# Neural Embeddings for Protein Graphs

arXiv: https://arxiv.org/abs/2306.04667 · HTML: https://mlsanity.com/paper/2306.04667/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 22 of its 70 references that are in the map.
- First posted on arXiv 7 Jun 2023.

## Builds on (most cited first, 22 of 22)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Learning Phrase Representations using RNN Encoder-Decoder for Statistical Machine Translation](https://mlsanity.com/paper/1406.1078/) (2014)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Deep Sets](https://mlsanity.com/paper/1703.06114/) (2017)
- [Poincar'e Embeddings for Learning Hierarchical Representations](https://mlsanity.com/paper/1705.08039/) (2017)
- [Long Range Graph Benchmark](https://mlsanity.com/paper/2206.08164/) (2022)
- [Weisfeiler and Lehman Go Cellular: CW Networks](https://mlsanity.com/paper/2106.12575/) (2021)
- [Neural Sheaf Diffusion: A Topological Perspective on Heterophily and Oversmoothing in GNNs](https://mlsanity.com/paper/2202.04579/) (2022)
- [Learning Deep Structure-Preserving Image-Text Embeddings](https://mlsanity.com/paper/1511.06078/) (2015)
- [Simplicial Neural Networks](https://mlsanity.com/paper/2010.03633/) (2020)
- [Topological Deep Learning: Going Beyond Graph Data](https://mlsanity.com/paper/2206.00606/) (2022)
- [Cell Complex Neural Networks](https://mlsanity.com/paper/2010.00743/) (2020)
- [Deep learning for molecular design - a review of the state of the art](https://mlsanity.com/paper/1903.04388/) (2019)
- [Drug Similarity Integration Through Attentive Multi-view Graph Auto-Encoders](https://mlsanity.com/paper/1804.10850/) (2018)
- [Neural Distance Embeddings for Biological Sequences](https://mlsanity.com/paper/2109.09740/) (2021)

## Abstract (arXiv)

Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches struggle to efficiently integrate the wealth of information contained in the protein sequence and structure. In this paper, we propose a novel framework for embedding protein graphs in geometric vector spaces, by learning an encoder function that preserves the structural distance between protein graphs. Utilizing Graph Neural Networks (GNNs) and Large Language Models (LLMs), the proposed framework generates structure- and sequence-aware protein representations. We demonstrate that our embeddings are successful in the task of comparing protein structures, while providing a significant speed-up compared to traditional approaches based on structural alignment. Our framework achieves remarkable results in the task of protein structure classification; in particular, when compared to other work, the proposed method shows an average F1-Score improvement of 26% on out-of-distribution (OOD) samples and of 32% when tested on samples coming from the same distribution as the training data. Our approach finds applications in areas such as drug prioritization, drug re-purposing, disease sub-type analysis and elsewhere.