Most of the checkpoints perform quite stable performance, yet here we provide details on exactly which we use in the manuscript.

1 Downstream: Zero-shot Structure-text Retrieval

1.1 DrugBank-Description

Type	Checkpoints	Tables/Figures in Manuscript
SMILES	pretrained_MoleculeSTM/SciBERT-MegaMolBART-3e-5-1-1e-4-1-InfoNCE-0.1-32-32	Figure 2 / Table 8 (ArXiv)
Graph	pretrained_MoleculeSTM/SciBERT-Graph-3e-5-1-1e-4-1-InfoNCE-0.1-32-32	Figure 2 / Table 8 (ArXiv)

1.2 DrugBank-Pharmacodynamics

Type	Checkpoints	Tables/Figures in Manuscript
SMILES	pretrained_MoleculeSTM_Raw/SciBERT-MegaMolBART-1e-5-1-1e-4-1-InfoNCE-0.1-32-32	Figure 2 / Table 9 (ArXiv)
Graph	pretrained_MoleculeSTM_Raw/SciBERT-Graph-1e-5-1-1e-4-1-InfoNCE-0.1-32-32	Figure 2 / Table 9 (ArXiv)

1.3 DrugBank-ATC

Type	Checkpoints	Tables/Figures in Manuscript
SMILES	pretrained_MoleculeSTM/SciBERT-MegaMolBART-1e-5-1-1e-4-1-InfoNCE-0.1-32-32	Figure 2 / Table 10 (ArXiv)
Graph	pretrained_MoleculeSTM/SciBERT-Graph-1e-5-1-1e-4-1-InfoNCE-0.1-32-32	Figure 2 / Table 10 (ArXiv)

2 Downstream: Zero-shot Text-based Molecule Editing

2.1 Single-objective molecule editing

Type	Checkpoints	Tables/Figures in Manuscript
SMILES	pretrained_MoleculeSTM_Raw/SciBERT-MegaMolBART-3e-5-1-1e-4-1-InfoNCE-0.1-32-32	Figure 4 / Figure 5 / Sec D.2
Graph	pretrained_MoleculeSTM/SciBERT-Graph-3e-5-1-1e-4-1-EBM_NCE-0.1-32-32	Figure 2 / Figure 5 / Sec D.2

2.2 Multi-objective molecule editing

Type	Checkpoints	Tables/Figures in Manuscript
SMILES	pretrained_MoleculeSTM/SciBERT-MegaMolBART-3e-5-1-1e-4-1-InfoNCE-0.1-32-32	Figure 4 / Figure 5 / Sec D.3
Graph	pretrained_MoleculeSTM/SciBERT-Graph-3e-5-1-1e-4-1-EBM_NCE-0.1-32-32	Figure 2 / Figure 5 / Sec D.3

2.3 Binding-affinity-based molecule editing

Type	Checkpoints	Tables/Figures in Manuscript
SMILES	pretrained_MoleculeSTM/SciBERT-MegaMolBART-1e-5-1-1e-4-1-EBM_NCE-0.1-32-32	Figure 4 / Figure 5 / Sec D.4
Graph	pretrained_MoleculeSTM/SciBERT-Graph-3e-5-1-1e-4-1-EBM_NCE-0.1-32-32	Figure 2 / Figure 5 / Sec D.4

2.4 Drug relevance editing

Type	Checkpoints	Tables/Figures in Manuscript
SMILES	pretrained_MoleculeSTM/SciBERT-MegaMolBART-1e-5-1-1e-4-1-EBM_NCE-0.1-32-32	Sec D.5
Graph	pretrained_MoleculeSTM/SciBERT-Graph-3e-5-1-1e-4-1-EBM_NCE-0.1-32-32	Sec D.5

2.5 Neighborhood searching

Type	Checkpoints	Tables/Figures in Manuscript
SMILES	pretrained_MoleculeSTM_Raw/SciBERT-MegaMolBART-3e-5-1-1e-4-1-InfoNCE-0.1-32-32	Figure 5 / Sec D.6

3 Downstream: Molecular Property Prediction

Type	Checkpoints	Tables/Figures in Manuscript
SMILES	pretrained_MoleculeSTM/SciBERT-MegaMolBART-1e-5-1-1e-4-1-EBM_NCE-0.1-32-32	Table 1
Graph	pretrained_MoleculeSTM/SciBERT-Graph-3e-5-1-1e-4-1-InfoNCE-0.1-32-32	Table 1