Next, I looked at the precision recall curves and it appears like every particle has the exact same score (-4.535172, a screenshot of the PRCcurve Jupyter notebook below) It extracted 10864881 particles, however when I tried to apply a score threshold (I used -2), there was nothing above this threshold. This was pretty surprising, so I double checked my input files to confirm they were what I thought they were before extracting a random epoch from a model to see what it was picking (I choose modelc, epoch 10). For every epoch in each model, the AUPRC is exactly the same and also pretty low (1.57444e-05, also shown in screenshot below). I then trained 6 models with 10 epochs, each differing only by the number or particles/image (I tried n=10, 50, 100, 200, 300, 500). I have a dataset of 2480 micrographs, and have picked a total of 1009 particles (using EMAN2), then split out a test set with 220 particles (21.8% total picked particles). I am using Topaz as a standalone program and there seems to be something going on when training the models.
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