SandboxAQ

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SandboxAQ 96

Thanks for open-sourcing this work! I'm potentially interested in some fine-tuning and have a few questions:

1. pIC50 conversion
   Is the correct conversion from pIC50 to your training scale (e.g., the regression target values in data/training_data.csv):
   binding_affinity = pIC50 - 6
   (Based on output being -log10(IC50_μM))

2. Default assay_batch_size=1 behavior
   With the default assay_batch_size=1, the CliffLoss relative component (90% weight) computes 0 pairs since you need ≥2 samples from the same assay for pairwise comparisons. Is this intentional, or should users increase assay_batch_size for training?

3. Recommended training hyperparameters
   What settings were used to train the released checkpoint? The OpenFold3 defaults (epoch_len=4, batch_size=1) seem like placeholders. Any guidance on:

• assay_batch_size
• epoch_len
• batch_size
• Number of epochs

4. Data source for query_ids
   Do the numeric query_id values map to BindingDB entry IDs? And do binding_affinity_dataset_* / PUBCHEM_* assay IDs correspond to BindingDB/PubChem assay IDs?

5. Pre-computed embeddings
   Are there plans to release the cached OpenFold3 embeddings, or is the expectation that users generate their own from scratch?

Thanks!