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arXiv · 2111.12951

Reliable Graph Neural Networks for Drug Discovery Under Distributional Shift

Kehang Han·Balaji Lakshminarayanan·Jeremiah Liu
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Abstract

The concern of overconfident mis-predictions under distributional shift demands extensive reliability research on Graph Neural Networks used in critical tasks in drug discovery. Here we first introduce CardioTox, a real-world benchmark on drug cardio-toxicity to facilitate such efforts. Our exploratory study shows overconfident mis-predictions are often distant from training data. That leads us to develop distance-aware GNNs: GNN-SNGP. Through evaluation on CardioTox and three established benchmarks, we demonstrate GNN-SNGP's effectiveness in increasing distance-awareness, reducing overconfident mis-predictions and making better calibrated predictions without sacrificing accuracy performance. Our ablation study further reveals the representation learned by GNN-SNGP improves distance-preservation over its base architecture and is one major factor for improvements.

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Kehang Han, Balaji Lakshminarayanan, Jeremiah Liu. 2021-11-25. Reliable Graph Neural Networks for Drug Discovery Under Distributional Shift. https://arxiv.org/abs/2111.12951

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