<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>

CC BY-SA 3.0
2017-12-01T09:14:50.883Z
2017-12-01T09:14:50.883Z
holmrenser
<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>

CC BY-SA 3.0
2017-12-01T08:23:26.227Z
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?
llrs
<proteins><machine-learning>
Proteins that cannot form biofilm?
# 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?  

---

## 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.)


---

