  The limited availability of annotations in small molecule datasets presents a
challenge to machine learning models. To address this, one common strategy is
to collaborate with additional auxiliary datasets. However, having more data
does not always guarantee improvements. Negative transfer can occur when the
knowledge in the target dataset differs or contradicts that of the auxiliary
molecule datasets. In light of this, identifying the auxiliary molecule
datasets that can benefit the target dataset when jointly trained remains a
critical and unresolved problem. Through an empirical analysis, we observe that
combining graph structure similarity and task similarity can serve as a more
reliable indicator for identifying high-affinity auxiliary datasets. Motivated
by this insight, we propose MolGroup, which separates the dataset affinity into
task and structure affinity to predict the potential benefits of each auxiliary
molecule dataset. MolGroup achieves this by utilizing a routing mechanism
optimized through a bi-level optimization framework. Empowered by the meta
gradient, the routing mechanism is optimized toward maximizing the target
dataset's performance and quantifies the affinity as the gating score. As a
result, MolGroup is capable of predicting the optimal combination of auxiliary
datasets for each target dataset. Our extensive experiments demonstrate the
efficiency and effectiveness of MolGroup, showing an average improvement of
4.41%/3.47% for GIN/Graphormer trained with the group of molecule datasets
selected by MolGroup on 11 target molecule datasets.
