Molecular graph representation learning is widely used in chemical and biomedical research. While pre-trained 2D graph encoders have demonstrated strong performance, they overlook the rich molecular domain knowledge associated with submolecular instances (atoms and bonds). While molecular pre-training approaches incorporate such knowledge into their pre-training objectives, they typically employ designs tailored to a specific type of knowledge, lacking the flexibility to integrate diverse knowledge present in molecules. Hence, reusing widely available and well-validated pre-trained 2D encoders, while incorporating molecular domain knowledge during downstream adaptation, offers a more practical alternative. In this work, we propose MolGA, which adapts pre-trained 2D graph encoders to downstream molecular applications by flexibly incorporating diverse molecular domain knowledge. First, we propose a molecular alignment strategy that bridge the gap between pre-trained topological representations with domain-knowledge representations. Second, we introduce a conditional adaptation mechanism that generates instance-specific tokens to enable fine-grained integration of molecular domain knowledge for downstream tasks. Finally, we conduct extensive experiments on eleven public datasets, demonstrating the effectiveness of MolGA.

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