Commits · 383bdcc0c59f69e1872c944bbd93e759ad346a1b · Lannoy, Carlos de / baseLess

Dec 09, 2021
- switch off complicated k-mer selection process for 16S k-mers · 383bdcc0
  Lannoy, Carlos de authored 3 years ago
  
  383bdcc0
- compile all elements of overarching model in single graph · 0faeea48
  Lannoy, Carlos de authored 3 years ago
  
  0faeea48
Dec 07, 2021
- express k-mer threshold as fraction of total rather than absolute int · 7b649606
  Carlos de Lannoy authored 3 years ago
  
  7b649606
- reduce number of simultaneously running compile_model to avoid mem issues · 13473cca
  Carlos de Lannoy authored 3 years ago
  
  13473cca
Dec 05, 2021
- properly add min-nb-models to compile_model parser · 0e9b2cc7
  Carlos de Lannoy authored 3 years ago
  
  0e9b2cc7
Dec 03, 2021
- Merge branch 'master' of git.wur.nl:lanno001/baseless · 71e55f92
  Carlos de Lannoy authored 3 years ago
  
  71e55f92
Dec 02, 2021
- 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
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 24, 2021
- Merge branch 'master' of git.wur.nl:lanno001/baseless · fd3a1006
  Carlos de Lannoy authored 3 years ago
  
  fd3a1006
- 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
- summarized stats for quick benchmark · 722849c1
  Carlos de Lannoy authored 3 years ago
  
  722849c1
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
- Set logit cutoff to 5 instead of 0 · 11b1d4c7
  Noordijk, Ben authored 3 years ago
  
  11b1d4c7
- Speedup: directly call model instead of via predict function · b50c353b
  Noordijk, Ben authored 3 years ago
  
  b50c353b
- Hyperparameter output · c8499789
  Noordijk, Ben authored 3 years ago
  
  c8499789
Nov 22, 2021
- Updated docstrings and removed unused function · 8abccdda
  Noordijk, Ben authored 3 years ago and Noordijk, Ben committed 3 years ago
  
  8abccdda
- Some commented lines to be used for debugging · 944b5177
  Noordijk, Ben authored 3 years ago
  
  944b5177
- More parameterfiles and changed num_kmer_switches to 1 · 5cf38f1f
  Noordijk, Ben authored 3 years ago
  
  5cf38f1f
Nov 21, 2021
- Max nb params now written without comma so it is interpreted as int D: · 4ef7fd6d
  Noordijk, Ben authored 3 years ago
  
  4ef7fd6d
Nov 19, 2021
- Added file used for development · 7f87d75b
  Noordijk, Ben authored 3 years ago
  
  7f87d75b
- Merge remote-tracking branch 'origin/ben_gru_dev' into ben_gru_dev · 2ecb99bb
  Noordijk, Ben authored 3 years ago
  
  # Conflicts: # hyperparameter_search/hyperparameter_ranges_cnn_test.yaml
  2ecb99bb
- All files as used for hyperparam optimisation · 3852c6c4
  Noordijk, Ben authored 3 years ago
  
  3852c6c4
- All files as used for hyperparam optimisation · d29f2f48
  Noordijk, Ben authored 3 years ago
  
  d29f2f48
- DB creation can now handle edge cases · f67ec03b
  Noordijk, Ben authored 3 years ago
  
  f67ec03b
Nov 18, 2021
- Updated docstring and decreased step size · c188067d
  Noordijk, Ben authored 3 years ago
  
  c188067d
- Correct number of negative examples is now stored in db and added check to... · 959894f8
  Noordijk, Ben authored 3 years ago
  
  Correct number of negative examples is now stored in db and added check to make sure negative examples never contain the target
  959894f8
Nov 17, 2021
- Merge remote-tracking branch 'origin/master' into ben_gru_dev · 91630450
  Noordijk, Ben authored 3 years ago
  
  91630450
- Bugfixed uncentered k-mers · 102f2140
  Noordijk, Ben authored 3 years ago
  
  102f2140
- Database building now more 'conservative' so we are absolutely sure about... · b34a3ca0
  Noordijk, Ben authored 3 years ago
  
  Database building now more 'conservative' so we are absolutely sure about correctness of positive examples
  b34a3ca0
- make logos and squiggle plots for tp and fp events · 338de017
  Carlos de Lannoy authored 3 years ago
  
  338de017
- k-mer uncentered now default for db building · e518ba7c
  Noordijk, Ben authored 3 years ago
  
  e518ba7c