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Sunyoung Kwon

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AAAI Conference 2025 Conference Paper

MORE: Molecule Pretraining with Multi-Level Pretext Task

Yeongyeong Son
Dasom Noh
Gyoungyoung Heo
Gyoung Jin Park
Sunyoung Kwon

Foundation models, serving as pretrained fundamental bases for a variety of downstream tasks, try to learn versatile, rich, and generalizable representations that can be quickly adopted through fine-tuning or even in a zero-shot manner for specific applications. Foundation models for molecular representation are no exception. Various pretext tasks have been proposed for pretraining molecular representations, but these approaches have focused on only single or partial properties. Molecules are complicated and require different perspectives depending on purposes: insights from local- or global-level, 2D-topology or 3D-spatial arrangement, and low- or high-level semantics. We propose Multi-level mOlecule gRaph prE-train (MORE) to consider these multiple aspects of molecules simultaneously. Experimental results demonstrate that our proposed method effectively learns comprehensive representations by showing outstanding performance in both linear probing and full fine-tuning. Notably, in quantification experiments of forgetting the pretrained models, MORE consistently exhibits minimal and stable parameter changes with the smallest performance gap, whereas other methods show substantial and inconsistent fluctuations with larger gaps. The effectiveness of individual pretext tasks varies depending on the problems being solved, which again highlights the need for a multi-level perspective. Scalability experiments reveal steady improvements of MORE as the dataset size increases, suggesting potential gains with larger datasets as well.

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NeurIPS Conference 2020 Conference Paper

Self-supervised Auxiliary Learning with Meta-paths for Heterogeneous Graphs

Dasol Hwang
Jinyoung Park
Sunyoung Kwon
Kyungmin Kim
Jung-Woo Ha
Hyunwoo J. Kim

Graph neural networks have shown superior performance in a wide range of applications providing a powerful representation of graph-structured data. Recent works show that the representation can be further improved by auxiliary tasks. However, the auxiliary tasks for heterogeneous graphs, which contain rich semantic information with various types of nodes and edges, have less explored in the literature. In this paper, to learn graph neural networks on heterogeneous graphs we propose a novel self-supervised auxiliary learning method using meta paths, which are composite relations of multiple edge types. Our proposed method is learning to learn a primary task by predicting meta-paths as auxiliary tasks. This can be viewed as a type of meta-learning. The proposed method can identify an effective combination of auxiliary tasks and automatically balance them to improve the primary task. Our methods can be applied to any graph neural networks in a plug-in manner without manual labeling or additional data. The experiments demonstrate that the proposed method consistently improves the performance of link prediction and node classification on heterogeneous graphs.

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