# An Effective GCN-based Hierarchical Multi-label classification for Protein Function Prediction

arXiv: https://arxiv.org/abs/2112.02810 · HTML: https://mlsanity.com/paper/2112.02810/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 8 of its 30 references that are in the map.
- First posted on arXiv 6 Dec 2021.

## Builds on (most cited first, 8 of 8)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Deep contextualized word representations](https://mlsanity.com/paper/1802.05365/) (2018)
- [Evaluating Protein Transfer Learning with TAPE](https://mlsanity.com/paper/1906.08230/) (2019)
- [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)
- [BERTology Meets Biology: Interpreting Attention in Protein Language Models](https://mlsanity.com/paper/2006.15222/) (2020)
- [DeepGO: Predicting protein functions from sequence and interactions using a deep ontology-aware classifier](https://mlsanity.com/paper/1705.05919/) (2017)

## Abstract (arXiv)

We propose an effective method to improve Protein Function Prediction (PFP) utilizing hierarchical features of Gene Ontology (GO) terms. Our method consists of a language model for encoding the protein sequence and a Graph Convolutional Network (GCN) for representing GO terms. To reflect the hierarchical structure of GO to GCN, we employ node(GO term)-wise representations containing the whole hierarchical information. Our algorithm shows effectiveness in a large-scale graph by expanding the GO graph compared to previous models. Experimental results show that our method outperformed state-of-the-art PFP approaches.