# GRAFT: Biological Graph and Hypergraph Benchmarks for Linked Gene Expression and Phenotypic Trait Prediction in Arabidopsis thaliana

arXiv: https://arxiv.org/abs/2606.27413 · HTML: https://mlsanity.com/paper/2606.27413/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 24 of its 72 references that are in the map.
- First posted on arXiv 25 Jun 2026.

## Builds on (most cited first, 24 of 24)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [A Unified Approach to Interpreting Model Predictions](https://mlsanity.com/paper/1705.07874/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering](https://mlsanity.com/paper/1606.09375/) (2016)
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- [Weisfeiler and Leman Go Neural: Higher-order Graph Neural Networks](https://mlsanity.com/paper/1810.02244/) (2018)
- [GNNExplainer: Generating Explanations for Graph Neural Networks](https://mlsanity.com/paper/1903.03894/) (2019)
- [Masked Label Prediction: Unified Message Passing Model for Semi-Supervised Classification](https://mlsanity.com/paper/2009.03509/) (2020)
- [Parameterized Explainer for Graph Neural Network](https://mlsanity.com/paper/2011.04573/) (2020)
- [Hypergraph Convolution and Hypergraph Attention](https://mlsanity.com/paper/1901.08150/) (2019)
- [UniGNN: a Unified Framework for Graph and Hypergraph Neural Networks](https://mlsanity.com/paper/2105.00956/) (2021)
- [Let Your Graph Do the Talking: Encoding Structured Data for LLMs](https://mlsanity.com/paper/2402.05862/) (2024)
- [GraphFramEx: Towards Systematic Evaluation of Explainability Methods for Graph Neural Networks](https://mlsanity.com/paper/2206.09677/) (2022)
- [Equivariant Hypergraph Diffusion Neural Operators](https://mlsanity.com/paper/2207.06680/) (2022)
- [Inhomogeneous Hypergraph Clustering with Applications](https://mlsanity.com/paper/1709.01249/) (2017)
- [Deep Leaf Segmentation Using Synthetic Data](https://mlsanity.com/paper/1807.10931/) (2018)
- [LLM-Guided Multi-View Hypergraph Learning for Human-Centric Explainable Recommendation](https://mlsanity.com/paper/2401.08217/) (2024)
- [MuSe-GNN: Learning Unified Gene Representation From Multimodal Biological Graph Data](https://mlsanity.com/paper/2310.02275/) (2023)
- [CYCLO: Cyclic Graph Transformer Approach to Multi-Object Relationship Modeling in Aerial Videos](https://mlsanity.com/paper/2406.01029/) (2024)
- [Beyond Graphs: Can Large Language Models Comprehend Hypergraphs?](https://mlsanity.com/paper/2410.10083/) (2024)
- [Self-Supervised Dynamic Hypergraph Recommendation based on Hyper-Relational Knowledge Graph](https://mlsanity.com/paper/2308.07752/) (2023)
- [NuTrea: Neural Tree Search for Context-guided Multi-hop KGQA](https://mlsanity.com/paper/2310.15484/) (2023)
- [CURSOR: Scalable Mixed-Order Hypergraph Matching with CUR Decomposition](https://mlsanity.com/paper/2402.16594/) (2024)

## Abstract (arXiv)

Understanding which genes control which traits in an organism remains one of the central challenges in biology. Despite significant advances in data collection technology, our ability to map genes to traits is still limited. This genome-to-phenome (G2P) challenge spans several problem domains, including plant breeding, and requires methods capable of reasoning over high-dimensional, heterogeneous, and biologically structured data. Current datasets and data repositories, however, are not well-equipped for this task. Current studies do not link gene expression and trait data, and most focus on very specific traits, limiting the breadth of possible correlations. To address this gap, we present the novel Gene-Graph Regression for Arabidopsis Functional Traits (GRAFT) dataset, a curated multi-modal dataset linking gene expression profiles with phenotypic trait measurements in Arabidopsis thaliana, a model organism in plant biology. GRAFT supports tasks such as phenotype prediction and interpretable graph learning. In addition, we benchmark conventional regression and explanatory baselines, including a biologically-informed hypergraph baseline, to validate gene-trait associations. To the best of our knowledge, this is the first dataset to provide multimodal gene information and heterogeneous trait or phenotype data for the same Arabidopsis thaliana specimens. With GRAFT, we aim to foster research to accurately understand the relationship between genotypes and phenotypes using gene information, higher-order gene pairings, and trait data from multiple sources.