Eric Libby

Oleksandr Cherendichenko, Josephine Solowiej-Wedderburn, Laura M. Carroll et al.

A fundamental challenge in microbial ecology is determining whether bacteria compete or cooperate in different environmental conditions. With recent advances in genome-scale metabolic models, we are now capable of simulating interactions between thousands of pairs of bacteria in thousands of different environmental settings at a scale infeasible experimentally. These approaches can generate tremendous amounts of data that can be exploited by state-of-the-art machine learning algorithms to uncover the mechanisms driving interactions. Here, we present Friend or Foe, a compendium of 64 tabular environmental datasets, consisting of more than 26M shared environments for more than 10K pairs of bacteria sampled from two of the largest collections of metabolic models. The Friend or Foe datasets are curated for a wide range of machine learning tasks -- supervised, unsupervised, and generative -- to address specific questions underlying bacterial interactions. We benchmarked a selection of the most recent models for each of these tasks and our results indicate that machine learning can be successful in this application to microbial ecology. Going beyond, analyses of the Friend or Foe compendium can shed light on the predictability of bacterial interactions and highlight novel research directions into how bacteria infer and navigate their relationships.

David H. Wolpert, Joshua A. Grochow, Eric Libby et al.

To analyze high-dimensional systems, many fields in science and engineering rely on high-level descriptions, sometimes called "macrostates," "coarse-grainings," or "effective theories". Examples of such descriptions include the thermodynamic properties of a large collection of point particles undergoing reversible dynamics, the variables in a macroeconomic model describing the individuals that participate in an economy, and the summary state of a cell composed of a large set of biochemical networks. Often these high-level descriptions are constructed without considering the ultimate reason for needing them in the first place. Here, we formalize and quantify one such purpose: the need to predict observables of interest concerning the high-dimensional system with as high accuracy as possible, while minimizing the computational cost of doing so. The resulting State Space Compression (SSC) framework provides a guide for how to solve for the {optimal} high-level description of a given dynamical system, rather than constructing it based on human intuition alone. In this preliminary report, we introduce SSC, and illustrate it with several information-theoretic quantifications of "accuracy", all with different implications for the optimal compression. We also discuss some other possible applications of SSC beyond the goal of accurate prediction. These include SSC as a measure of the complexity of a dynamical system, and as a way to quantify information flow between the scales of a system.