Digging Deeper into Thompson Sampling - A Guest Blog Post by Patrick Riley
This week is a special Pat substitution. Pat(rick) Riley is taking over this blog post for a follow up on our Thompson Sampling paper. In our recent paper Thompson Sampling─An Efficient Method for Searching Ultralarge Synthesis on Demand Databases we showed how you could use the classic Thompson Sampling algorithm to select each reagent in a combinatorial library to conduct an efficient search for a variety of scoring functions. Eagle-eyed readers probably noticed that for ROCS, we presented results searching 0.1% of the library and for docking we searched 1% because "docking with TS requires more sampling than ... ROCS". But why is docking harder for a Thompson Sampling based search than ROCS? This post gives an answer to that question. A Visual Version Remember that in Thompson Sampling, for each component in a reaction, you track statistics for each possible reagent. Each reagent is associated with a distribution of scores for complete molecules because the reagent c