EnzymeRSI：面向酶设计的双循环递归自改进系统

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Abstract:Improvement in enzyme engineering is usually pursued by optimising which candidates to assay within a fixed model and workflow; when the bottleneck arises from a mismatched method or a failing workflow, that route is difficult to escape. We present EnzymeRSI, a dual-loop system for recursive self-improvement (RSI). The outer loop evolves harness assets without changing model weights, the inner loop develops prediction and selection algorithms under controlled conditions, and a cloud laboratory system is specified to close the physical loop with quality-controlled feedback. By updating its prediction strategy through iterative comparison, the outer loop raised the mean development-set Spearman correlation on ProteinGym by 0.044 across five assays, reaching 0.335 on CD19 and 0.683 on OPSD (rhodopsin); of the two first places, only CD19 was produced by the outer loop itself. In the self-improvement of the ThermoMPNN algorithm the inner loop reached a PCC of 0.849, and on TadA-Bench it reached a Spearman correlation of 0.307 in 1.13 h. In three prospective wet-lab tests of the system's experimental decision-making, 10 of the 32 candidates that had not been pre-specified for the luciferase RLuc showed at least twice the wild-type activity; a recommended variant of the cytidine deaminase A3A raised 5mC conversion to 90.2%; and path selection in evolution raised the catalytic efficiency of the DNA polymerase KOD-E on a modified substrate to 31.1 times that of the parent. By treating the organisation of the research workflow and the development of algorithms as a single falsifiable dry-to-wet loop, this work offers an evolutionary paradigm for moving beyond the blind spots of a fixed method and for autonomous enzyme engineering.

Submission history

From: YueJie Hou [view email]
[v1] Wed, 4 Nov 2026 10:54:35 UTC (1,760 KB)