Steven-GUHK

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Question about training a DeepMicrobes model to predict the taxonomy from phylum to species

> 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...

Question about training a DeepMicrobes model to predict the taxonomy from phylum to species

> 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...

Question about training a DeepMicrobes model to predict the taxonomy from phylum to species

Thanks for your patience. It was my mistake that I only looked at the GitHub steps and forgot that you mentioned you use ART to simulate the reads. According to...

Question about training a DeepMicrobes model to predict the taxonomy from phylum to species

Thanks for your advice. I have successfully run the training step using the command: `nohup python DeepMicrobes.py --input_tfrec=train.tfrec --model_name=attention --model_dir=weights_phylum --num_classes=36 --train_epochs=1> train.log 2>train-error.log &` Because I have 36 classes...

Question about training a DeepMicrobes model to predict the taxonomy from phylum to species

Therefore, if I want to reduce the training time, I can set a larger `batch_size` but make sure that the total steps are more than the value of `_save_checkpoints_steps`. The...

Question about training a DeepMicrobes model to predict the taxonomy from phylum to species

Another question is I saw you mention that `Recommended batch size for training on thousands of species is 2048 or 4096. Try a lower value when training on fewer classes.`...