Skip to content

Upstream bootstrap upd

Marcus Hardt requested to merge upstream_bootstrap_upd into main

Created by: albazarova

The up-to-date branch for bootstrapping task.

Includes:

Bootstrapping task: replacing custom number of sequences (default 50% of the MSA) in the MSA by the bootstrapped ones.

  • Loss per sequence
  • Loss per base pair. Two options: comparing each bootstrapped sequence to the replaced sequence/comparing each bootstrapped sequence to the closest one in the MSA
  • Mean absolute error loss: predicting the normalised hamming distance between the bootstrapped sequence and the replaced/closest one

Jigsaw task amended with the one where columns are frozen: all sequences in the MSA are shuffled in the same way

max_seqlen in the MSAmodel both in train.py and in train_downstream.py is hardwired to what it should be

Merge request reports

A HIFIS Service | Privacy | Imprint | Support | Documentation | Changelog