Commits · 30b35d319ade79664714dfe82517f02e01739d43 · Lannoy, Carlos de / baseLess

Mar 30, 2022
- Now use 95% alignment cutoff for guppy · 30b35d31
  Noordijk, Ben authored 2 years ago
  
  30b35d31
Dec 10, 2021
- Some more debug scripts · b715e0e9
  Noordijk, Ben authored 3 years ago
  
  b715e0e9
Dec 09, 2021
- compile_model.py now prints how many k-mers it saves · ae847ffc
  Noordijk, Ben authored 3 years ago
  
  ae847ffc
- Runtime of baseless now plotted · 430d45d1
  Noordijk, Ben authored 3 years ago
  
  430d45d1
- Accuracy also inferred from baseless now · 30012bc4
  Noordijk, Ben authored 3 years ago
  
  30012bc4
- Bugfixed naive inference · 967d96e8
  Noordijk, Ben authored 3 years ago
  
  967d96e8
Dec 08, 2021
- Added naive inference · 91074cf3
  Noordijk, Ben authored 3 years ago
  
  91074cf3
Dec 06, 2021
- Some debug scripts modified / added · 4dd89189
  Noordijk, Ben authored 3 years ago
  
  4dd89189
- Store only 1 example read by default to save space · e5cbd555
  Noordijk, Ben authored 3 years ago
  
  e5cbd555
- Show fewer kmer labels in nn performance plot · 69f834fb
  Noordijk, Ben authored 3 years ago
  
  69f834fb
- Runtime plot is now a stripplot instead of bar chart · bb2ad105
  Noordijk, Ben authored 3 years ago
  
  bb2ad105
Dec 03, 2021
- Debug changes · 9803e772
  Noordijk, Ben authored 3 years ago
  
  9803e772
- Now compile model compiles from all kmers found in target for which we train models · d02b1259
  Noordijk, Ben authored 3 years ago
  
  d02b1259
Dec 02, 2021
- Fixed file not found error · 3955b2bc
  Noordijk, Ben authored 3 years ago
  
  3955b2bc
- DB building now adds 2 negative examples per read that contains target, or 1... · 0491058e
  Noordijk, Ben authored 3 years ago
  
  DB building now adds 2 negative examples per read that contains target, or 1 negative example in case target is not in read
  0491058e
- Merge remote-tracking branch 'origin/master' into ben_gru_dev · 460bcc29
  Noordijk, Ben authored 3 years ago
  
  # Conflicts: # argparse_dicts.py # inference/InferenceModel.py # run_production_pipeline.py
  460bcc29
- Threshold now parameter in InferenceModel.py · a597d2ca
  Noordijk, Ben authored 3 years ago
  
  a597d2ca
- Plots now saved as svg and only one contains the legend · a0b22256
  Noordijk, Ben authored 3 years ago
  
  a0b22256
- make min nb models arg, small fixes · dec89520
  Lannoy, Carlos de authored 3 years ago
  
  dec89520
Nov 30, 2021
- overhaul threshold analysis, add precision recall plot · 83e37100
  Lannoy, Carlos de authored 3 years ago
  
  83e37100
- add f1 to summary table · fcdb00a7
  Lannoy, Carlos de authored 3 years ago
  
  fcdb00a7
Nov 29, 2021
- fixes for benchmarking and thresholding · 66da9665
  Lannoy, Carlos de authored 3 years ago
  
  66da9665
- Debug script updated · 5bed22ff
  Noordijk, Ben authored 3 years ago
  
  5bed22ff
- Remove titles and k-mer labels from k-mer library plots · d7fc412d
  Noordijk, Ben authored 3 years ago
  
  d7fc412d
- Only plot legend for library size of 1000 · ce749b55
  Noordijk, Ben authored 3 years ago
  
  ce749b55
- Built-in predict function of CNN now directly calls model to be faster · 483c3954
  Noordijk, Ben authored 3 years ago
  
  483c3954
- compare_run_times.py now plots time per read in seconds · 280a7b80
  Noordijk, Ben authored 3 years ago
  
  280a7b80
- Squigglenet runtime added · b3672d61
  Noordijk, Ben authored 3 years ago and Noordijk, Ben committed 3 years ago
  
  b3672d61
Nov 26, 2021
- on the fly training should only pick k-mers from discernible k-mer list · 7cc65f8a
  Lannoy, Carlos de authored 3 years ago
  
  7cc65f8a
- debugged threshold optimization · d3c668f3
  Lannoy, Carlos de authored 3 years ago
  
  d3c668f3
- small fix · 0b9edbeb
  Lannoy, Carlos de authored 3 years ago
  
  0b9edbeb
- add logit and kmer threshold search code · 254c57a8
  Lannoy, Carlos de authored 3 years ago
  
  254c57a8
- run production pipeline on the fly during compilation · 4f6af55b
  Lannoy, Carlos de authored 3 years ago
  
  4f6af55b
- better k-mer selection for compiled 16S models · d30580b4
  Lannoy, Carlos de authored 3 years ago
  
  d30580b4
Nov 25, 2021
- Ability to save fewer reads when building db to save data · f4e62b8d
  Noordijk, Ben authored 3 years ago
  
  f4e62b8d
- Bugfixed build_db to save example reads · 76d243fc
  Noordijk, Ben authored 3 years ago
  
  76d243fc
Nov 24, 2021
- Run production pipeline can now be used for 5-fold cv with index file · 3b525fc2
  Noordijk, Ben authored 3 years ago
  
  3b525fc2
- Merge branch 'ben_gru_dev' into 'master' · 02097f5a
  Lannoy, Carlos de authored 3 years ago
  
  compare_accuracy.py now saves confusion matrices and can be called on the... See merge request !5
  02097f5a
Nov 23, 2021
- better timeseries plot · fdfba74c
  Carlos de Lannoy authored 3 years ago
  
  fdfba74c
- Debug script added · 25792824
  Noordijk, Ben authored 3 years ago
  
  25792824