# Graph algorithms for predicting subcellular localization at the pathway level

arXiv: https://arxiv.org/abs/2212.05991 · HTML: https://mlsanity.com/paper/2212.05991/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 6 of its 55 references that are in the map.
- First posted on arXiv 12 Dec 2022.

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

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [How Attentive are Graph Attention Networks?](https://mlsanity.com/paper/2105.14491/) (2021)
- [A Tutorial on Modeling and Inference in Undirected Graphical Models for Hyperspectral Image Analysis](https://mlsanity.com/paper/1801.08268/) (2018)

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

- [Product Manifold Representations for Learning on Biological Pathways](https://mlsanity.com/paper/2401.15478/) (2024)

## Abstract (arXiv)

Protein subcellular localization is an important factor in normal cellular processes and disease. While many protein localization resources treat it as static, protein localization is dynamic and heavily influenced by biological context. Biological pathways are graphs that represent a specific biological context and can be inferred from large-scale data. We develop graph algorithms to predict the localization of all interactions in a biological pathway as an edge-labeling task. We compare a variety of models including graph neural networks, probabilistic graphical models, and discriminative classifiers for predicting localization annotations from curated pathway databases. We also perform a case study where we construct biological pathways and predict localizations of human fibroblasts undergoing viral infection. Pathway localization prediction is a promising approach for integrating publicly available localization data into the analysis of large-scale biological data.