# PhenoLinker: Phenotype-Gene Link Prediction and Explanation using Heterogeneous Graph Neural Networks

arXiv: https://arxiv.org/abs/2402.01809 · HTML: https://mlsanity.com/paper/2402.01809/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 7 of its 72 references that are in the map.
- First posted on arXiv 2 Feb 2024.

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

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [Axiomatic Attribution for Deep Networks](https://mlsanity.com/paper/1703.01365/) (2017)
- [Captum: A unified and generic model interpretability library for PyTorch](https://mlsanity.com/paper/2009.07896/) (2020)
- [Graph Based Link Prediction between Human Phenotypes and Genes](https://mlsanity.com/paper/2105.11989/) (2021)
- [Integrating Transductive And Inductive Embeddings Improves Link Prediction Accuracy](https://mlsanity.com/paper/2108.10108/) (2021)
- [Introducing New Node Prediction in Graph Mining: Predicting All Links from Isolated Nodes with Graph Neural Networks](https://mlsanity.com/paper/2401.05468/) (2024)

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

- [G2PDiffusion: Cross-Species Genotype-to-Phenotype Prediction via Evolutionary Diffusion](https://mlsanity.com/paper/2502.04684/) (2025)

## Abstract (arXiv)

The association of a given human phenotype to a genetic variant remains a critical challenge for biology. We present a novel system called PhenoLinker capable of associating a score to a phenotype-gene relationship by using heterogeneous information networks and a convolutional neural network-based model for graphs, which can provide an explanation for the predictions. This system can aid in the discovery of new associations and in the understanding of the consequences of human genetic variation.