Michael A. Cianfrocco

Quanfu Fan, Yilai Li, Yuguang Yao et al.

Single-particle cryo-electron microscopy (cryo-EM) has become one of the mainstream structural biology techniques because of its ability to determine high-resolution structures of dynamic bio-molecules. However, cryo-EM data acquisition remains expensive and labor-intensive, requiring substantial expertise. Structural biologists need a more efficient and objective method to collect the best data in a limited time frame. We formulate the cryo-EM data collection task as an optimization problem in this work. The goal is to maximize the total number of good images taken within a specified period. We show that reinforcement learning offers an effective way to plan cryo-EM data collection, successfully navigating heterogenous cryo-EM grids. The approach we developed, cryoRL, demonstrates better performance than average users for data collection under similar settings.

Lai Wei, Ambuj Tewari, Michael A. Cianfrocco

We introduce a latency-aware contextual bandit framework that generalizes the standard contextual bandit problem, where the learner adaptively selects arms and switches decision sets under action delays. In this setting, the learner observes the context and may select multiple arms from a decision set, with the total time determined by the selected subset. The problem can be framed as a special case of semi-Markov decision processes (SMDPs), where contexts and latencies are drawn from an unknown distribution. Leveraging the Bellman optimality equation, we design the contextual online arm filtering (COAF) algorithm, which balances exploration, exploitation, and action latency to minimize regret relative to the optimal average-reward policy. We analyze the algorithm and show that its regret upper bounds match established results in the contextual bandit literature. In numerical experiments on a movie recommendation dataset and cryogenic electron microscopy (cryo-EM) data, we demonstrate that our approach efficiently maximizes cumulative reward over time.