What Makes a Bacterial Model a Good Reservoir Computer? Predicting Performance from Separability and Similarity

TL;DR

This study explores bacterial metabolic models as physical reservoirs for computation, demonstrating their potential for nonlinear classification tasks and analyzing how dynamical properties predict performance.

Contribution

It introduces a method to predict reservoir computing performance from bacterial metabolic dynamics and compares different microbial models' computational capabilities.

Findings

Several microbial models achieved high classification accuracy.

Trade-off observed between convergence speed and maximum accuracy.

Gene deletions in E. coli reduce dynamical richness for computation.

Abstract

Biological systems are promising substrates for computation because they naturally process environmental information through complex internal dynamics. In this study, we investigate whether bacterial metabolic models can act as physical reservoirs and whether their computational performance can be predicted from dynamical properties linked to separability and similarity. We simulated the growth dynamics of five bacterial species, one yeast species, and 29 Escherichia coli single-gene deletion mutants using dynamic flux balance analysis (dFBA), with glucose and xylose concentrations as inputs and growth curves as reservoir states. Computational performance was assessed on random nonlinear classification tasks using a linear readout, while reservoir properties linked to separability and similarity were characterised through kernel and generalisation ranks computed from growth-curve state matrices. Several microbial models achieved high classification accuracy, showing that bacterial metabolic dynamics can support nonlinear computation. Clear differences were observed between species, with some models converging more rapidly and others reaching higher maximum accuracy, revealing a trade-off between convergence speed and peak performance. In contrast, all E. coli mutants were dominated by the wild-type model, suggesting that gene deletions reduce the dynamical richness required for efficient computation. The difference between kernel and generalisation ranks was generally associated with improved accuracy, but deviations across models and sensitivity at low rank values limited its predictive power in practice. Overall, these results show that bacterial metabolic models constitute promising substrates for reservoir computing and provide a first step towards identifying microbial strains with favourable computational properties for future experimental implementations.