optimize_augustus.pl results in lower prediction accuracy??
Posted: Fri Jul 01, 2016 2:22 pm
Hello,
I'm getting some strange results from optimize_augustus.pl, essentially it is not resulting in improving the training parameters. I'm using ~ 1200 high quality models that I split into a test set (200) and training set, run etraining, run an initial prediction with augustus which yields gene level sensitivity at 0.745 and specificity 0.73. I then run the optimize_augustus.pl script, after it is complete, the gene level prediction sensitivity is now 0.733 and specificity is 0.707. So it seems like after "optimization" the prediction ability is actually worse. I've seen a very similar pattern with different genomes and gene models. I'm running augustus v3.2.1 compiled using gcc-5.
Thanks,
Jon
I'm getting some strange results from optimize_augustus.pl, essentially it is not resulting in improving the training parameters. I'm using ~ 1200 high quality models that I split into a test set (200) and training set, run etraining, run an initial prediction with augustus which yields gene level sensitivity at 0.745 and specificity 0.73. I then run the optimize_augustus.pl script, after it is complete, the gene level prediction sensitivity is now 0.733 and specificity is 0.707. So it seems like after "optimization" the prediction ability is actually worse. I've seen a very similar pattern with different genomes and gene models. I'm running augustus v3.2.1 compiled using gcc-5.
Thanks,
Jon