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CHANGELOG.md

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To Do

  • Expand test suite to include function unittests (maximize coverage)
  • Add multi-gpu support (issue #6)
  • support for loading embeddings on the fly to reduce memory usage (issue #11)

v0

v0.2

v0.2.2

  • Resolve #35 to use require_dataset -- can now add multiple .fasta files to the same h5 file
  • Update pretrained API and docs to include Topsy-Turvy
  • Add retry decorator to get_pretrained if download fails
  • Add ability to set a random seed for training
  • Update evaluate code to also store metrics in a file

v0.2.1: 2022-06-28 -- Bug fixes

  • Add biopython to setup.py

v0.2.0: 2022-06-24 -- Integration of Topsy Turvy

  • Integrate Topsy-Turvy to allow for top-down supervision
  • Use utils.log function across all commands
  • Speed up loading embeddings into memory using parallel processing
  • Update fasta parse and write to use BioPython SeqIO (better error checking)
  • More comprehensive test suite for main commands

v0.1

v0.1.9: 2022-03-07 -- Minor bug fixes

  • Updated model loading on new version to handle re-named parameters
  • Updated cpu-only loading during prediction with map_location

v0.1.8: 2022-02-08 -- Finalized training bug fix

  • Resolve #24 by fixing training
  • Can now run dscript train --train data/pairs/human_train.tsv --test data/pairs/human_test.tsv --embedding /afs/csail/u/s/samsl/Work/databases/STRING/homo.sapiens/human_nonRed.h5 --output [output] --save-prefix [prefix] --device 0 to replicate paper results
  • Updated code formatting with black and pre-commit

v0.1.7-dev9: 2022-02-07 -- Update training code to be clean again

  • Following previous update, addresses #24 by fixing model training while maintaining preferred API and command line usage

v0.1.7-dev1: 2021-12-16 -- Major overhaul in training

  • Fixed significant bug in how training was run by reverting to older code
  • Should address issue #24: unable to replicate paper results
  • To do: code cleaning to bring up to formatting standards while maintaining performance

v0.1.6: 2021-09-06 -- Bug Fix - Augmentation and proper defaults

  • Augmentation fix in v0.1.5 was bugged still and would throw an error, now resets index
  • Change --use-w and --augment to --no-w and --no-augment with store false

v0.1.5: 2021-06-23 -- Bug Fix - Augment and Documentation

  • Updated package level imports
  • Updated documentation
  • Fixed issue #13: improper augmentation of data
  • Fixed issue #12: overwrites cmap data sets if they already exist

v0.1.4: 2021-03-05 -- Bug Fix - Typo in ContactModule.forward()

  • Fixed issue #7: bug which would crash contact module if called directly

v0.1.3: 2021-02-17 -- Bug Fix - Pairs too large for GPU

  • Fixed issues #3, #4
  • Basic logging system implemented to report skipped pairs
  • Fixed wrong variable name in loading from sequence file
  • Updated documentation

v0.1.2: 2020-11-30 -- Bug Fix - Eval Mode

  • Model should be put into eval() mode before prediction or evaluation, and when new models are downloaded - this makes the output deterministic by disabling dropout layers

v0.1.1: 2020-11-18 -- First Beta Release