Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function

Yuanchen Zhao, Otto X Cordero and Mikhail Tikhonov

PLOS Computational Biology, 2024, vol. 20, issue 11, 1-17

Abstract: Microbial communities play key roles across diverse environments. Predicting their function and dynamics is a key goal of microbial ecology, but detailed microscopic descriptions of these systems can be prohibitively complex. One approach to deal with this complexity is to resort to coarser representations. Several approaches have sought to identify useful groupings of microbial species in a data-driven way. Of these, recent work has claimed some empirical success at de novo discovery of coarse representations predictive of a given function using methods as simple as a linear regression, against multiple groups of species or even a single such group (the ensemble quotient optimization (EQO) approach). Modeling community function as a linear combination of individual species’ contributions appears simplistic. However, the task of identifying a predictive coarsening of an ecosystem is distinct from the task of predicting the function well, and it is conceivable that the former could be accomplished by a simpler methodology than the latter. Here, we use the resource competition framework to design a model where the “correct” grouping to be discovered is well-defined, and use synthetic data to evaluate and compare three regression-based methods, namely, two proposed previously and one we introduce. We find that regression-based methods can recover the groupings even when the function is manifestly nonlinear; that multi-group methods offer an advantage over a single-group EQO; and crucially, that simpler (linear) methods can outperform more complex ones.Author summary: Natural microbial communities are highly complex, making predictive modeling difficult. One appealing approach is to make their description less detailed, rendering modeling more tractable while hopefully still retaining some predictive power. The Tree of Life naturally provides one possible method for building coarser descriptions (instead of thousands of strains, we could think about hundreds of species; or dozens of families). However, it is known that useful descriptions need not be taxonomically coherent, as illustrated, for example, by the so-called functional guilds. This prompted the development of computational methods seeking to propose candidate groupings in a data-driven manner. In this computational study, we examine one class of such methods, recently proposed in the microbial context. Quantitatively testing their performance can be difficult, as the answer they “should” recover is often unknown. Here, we overcome this difficulty by testing these methods on synthetic data from a model where the ground truth is known by construction. Curiously, we demonstrate that simpler approaches, rather than suffering from this simplicity, can in fact be more robust.

Date: 2024
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1012590

DOI: 10.1371/journal.pcbi.1012590

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