Implicit degree bias in the link prediction task

Rachith Aiyappa, Xin Wang, Munjung Kim, Ozgur Can Seckin, Jisung Yoon, Yong-Yeol Ahn, Sadamori Kojaku

Keywords: link prediction, graph machine learning, sampling bias, benchmark

TL;DR: We show that common link prediction benchmarks are biased by node degree, leading to misleading performance favoring methods which overfit to node degree. We propose a correction and highlight its advantages.

Abstract: Link prediction---a task of distinguishing actual hidden edges from random unconnected node pairs---is one of the quintessential tasks in graph machine learning. Despite being widely accepted as a universal benchmark and a downstream task for representation learning, the link prediction benchmark's validity has rarely been questioned. Here, we show that the common edge sampling procedure in the link prediction task has an implicit bias toward high-degree nodes. This produces a highly skewed evaluation that favors methods overly dependent on node degree. In fact a ``null'' link prediction method based solely on node degree can yield nearly optimal performance in this setting. We propose a degree-corrected link prediction benchmark that offers a more reasonable assessment and better aligns with the performance on the recommendation task. Finally, we demonstrate that the degree-corrected benchmark can more effectively train graph machine-learning models by reducing overfitting to node degrees and facilitating the learning of relevant structures in graphs.

Primary Area: learning on graphs and other geometries & topologies

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Submission Number: 10567