Online Surrogate Repair: Decoupling High-Fidelity Feedback from Search Length in Closed-Loop Discovery

Closed-loop AI scientists can generate candidate designs at low marginal computational cost, whereas reliable feedback may require wet-lab synthesis, characterization, or high-fidelity computation. Addressing this imbalance through custom laboratory automation remains infrastructure-intensive and costly, while replacing new experiments with a fixed surrogate leaves persistent model errors that can be amplified by optimization. We propose online surrogate repair (OSR), a closed-loop algorithm that uses sparse high-fidelity evaluations to update the surrogate throughout a longer agent search conducted primarily with inexpensive surrogate feedback. An acquisition rule selects which designs from the agent's accumulated proposals receive high-fidelity evaluation, and the resulting labels update the surrogate used in subsequent episodes. Across controlled synthetic environments, we demonstrate that improving global surrogate fit does not necessarily reduce maximum regret, whereas Q90-UCB and expected improvement (EI) substantially reduce regret by directing evaluations toward regions that determine the optimizer's decisions. On MADE, controls receiving high-fidelity feedback after every episode require 6.36--7.23× more oracle queries to match Online EI under two LLM orchestrators and 10.27× more under the non-LLM Chemeleon+MLIP workflow. Online surrogate repair introduces a novel third feedback regime between fixed-surrogate operation and high-fidelity feedback after every episode, separating the frequency of high-fidelity evaluation from the duration of the agent's search.