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This paper introduces algorithmically controlled stochastic synthesis for molecular discovery, addressing the challenge of finding molecules with rare properties in sparse search spaces. By synthesizing and testing complex mixtures of molecules rather than individual compounds, the method deconvolutes molecule-activity relationships to extract maximal information per experiment. This approach significantly reduces the experimental cost, achieving an order of magnitude improvement in finding active molecules on simulated protein fitness landscapes compared to standard Bayesian optimization.
Discovering molecules with rare properties can now be an order of magnitude faster by testing complex mixtures and deconvoluting activity, slashing experimental costs from $\mathcal{O}(d)$ to $\mathcal{O}(\log d)$ or $\mathcal{O}(1)$.
Machine learning can accelerate molecular discovery by designing molecules and planning experiments. However, many scientific challenges demand molecules with very rare properties, and in this sparse setting, existing algorithms offer little gain over random guessing. We propose a method to efficiently search large regions of molecular space using algorithmically controlled stochastic synthesis. Rather than design, make and test individual molecules, we design and make complex mixtures, test them as a pool, then deconvolute the molecule-activity map. We optimize synthesis to encode maximal information. Theoretically, this approach can reduce the number of experiments required to find the optimal molecule among $d$ candidates from $\mathcal{O}(d)$ to $\mathcal{O}(\log d)$ or $\mathcal{O}(1)$. In simulation, on estimated protein fitness landscapes, it finds active molecules with an order of magnitude fewer experiments than existing Bayesian optimization methods.
