Code

Add beam search peptide decoding#87

Code

Merged

bittremieux merged 44 commits intomainNoble-Lab/casanovo:mainfrom beamsearch_melihNoble-Lab/casanovo:beamsearch_melihCopy head branch name to clipboardNov 18, 2022

+1,077-66

Commits

Commits on Nov 2, 2022

• Add beam search

  melihyilmaz

  committed
  0710ee8

• Delete print statements

  melihyilmaz

  authored
  0476618

Commits on Nov 3, 2022

• Automatically download model weights (#68) (#88)

  Show description for bfbffa6
  

  3 peopleauthored
  bfbffa6

• Automatically download model weights (#68) (#89)

  Show description for bc7d350
  

  3 peopleauthored
  bc7d350

Commits on Nov 5, 2022

• Break beam search to testable subfunctions

  melihyilmaz

  committed
  dc77f1b

• Automatically download model weights (#68)

  melihyilmaz

  committed
  bab7072

Commits on Nov 6, 2022

• Fix precursor m/z termination and filtering

  melihyilmaz

  committed
  3f0576e

• Add unit testing for beam search

  melihyilmaz

  committed
  6f39e1c

• Add beamsearch comments and fix formatting

  melihyilmaz

  committed
  5d61868

Commits on Nov 8, 2022

• Merge branch 'main' into beamsearch_melih

  melihyilmaz

  committed
  be05748

Commits on Nov 9, 2022

• Address requested changes and minor fixes

  melihyilmaz

  committed
  3c81755

• Add more unit tests for beam search

  melihyilmaz

  committed
  75c9b50

Commits on Nov 14, 2022

• Check NH3 loss for early stopping

  melihyilmaz

  committed
  b962453

• Consistent parameter order

  bittremieux

  committed
  9050fc8

• Update docstrings

  bittremieux

  committed
  592efb0

• Remove unused precursors parameter

  bittremieux

  committed
  426ece8

• Update beam matching mask in a level higher

  bittremieux

  committed
  fcb006c

• Minor refactoring to avoid code duplication

  bittremieux

  committed
  6bc2ba4

• Update imports

  bittremieux

  committed
  cbdcacc

• Simplification refactoring

  bittremieux

  committed
  646f9dc

• Fix unit tests

  bittremieux

  committed
  616c0c4

Commits on Nov 15, 2022

• Merge remote-tracking branch 'origin/main' into beamsearch_melih

  bittremieux

  committed
  66c1b2e

• Simplify predicted peptide caching

  bittremieux

  committed
  c705b0e

• Simplify predicted peptide caching

  bittremieux

  committed
  cbeefa7

• Simplify predicted peptide caching

  bittremieux

  committed
  6e3b6da

• Unify predicted peptide caching

  bittremieux

  committed
  1a3bcb1

• Restrict tensor reshape to subfunction and minor fixes

  melihyilmaz

  committed
  c2ec4d2

• Finish beams when all isotopes exceed the precursor m/z tolerance

  bittremieux

  committed
  62c51ae

• Generalize look-ahead for tokens with negative mass

  bittremieux

  committed
  57b5b31

• Remove greedy decoding functionality

  bittremieux

  committed
  b65aaca

• Merge branch 'main' into beamsearch_melih

  melihyilmaz

  committed
  eb08c5b

• Handle case with unfinished beams and add test

  melihyilmaz

  committed
  a2f9a3d

Commits on Nov 16, 2022

• Merge branch 'main' into beamsearch_melih

  melihyilmaz

  committed
  bc64949

• Upgrade required depthcharge version

  melihyilmaz

  authored
  63262e9

• Use detokenize function

  melihyilmaz

  committed
  03b9172

• Add test for negative mass-aware termination

  melihyilmaz

  committed
  412093b

• Fix egative mass-aware beam termination

  melihyilmaz

  committed
  3126e14

• Minor refactoring

  bittremieux

  committed
  053967e

Commits on Nov 17, 2022

• Add test for dummy output at max length

  melihyilmaz

  committed
  bdfa915

• Fixed and refactored peptide and scocre mzTab outputs

  melihyilmaz

  committed
  0c6c0f0

• Add tests for peptide and score output formatting

  melihyilmaz

  committed
  e50bf90

• Small fixes

  bittremieux

  committed
  7e934f5

Commits on Nov 18, 2022

• Update changelog

  bittremieux

  committed
  10df5e0

• Fix changelog update

  bittremieux

  committed
  f4fa6c8