Maxat Kulmanov

Could you please remind me where is this file referenced?

To evaluate CAFA3, we ran cafa3_data.py script to generate cafa test_data.pkl and the run our model to get the predictions.pkl. The data is available here https://deepgo.cbrc.kaust.edu.sa/data/data-cafa.tar.gz

Hi, You need to use this tool to get the same results as in the paper for CAFA3 evaluation https://github.com/ashleyzhou972/CAFA_assessment_tool If I remember correctly this file should have the txt...

I think I have used [evaluate_cafa3.py](https://github.com/bio-ontology-research-group/deepgoplus/blob/master/evaluate_cafa3.py) script to generate them. Uncomment lines 124-132

Hi, I need to rerun everything and check before I can give an answer for this. One possible reason might be the ontology version, or if you re-train the model...

Hello, evaluate_cafa3.py script has a parameter for sub ontology selection '--ont', you need to run it three times with 'mf', 'bp' and 'cc' parameters. To get 'all' file just concatenate...

Hi, It needs a PPI file from STRING Database which is available in the data folder downloaded from here https://doi.org/10.5281/zenodo.3779900

Yes, that's right

If I understand correctly {on}_go_1.pickle files store the prediction terms, right? Are you using the same files for both datasets? If I use the same files I don't get very...

Dear @YueCao2017, @YueCao94, Could you please help? Thank you.