# ProteinRPN: Towards Accurate Protein Function Prediction with Graph-Based Region Proposals

arXiv: https://arxiv.org/abs/2409.00610 · HTML: https://mlsanity.com/paper/2409.00610/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 6 of its 36 references that are in the map.
- First posted on arXiv 1 Sep 2024.

## Builds on (most cited first, 6 of 6)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks](https://mlsanity.com/paper/1506.01497/) (2015)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Hyperbolic Attention Networks](https://mlsanity.com/paper/1805.09786/) (2018)
- [DeepGO: Predicting protein functions from sequence and interactions using a deep ontology-aware classifier](https://mlsanity.com/paper/1705.05919/) (2017)

## Abstract (arXiv)

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.