Efficient Data Selection for Training Genomic Perturbation Models

• URL: http://arxiv.org/abs/2503.14571v6
• Date: Sun, 19 Oct 2025 18:39:32 GMT
• Title: Efficient Data Selection for Training Genomic Perturbation Models
• Authors: George Panagopoulos, Johannes F. Lutzeyer, Sofiane Ennadir, Michalis Vazirgiannis, Jun Pang,
• Abstract summary: We focus on graph neural network-based gene perturbation models.<n>We propose a subset selection method that, unlike active learning, selects the training perturbations in one shot.
• Score: 32.968559353907004
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Genomic studies face a vast hypothesis space, while interventions such as gene perturbations remain costly and time-consuming. To accelerate such experiments, gene perturbation models predict the transcriptional outcome of interventions. Since constructing the training set is challenging, active learning is often employed in a "lab-in-the-loop" process. While this strategy makes training more targeted, it is substantially slower, as it fails to exploit the inherent parallelizability of Perturb-seq experiments. Here, we focus on graph neural network-based gene perturbation models and propose a subset selection method that, unlike active learning, selects the training perturbations in one shot. Our method chooses the interventions that maximize the propagation of the supervision signal to the model. The selection criterion is defined over the input knowledge graph and is optimized with submodular maximization, ensuring a near-optimal guarantee. Experimental results across multiple datasets show that, in addition to providing months of acceleration compared to active learning, the method improves the stability of perturbation choices while maintaining competitive predictive accuracy.

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