Conformal prediction for the design problem

In many real-world deployments of machine learning, we use a prediction algorithm to choose what data to test next. For example, in the protein design problem, we have a regression model that predicts some real-valued property of a protein sequence, which we use to propose new sequences believed to exhibit higher property values than observed in the training data. Since validating designed sequences in the wet lab is typically costly, it is important to know how much we can trust the model's predictions. In such settings, however, there is a distinct type of distribution shift between the training and test data: one where the training and test data are statistically dependent, as the latter is chosen based on the former. Consequently, the model's error on the test data -- that is, the designed sequences -- has some non-trivial relationship with its error on the training data. Herein, we introduce a method to quantify predictive uncertainty in such settings. We do so by constructing confidence sets for predictions that account for the dependence between the training and test data. The confidence sets we construct have finite-sample guarantees that hold for any prediction algorithm, even when a trained model chooses the test-time input distribution. As a motivating use case, we demonstrate how our method quantifies uncertainty for the predicted fitness of designed protein using several real data sets.