# Mamba-driven multi-perspective structural understanding for molecular ground-state conformation prediction

arXiv: https://arxiv.org/abs/2511.09564 · HTML: https://mlsanity.com/paper/2511.09564/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Core SSM architectures for language, one of 10 directions in State-space sequence models (S4, Mamba).
- Builds on 17 of its 51 references that are in the map.
- First posted on arXiv 10 Nov 2025.

## Placed in

- State-space sequence models (S4, Mamba) / [Core SSM architectures for language](https://mlsanity.com/ssm/core-ssm-architectures-for-language/)

## Builds on (most cited first, 17 of 17)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [Efficiently Modeling Long Sequences with Structured State Spaces](https://mlsanity.com/paper/2111.00396/) (2021)
- [Vision Mamba: Efficient Visual Representation Learning with Bidirectional State Space Model](https://mlsanity.com/paper/2401.09417/) (2024)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [How Attentive are Graph Attention Networks?](https://mlsanity.com/paper/2105.14491/) (2021)
- [Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs](https://mlsanity.com/paper/2206.11990/) (2022)
- [DeeperGCN: All You Need to Train Deeper GCNs](https://mlsanity.com/paper/2006.07739/) (2020)
- [MoE-Mamba: Efficient Selective State Space Models with Mixture of Experts](https://mlsanity.com/paper/2401.04081/) (2024)
- [MambaByte: Token-free Selective State Space Model](https://mlsanity.com/paper/2401.13660/) (2024)
- [MambaMixer: Efficient Selective State Space Models with Dual Token and Channel Selection](https://mlsanity.com/paper/2403.19888/) (2024)
- [Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs](https://mlsanity.com/paper/2110.01717/) (2021)
- [Mamba Modulation: On the Length Generalization of Mamba](https://mlsanity.com/paper/2509.19633/) (2025)
- [Do Deep Learning Methods Really Perform Better in Molecular Conformation Generation?](https://mlsanity.com/paper/2302.07061/) (2023)
- [EvoBrain: Dynamic Multi-Channel EEG Graph Modeling for Time-Evolving Brain Networks](https://mlsanity.com/paper/2509.15857/) (2025)
- [Orochi: Versatile Biomedical Image Processor](https://mlsanity.com/paper/2509.22583/) (2025)
- [A Survey of Deep Learning Methods in Protein Bioinformatics and its Impact on Protein Design](https://mlsanity.com/paper/2501.01477/) (2025)

## Abstract (arXiv)

A comprehensive understanding of molecular structures is important for the prediction of molecular ground-state conformation involving property information. Meanwhile, state space model (e.g., Mamba) has recently emerged as a promising mechanism for long sequence modeling and has achieved remarkable results in various language and vision tasks. However, towards molecular ground-state conformation prediction, exploiting Mamba to understand molecular structure is underexplored. To this end, we strive to design a generic and efficient framework with Mamba to capture critical components. In general, molecular structure could be considered to consist of three elements, i.e., atom types, atom positions, and connections between atoms. Thus, considering the three elements, an approach of Mamba-driven multi-perspective structural understanding (MPSU-Mamba) is proposed to localize molecular ground-state conformation. Particularly, for complex and diverse molecules, three different kinds of dedicated scanning strategies are explored to construct a comprehensive perception of corresponding molecular structures. And a bright-channel guided mechanism is defined to discriminate the critical conformation-related atom information. Experimental results on QM9 and Molecule3D datasets indicate that MPSU-Mamba significantly outperforms existing methods. Furthermore, we observe that for the case of few training samples, MPSU-Mamba still achieves superior performance, demonstrating that our method is indeed beneficial for understanding molecular structures.