Overview Welcome to the Friend or Foe Collection! Friend or Foe is a collection of synthetic environmental tabular datasets generated by solving metabolic models for 10,000 pairs of bacteria. This README contains the description of the Friend or Foe collection of bacterial datasets. The general tree structure of the repository is described by Friend or Foe Structure figure. Friend or Foe Collection (panel a) contains data suitable for 5 different ML methods stored in corresponding folders (panel b): Classification, Regression, Transfer Learning, Clustering and Generative modeling. Each folder contains data obtained from two sources of metabolic models, AGORA and CARVEME (panel c). For each source there is 100 and 50 additional compounds used in the metabolic modeling and the data corresponds to each folder panel d. Next on the panel e, the datasets are named according to the Table 3 in the manuscript, i.e Binary Classification for Facultative Cooperation vs Competition is BC I. Finally, each subfolder contains .csv train/test files. Note that for Clustering task data is stored as raw .npy arrays for compilatibility with clustering algorightms (see manuscript). In addition to tabula…
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