How can I find out what class each of the columns in the probabilities output correspond to using Keras for a multi-class classification problem?
The class_indices attribute in Keras’ flow_from_directory(directory) creates a dictionary of the classes and their index in the output array:

classes: optional list of class subdirectories (e.g. [‘dogs’, ‘cats’]). Default: None. If not provided, the list of classes will be
automatically inferred from the subdirectory names/structure under
directory, where each subdirectory will be treated as a different
class (and the order of the classes, which will map to the label
indices, will be alphanumeric). The dictionary containing the mapping
from class names to class indices can be obtained via the attribute
class_indices.

Source
I would be interested to see how people have incorporated this into their workflow/scripts though...