# GLaDiGAtor: Language-Model-Augmented Multi-Relation Graph Learning for Predicting Disease-Gene Associations

arXiv: https://arxiv.org/abs/2602.18769 · HTML: https://mlsanity.com/paper/2602.18769/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 13 of its 45 references that are in the map.
- First posted on arXiv 21 Feb 2026.

## Builds on (most cited first, 13 of 13)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [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)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [node2vec: Scalable Feature Learning for Networks](https://mlsanity.com/paper/1607.00653/) (2016)
- [DeepWalk: Online Learning of Social Representations](https://mlsanity.com/paper/1403.6652/) (2014)
- [Representation Learning on Graphs with Jumping Knowledge Networks](https://mlsanity.com/paper/1806.03536/) (2018)
- [MixHop: Higher-Order Graph Convolutional Architectures via Sparsified Neighborhood Mixing](https://mlsanity.com/paper/1905.00067/) (2019)
- [struc2vec: Learning Node Representations from Structural Identity](https://mlsanity.com/paper/1704.03165/) (2017)
- [SkipGNN: Predicting Molecular Interactions with Skip-Graph Networks](https://mlsanity.com/paper/2004.14949/) (2020)
- [Predicting Biomedical Interactions with Higher-Order Graph Convolutional Networks](https://mlsanity.com/paper/2010.08516/) (2020)
- [ResMGCN: Residual Message Graph Convolution Network for Fast Biomedical Interactions Discovering](https://mlsanity.com/paper/2311.07632/) (2023)

## Abstract (arXiv)

Understanding disease-gene associations is essential for unravelling disease mechanisms and advancing diagnostics and therapeutics. Traditional approaches based on manual curation and literature review are labour-intensive and not scalable, prompting the use of machine learning on large biomedical data. In particular, graph neural networks (GNNs) have shown promise for modelling complex biological relationships. To address limitations in existing models, we propose GLaDiGAtor (Graph Learning-bAsed DIsease-Gene AssociaTiOn pRediction), a novel GNN framework with an encoder-decoder architecture for disease-gene association prediction. GLaDiGAtor constructs a heterogeneous biological graph integrating gene-gene, disease-disease, and gene-disease interactions from curated databases, and enriches each node with contextual features from well-known language models (ProtT5 for protein sequences and BioBERT for disease text). In evaluations, our model achieves superior predictive accuracy and generalisation, outperforming 14 existing methods. Literature-supported case studies confirm the biological relevance of high-confidence novel predictions, highlighting GLaDiGAtor's potential to discover candidate disease genes. These results underscore the power of graph convolutional networks in biomedical informatics and may ultimately facilitate drug discovery by revealing new gene-disease links. The source code and processed datasets are publicly available at https://github.com/HUBioDataLab/GLaDiGAtor.