GNNs which usually suffer from oversmoothing and oversquashing, MPPH provides a more comprehensive and interpretable characterization of molecular data topology. We substantiate our approach with theoretical stability guarantees and demonstrate its superior performance over existing state-of-the-art methods in predicting molecular properties through extensive evaluations on the MoleculeNet benchmark datasets.