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I am trying to build a machine learning training set for bacterial protein sequences that form biofilm, and that cannot. I collected the positive sequences from the GO ontology website but for negative sequences I am not sure which sequences to incorporate into my training set.

Can anyone point me to resources for proteins sequences that are known to be not capable of forming biofilms?

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  • $\begingroup$ Maybe I am wrong but all the proteins you don't have as your positive set is your negative set. How do you select the biofilm capable proteins? By those annotated with a specific GO term? $\endgroup$ – llrs Dec 1 '17 at 8:23
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One option is to treat all proteins that are not explicitly known to form a biofilm as proteins that are incapable of doing so, but this will likely result in many false negatives.

You could take a look at one-class classification and positive-unlabeled (PU) learning. Both are techniques specifically designed for these kind of problems where only one of the two classes is known. (In this case: only biofilm forming proteins are known.)

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