AGP: A Novel Arabidopsis thaliana Genomics-Phenomics Dataset and its HyperGraph Baseline Benchmarking

TL;DR

This paper introduces AGP, a comprehensive multi-modal Arabidopsis thaliana dataset linking gene expression and phenotypes, and benchmarks hypergraph models for gene-trait prediction, advancing plant genomics research.

Contribution

The paper presents the first integrated multi-modal genomics-phenomics dataset for Arabidopsis thaliana and evaluates a biologically-informed hypergraph baseline for gene-trait association tasks.

Findings

Hypergraph baseline effectively models gene-trait relationships.

AGP dataset enables multi-faceted analysis of gene-phenotype links.

Benchmark results highlight potential for improved predictive models.

Abstract

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 models capable of reasoning over high-dimensional, heterogeneous, and biologically structured data. Currently, however, many datasets solely capture genetic information or solely capture phenotype information. Additionally, phenotype data is very heterogeneous, which many datasets do not fully capture. The critical drawback is that these datasets are not integrated, that is, they do not link with each other to describe the same biological specimens. This limits machine learning models' ability to be informed on the various aspects of these specimens, impacting the breadth of correlations learned, and therefore their ability to make more accurate predictions. To address this gap, we present the Arabidopsis Genomics-Phenomics (AGP) Dataset, a curated multi-modal dataset linking gene expression profiles with phenotypic trait measurements in Arabidopsis thaliana, a model organism in plant biology. AGP 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 that provides multi-modal gene information and heterogeneous trait or phenotype data for the same Arabidopsis thaliana specimens. With AGP, we aim to foster the research community towards accurately understanding the connection between genotypes and phenotypes using gene information, higher-order gene pairings, and trait data from several sources.