New Workflow: LDA then XGBoost

[jcharkow]

New workflow which first runs LDA and then runs XGBoost using the LDA results as the main score. This helps prevent pi0 errors that run into with XGBoost.

Overall, the results seem quite comparable to just running XGBoost on my dataset.

[jcharkow]

Doing eFDR / FDR identification curves with different workflows we can se that LDA_XGBoost is quite similar to XGBoost in terms of overfitting and actually overfits slightly less than XGBoost but all results look reasonable.

Here are PyProphet reports for different classifiers for diaPASEF single injection with an experimental library. pyprophet_reports.zip