The RL-AL Baseline, in the ROCS and ADV case, finds a maximum of 35 and 37 scaffolds respectively, therefore the time to find more scaffolds cannot be compared directly. In the time it took the RL Baseline to find 35 scaffolds the RL-AL Optimized & RL MPO condition identify ~500 & 185 scaffolds for a ~15 & ~6× enrichment (Figure ), for ROCS and ADV respectively. For ROCS, selecting either MPO or optimized configurations did not significantly change the number of hits found per second. For RL optimized with ADV, there was a 68-& 11-fold increase in hits found per second compared to the RL-Baseline & RL-AL MPO (Computed from the assumption AL CPUtime -MPO time ≈ AL CPUtime , see Supporting Text 1 for hardware information).