# Enhancing Multimodal Protein Function Prediction Through Dual-Branch Dynamic Selection with Reconstructive Pre-Training

arXiv: https://arxiv.org/abs/2511.04040 · HTML: https://mlsanity.com/paper/2511.04040/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 7 of its 31 references that are in the map.
- First posted on arXiv 6 Nov 2025.

## Builds on (most cited first, 7 of 7)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [Vision Mamba: Efficient Visual Representation Learning with Bidirectional State Space Model](https://mlsanity.com/paper/2401.09417/) (2024)
- [ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing](https://mlsanity.com/paper/2007.06225/) (2020)
- [How to Train Your HiPPO: State Space Models with Generalized Orthogonal Basis Projections](https://mlsanity.com/paper/2206.12037/) (2022)
- [t-viSNE: Interactive Assessment and Interpretation of t-SNE Projections](https://mlsanity.com/paper/2002.06910/) (2020)
- [Artificial Intelligence for Drug Discovery: Are We There Yet?](https://mlsanity.com/paper/2307.06521/) (2023)

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

- [Neighbor-aware Instance Refining with Noisy Labels for Cross-Modal Retrieval](https://mlsanity.com/paper/2512.24064/) (2025)

## Abstract (arXiv)

Multimodal protein features play a crucial role in protein function prediction. However, these features encompass a wide range of information, ranging from structural data and sequence features to protein attributes and interaction networks, making it challenging to decipher their complex interconnections. In this work, we propose a multimodal protein function prediction method (DSRPGO) by utilizing dynamic selection and reconstructive pre-training mechanisms. To acquire complex protein information, we introduce reconstructive pre-training to mine more fine-grained information with low semantic levels. Moreover, we put forward the Bidirectional Interaction Module (BInM) to facilitate interactive learning among multimodal features. Additionally, to address the difficulty of hierarchical multi-label classification in this task, a Dynamic Selection Module (DSM) is designed to select the feature representation that is most conducive to current protein function prediction. Our proposed DSRPGO model improves significantly in BPO, MFO, and CCO on human datasets, thereby outperforming other benchmark models.