Post #2749777
2026-05-19 08:58 UTC
I've been wondering about role of reference assembly contiguity when training/tuning a basecaller model.
Figured out how to export ONT's pytorch weights to hdf5 for processing in #Julia with NNlib, and attention map generated from POD5 is fascinating. Whatever is happening in there, the basecaller behavior differs quite a bit.
#bioinformatics
Replies (1)
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@naturepoker@genomic.social 2026-05-19 09:20
Main difference being that weights trained on complete genome reference keeps on looking toward other distant signals to make a call on current input, while contig level genome reference trained model constantly focuses on immediate signal neighbors more often than not.