How to Spend Your Oracle Budget: Practical Guidance for Protein Structure Prediction Models
Foundation models for protein structure prediction remain unreliable on certain targets. External oracles can flag and correct these failures, but biological oracles are expensive, making oracle budget a critical constraint. Existing guidance methods, such as FK-steering, DPO, and Best K-of-N sampling, differ in how they spend this budget, yet no systematic comparison exists to guide method selection. To bridge this gap, we benchmark these methods alongside the recently proposed Optimisation Over Outputs (O3), which applies off-the-shelf optimisers within a generative model's latent subspace. We extend the usage of O3 to protein structure prediction models. Overall, our work provides the ...
| Authors | Aleksandra Kalisz, Jack Simons, Krisztina Sinkovics et al. |
|---|---|
| Primary category | cs.AI |
| Published | 12 August 2026 |
| Last updated at source | 12 August 2026 |
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