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Data-driven design is making headway into a number of application areas, including protein, small-molecule, and materials engineering. The design goal is to construct an object with desired properties, such as a protein that binds to a therapeutic target, or a superconducting material with a higher critical temperature than previously observed. To that end, costly experimental measurements are being replaced with calls to high-capacity regression models trained on labeled data, which can be leveraged in an in silico search for design candidates. However, the design goal necessitates moving into regions of the design space beyond where such models were trained. Therefore, one can ask: should the regression model be altered as the design algorithm explores the design space, in the absence of new data? Herein, we answer this question in the affirmative. In particular, we (i) formalize the data-driven design problem as a non-zero-sum game, (ii) develop a principled strategy for retraining the regression model as the design algorithm proceeds---what we refer to as autofocusing, and (iii) demonstrate the promise of autofocusing empirically.
We present a probabilistic modeling framework and adaptive sampling algorithm wherein unsupervised generative models are combined with black box predictive models to tackle the problem of input design. In input design, one is given one or more stocha
Designing novel protein sequences for a desired 3D topological fold is a fundamental yet non-trivial task in protein engineering. Challenges exist due to the complex sequence--fold relationship, as well as the difficulties to capture the diversity of
Scientists and engineers employ stochastic numerical simulators to model empirically observed phenomena. In contrast to purely statistical models, simulators express scientific principles that provide powerful inductive biases, improve generalization
Uncertainty quantification (UQ) is an important component of molecular property prediction, particularly for drug discovery applications where model predictions direct experimental design and where unanticipated imprecision wastes valuable time and r
Background: During the early stages of hospital admission, clinicians must use limited information to make diagnostic and treatment decisions as patient acuity evolves. However, it is common that the time series vital sign information from patients t