Answers.Body: <p>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.</p>
  
  <p>You could take a look at <a href="https://en.wikipedia.org/wiki/One-class_classification" rel="nofollow noreferrer">one-class classification and positive-unlabeled (PU) learning</a>. 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.)</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-12-01T09:14:50.883Z
Answers.LastActivityDate: 2017-12-01T09:14:50.883Z
Answers.UserDisplayName: holmrenser
Body: <p>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.</p>
  
  <p>Can anyone point me to resources for proteins sequences that are known to be not capable of forming biofilms?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-01T08:23:26.227Z
Comments.Text: 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?
Comments.UserDisplayName: llrs
Tags: <proteins><machine-learning>
Title: Proteins that cannot form biofilm?
ThreadText: # Proteins that cannot form biofilm?
  
  (Asked by: username_0 on 2017-11-30)
  
  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?
  
  **Tags:** proteins, machine-learning
  
  > **Comments:**
  > **username_1**: 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?  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2017-12-01. Score: 2
  
  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](https://en.wikipedia.org/wiki/One-class_classification). 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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