用细菌代谢模型做计算,性能可由动态分离性预测。
What Makes a Bacterial Model a Good Reservoir Computer? Predicting Performance from Separability and Similarity

- 基于代谢模型模拟生长曲线,作为物理储备池。
- 不同菌种性能差异大,野生型大肠杆菌表现最优。
- 模型动态分离性与计算精度相关,适合生物计算研究者。
生物系统因其复杂内部动态天然处理环境信息,是计算的潜在载体。本研究探讨细菌代谢模型能否作为物理储备池,并验证其计算性能是否可由与可分性和相似性相关的动力学特性预测。通过动态通量平衡分析(dFBA)模拟五种细菌、一种酵母及29株大肠杆菌单基因敲除突变体的生长动态,以葡萄糖和木糖浓度为输入,生长曲线作为储备池状态。在随机非线性分类任务上使用线性读出评估计算性能,通过生长曲线状态矩阵计算核秩和泛化秩来表征可分性与相似性。多个微生物模型实现高分类准确率,表明细菌代谢动态可支持非线性计算。物种间差异显著,部分模型收敛更快,另一些达到更高峰值准确率,揭示收敛速度与最高性能间的权衡。所有大肠杆菌突变体均被野生型主导,说明基因删除降低了计算所需的动力学丰富性。核秩与泛化秩之差通常关联更高准确率,但跨模型差异及低秩时的敏感性限制了实际预测能力。结果表明,细菌代谢模型是储备计算的有前景基底,为未来实验筛选优良菌株提供初步依据。
原文摘要 · Abstract (English)
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.
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