MicrobeLab

For prediction, the batch size has no effect on the results, so I tend to use the largest batch size that fits into memory. For training, batch size is an...

Hi, I have not encountered a similar error. It seems that the number of classes was left as the default 2505. Not sure why.

Yes, num_classes parameter is the final number of predicted classes. The default value is 2505 and should be changed to exact number of output nodes. The '3000' is just a...

It is set as a parameter as --num_classes=120, not internally. By the way, not sure the meaning of classification when there is only one possible category.

Hi! The script attempts to parse the number placed in the header after the first "|". The prefix can be any word and is just used to distinguish the sequences...

You will need to perform read simulation to break the complete genomes into short fragments since the model takes as input short reads during prediction. The TFRecord files should be...

The Read simulation step is compulsory. Otherwise the range of read length in training and prediction will be unmatched. Yes, you should concatenate all the simulated reads.

It is recommended to first determine a total number of reads for each class for class balance purpose, and then calculate the -f. But the exact number of reads depends...

Our training scheme is that if more training steps are needed, simulate more reads (not repeatedly train on the same data), so the epoch is 1. The number of step...

You may modify the code by yourself to set the frequency of checkpoint saving. The batch size can be a hyper parameter that affects model performance. Yes the script does...