cdanielmachado / carveme_paper Goto Github PK

Can you please provide the column titles of the tsv ouput file?
Thanks!

Hi Daniel :)
I am trying to use your benchmark to analyse some models I just created and I noticed that your script are working with framed and python 2, I was thinking of moving the scripts to python 3 as cplex is dropping python 2. Any chance you have already moved the code to reframed and python 3? If this is the case, may I have the link to that?

Best,
Arianna

Dear Daniel,
I would like to ask for your support regarding the use of Biolog benchmarks.ipynb.
I tried to use it to check whether or not the metrics (Specificity, F1-score, Precision, Accuracy, Sensitivity) of a model change after the use of a putative gap fill approach and in which measure.
It worked well when I used Biolog for the gap-filled models of the organisms you also used for your benchmarks, using fbc2 flavor options.
However, when I used Biolog with a new model reconstructed with CarveMe, False positive and True positive result to be null both before and after the gap fill.

[{'Accuracy': 0.5163934426229508,
'F1-score': 0.0,
'FN': 59,
'FP': 0,
'Precision': 0,
'Sensitivity': 0.0,
'Specificity': 1.0,
'TN': 63,
'TP': 0},
{'Accuracy': 0.5163934426229508,
'F1-score': 0.0,
'FN': 59,
'FP': 0,
'Precision': 0,
'Sensitivity': 0.0,
'Specificity': 1.0,
'TN': 63,
'TP': 0}]

I'm pretty sure it cannot be possible because it also happens in the model created with CarveMe without attempting gap filling.
Do you think the problem could be in the medium definition, in the handling of models, or what else?

Sincerely,
Arianna