Comments (2)
Thanks for pointing this out. The DNA sequences stored as float16's are responsible for the high memory usage. I originally made that choice to allow for storing N's as 0.25 vectors, but I haven't found that to be very helpful in the years since. I just pushed a new commit to store them as booleans, which cuts the memory usage in half. (Python unfortunately uses 8 bits for a boolean.)
I also removed the "-r" option, which permutes the sequences before dividing into train/valid/test according to the current order. I believe the script should always permute, since input BED files will often be nonrandomly ordered. I recommend that you regenerate your training dataset with the new commit.
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Thank you, @davek44 ! Let me play around with the new commit
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Related Issues (20)
- Training aways converges after 2 or 3 epochs HOT 4
- Training takes too long HOT 3
- Pre-trained Weights? HOT 1
- Torch-HDF5 Failure during Writing Output by basset_motifs_predict.lua HOT 3
- First Epoch Loss is Bigger than Expected HOT 2
- Nucleotide Order in Motif Heatmap Reversed HOT 1
- how are filters combined HOT 2
- Error in running basset_sat_vcf.py HOT 1
- Convolutional layers - padding and bias HOT 1
- input and target size mismatch when running test.lua HOT 3
- Citation on README HOT 1
- Prediction tasks specification HOT 1
- Docker image Lua and Python setups wrong
- how to install 'convnet' module HOT 1
- ENUM error when running basset_train.lua HOT 7
- preprocess_features.py file is generating empty output bed files HOT 2
- bedtools getfasta skipping problem HOT 1
- Used in non human species HOT 1
- Original dataset Basset is trained on HOT 1
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