Designing biochemical circuits with tree search

Discovering biochemical circuits that exhibit a desired behavior is an outstanding problem in biological engineering. The traditional approach of enumerating every possible circuit topology becomes intractable for circuits with more than four components due to combinatorial scaling of the search space. Here, we use Monte Carlo Tree Search (MCTS), a reinforcement learning (RL) algorithm, to optimize circuit topology for a target phenotype by approaching circuit design as a sequence of assembly decisions. Our RL-based design framework, which we call CircuiTree, efficiently and comprehensively finds robust designs for three-component oscillators by prioritizing sparsity. CircuiTree can also infer candidate network motifs from its search results, producing similar results to enumeration. Using parallel MCTS, we scale this workflow up to five components and find that highly fault-tolerant designs use a novel strategy, which we call motif multiplexing. Multiplexed circuits contain many overlapping network motifs that each activate in different mutational scenarios. The evolutionary robustness of multiplexing may explain the ubiquity of multiple sub-oscillators in circadian clock circuits. Overall, CircuiTree provides the first scalable computational platform for designing biochemical circuits.