Converting the regression MIC value problem to a classification problem AMP vs. non-AMP. How?

[qm-intel]

@jswitten

I am trying to use your GRAMPA dataset as a binary classification problem to train my model. As far as If I understood, You use two files for the classification problem:

• UniPort file all samples (class 0) in this file is considered as a negative class (non-antimicrobial peptides)

for example, this specific strain has 14 samples and the term OS=Arabidopsis thaliana is bacteria species, is my understanding correct? sp|F4HPR5|DRP5A_ARATH Dynamin-related protein 5A OS=Arabidopsis thaliana OX=3702 GN=DRP5A PE=2 SV=1 MANSNTYLTTPTKTPSSRRNQQSQSKMQSHSKDPINAESRSRFEAYNRLQAAAVAFGEKL PIPEIVAIGGQSDGKSSLLEALLGFRFNVREVEMGTRRPLILQMVHDLSALEPRCRFQDE DSEEYGSPIVSATAVADVIRSRTEALLKKTKTAVSPKPIVMRAEYAHCPNLTIIDTPGFV LKAKKGEPETTPDEILSMVKSLASPPHRILLFLQQSSVEWCSSLWLDAVREIDSSFRRTI VVVSKFDNRLKEFSDRGEVDRYLSASGYLGENTRPYFVALPKDRSTISNDEFRRQISQVD TEVIRHLREGVKGGFDEEKFRSCIGFGSLRDFLESELQKRYKEAAPATLALLEERCSEVT DDMLRMDMKIQATSDVAHLRKAAMLYTASISNHVGALIDGAANPAPEQWGKTTEEERGES GIGSWPGVSVDIKPPNAVLKLYGGAAFERVIHEFRCAAYSIECPPVSREKVANILLAHAG RGGGRGVTEASAEIARTAARSWLAPLLDTACDRLAFVLGSLFEIALERNLNQNSEYEKKT ENMDGYVGFHAAVRNCYSRFVKNLAKQCKQLVRHHLDSVTSPYSMACYENNYHQGGAFGA YNKFNQASPNSFCFELSDTSRDEPMKDQENIPPEKNNGQETTPGKGGESHITVPETPSPD QPCEIVYGLVKKEIGNGPDGVGARKRMARMVGNRNIEPFRVQNGGLMFANADNGMKSSSA YSEICSSAAQHFARIREVLVERSVTSTLNSGFLTPCRDRLVVALGLDLFAVNDDKFMDMF VAPGAIVVLQNERQQLQKRQKILQSCLTEFKTVARSL

• and all sequences in grampa.csv are antimicrobial peptides or possitive class (class 1)

Is my understanding correct?

If yes, can you please explain which Uniport file in your fasta files folder [Fasta Files](https://github.com/zswitten/Antimicrobial-Peptides/tree/master/data/Fasta_files) can be used as negative class?

Thanks

[zswitten]

Thanks for looking into GRAMPA. @jswitten answered this question in this thread: https://github.com/zswitten/Antimicrobial-Peptides/issues/8#issuecomment-1459280654.

[jswitten]

(Also, completely unimportant but incidentally arabidopsis is not a bacteria it's a plant often used as a model organism for plant biology)