# Topology-Aware Multiscale Mixture of Experts for Efficient Molecular Property Prediction

arXiv: https://arxiv.org/abs/2601.12637 · HTML: https://mlsanity.com/paper/2601.12637/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Placed in MoE theory and gating functions, one of 12 directions in Mixture-of-experts.
- Builds on 26 of its 52 references that are in the map.
- First posted on arXiv 19 Jan 2026.

## Placed in

- Mixture-of-experts / [MoE theory and gating functions](https://mlsanity.com/moe/moe-theory-and-gating-functions/)

## Builds on (most cited first, 26 of 26)

- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Outrageously Large Neural Networks: The Sparsely-Gated Mixture-of-Experts Layer](https://mlsanity.com/paper/1701.06538/) (2017)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [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)
- [Masked Label Prediction: Unified Message Passing Model for Semi-Supervised Classification](https://mlsanity.com/paper/2009.03509/) (2020)
- [Equivariant message passing for the prediction of tensorial properties and molecular spectra](https://mlsanity.com/paper/2102.03150/) (2021)
- [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)
- [ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction](https://mlsanity.com/paper/2010.09885/) (2020)
- [Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules](https://mlsanity.com/paper/2011.14115/) (2020)
- [ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction](https://mlsanity.com/paper/2106.06130/) (2021)
- [Graph Mixture of Experts: Learning on Large-Scale Graphs with Explicit Diversity Modeling](https://mlsanity.com/paper/2304.02806/) (2023)
- [polyBERT: A chemical language model to enable fully machine-driven ultrafast polymer informatics](https://mlsanity.com/paper/2209.14803/) (2022)
- [Persistence Curves: A canonical framework for summarizing persistence diagrams](https://mlsanity.com/paper/1904.07768/) (2019)
- [Polymer Informatics with Multi-Task Learning](https://mlsanity.com/paper/2010.15166/) (2020)
- [GraphMoRE: Mitigating Topological Heterogeneity via Mixture of Riemannian Experts](https://mlsanity.com/paper/2412.11085/) (2024)
- [GraphMETRO: Mitigating Complex Graph Distribution Shifts via Mixture of Aligned Experts](https://mlsanity.com/paper/2312.04693/) (2023)
- [Node-wise Filtering in Graph Neural Networks: A Mixture of Experts Approach](https://mlsanity.com/paper/2406.03464/) (2024)
- [Learning Topology-Specific Experts for Molecular Property Prediction](https://mlsanity.com/paper/2302.13693/) (2023)
- [Molecular geometric deep learning](https://mlsanity.com/paper/2306.15065/) (2023)
- [DA-MoE: Addressing Depth-Sensitivity in Graph-Level Analysis through Mixture of Experts](https://mlsanity.com/paper/2411.03025/) (2024)
- [Molecular topological deep learning for polymer property prediction](https://mlsanity.com/paper/2410.04765/) (2024)
- [Fast, Accurate and Interpretable Graph Classification with Topological Kernels](https://mlsanity.com/paper/2509.17693/) (2025)

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

- [Periodic Topological Deep Learning for Polymer Design and Discovery](https://mlsanity.com/paper/2605.26833/) (2026)

## Abstract (arXiv)

Many molecular properties depend on 3D geometry, where non-covalent interactions, stereochemical effects, and medium- to long-range forces are determined by spatial distances and angles that cannot be uniquely captured by a 2D bond graph. Yet most 3D molecular graph neural networks still rely on globally fixed neighborhood heuristics, typically defined by distance cutoffs and maximum neighbor limits, to define local message-passing neighborhoods, leading to rigid, data-agnostic interaction budgets. We propose Multiscale Interaction Mixture of Experts (MI-MoE) to adapt interaction modeling across geometric regimes. Our contributions are threefold: (1) we introduce a distance-cutoff expert ensemble that explicitly captures short-, mid-, and long-range interactions without committing to a single cutoff; (2) we design a topological gating encoder that routes inputs to experts using filtration-based descriptors, including persistent homology features, summarizing how connectivity evolves across radii; and (3) we show that MI-MoE is a plug-in module that consistently improves multiple strong 3D molecular backbones across diverse molecular and polymer property prediction benchmark datasets, covering both regression and classification tasks. These results highlight topology-aware multiscale routing as an effective principle for 3D molecular graph learning.