Commits · b2747817caac8f34a3392545b20e8c0916b1a1fa · Lannoy, Carlos de / baseLess

Nov 08, 2021
- Database building now randomises and stores example reads by default · b2747817
  Noordijk, Ben authored 3 years ago
  
  b2747817
- Changed model loading and added docstrings · bc10ef08
  Noordijk, Ben authored 3 years ago
  
  bc10ef08
Nov 05, 2021
- More comments that show what is temporary and should be fixed · a133f0c7
  Noordijk, Ben authored 3 years ago
  
  a133f0c7
- Merge remote-tracking branch 'origin/master' into ben_dev · 9be29699
  Noordijk, Ben authored 3 years ago
  
  # Conflicts: # CnnParameterFile.yaml # compare_benchmark_performance/compare_accuracy.py # compare_benchmark_performance/compare_run_times.py
  9be29699
- Changed predict function so it predicts properly when called from run_inference.py. · fec53958
  Noordijk, Ben authored 3 years ago
  
  However, CNN call is hardcoded now in an ugly way.
  fec53958
- Updated docstrings and removed unused function · f4a9f6e2
  Noordijk, Ben authored 3 years ago
  
  f4a9f6e2
- Merge remote-tracking branch 'origin/ben_dev' into ben_dev · 5f8e3fcc
  Noordijk, Ben authored 3 years ago
  
  5f8e3fcc
- Merge branch 'ben_dev' into 'master' · 1d29d7fb
  Lannoy, Carlos de authored 3 years ago
  
  Added data preparation, hyperparameter optimisation, benchmarking code and k-mer library visualisation See merge request !3
  1d29d7fb
- Added data preparation, hyperparameter optimisation, benchmarking code and... · 1f2e0dff
  Noordijk, Ben authored 3 years ago and Lannoy, Carlos de committed 3 years ago
  
  Added data preparation, hyperparameter optimisation, benchmarking code and k-mer library visualisation
  1f2e0dff
- Save confusion matrix plots · 841ebff8
  Noordijk, Ben authored 3 years ago
  
  841ebff8
- Merge branch 'master' into 'ben_dev' · aa282e1c
  Lannoy, Carlos de authored 3 years ago
  
  # Conflicts: # CnnParameterFile.yaml
  aa282e1c
- adapt threshold to logits · 3bc98026
  Carlos de Lannoy authored 3 years ago
  
  3bc98026
- add inference model class, more diverse neg examples, misc · 806d8816
  Carlos de Lannoy authored 3 years ago
  
  806d8816
- strided reads · d5aa0682
  Carlos de Lannoy authored 3 years ago
  
  d5aa0682
- remove old clutter · 78e5bc80
  Carlos de Lannoy authored 3 years ago
  
  78e5bc80
- Saves to correct file names now · cb35d96e
  Noordijk, Ben authored 3 years ago
  
  cb35d96e
- Squigglenet runtime added · e3f795fa
  Noordijk, Ben authored 3 years ago
  
  e3f795fa
Nov 04, 2021
- Confusion matrix is now inferred from benchmark output, too · 244ca3ba
  Noordijk, Ben authored 3 years ago
  
  244ca3ba
- Merge remote-tracking branch 'origin/master' into ben_dev · 58f2f684
  Noordijk, Ben authored 3 years ago
  
  # Conflicts: # nns/Cnn_test.py
  58f2f684
- Proper squigglenet parser added now · e28c0d1c
  Noordijk, Ben authored 3 years ago
  
  e28c0d1c
Nov 03, 2021
- Squigglenet parsing stub · f55af93f
  Noordijk, Ben authored 3 years ago
  
  f55af93f
- fix accidental float-to-int casting, fix predict function · 9f2fe975
  Carlos de Lannoy authored 3 years ago
  
  9f2fe975
- Added script to visualise k-mer libraries · 8ece41cb
  Noordijk, Ben authored 3 years ago
  
  8ece41cb
- visualise_ground_truth_file.py can now be run from command line · 030cbcd5
  Noordijk, Ben authored 3 years ago
  
  030cbcd5
- Added support for multiprocessing, assert that input files are present and... · 5b0791b3
  Noordijk, Ben authored 3 years ago
  
  Added support for multiprocessing, assert that input files are present and fixed bug in F1 calculation for some species
  5b0791b3
- visualise_ground_truth_file.py now also shows species abundance · b9049d1d
  Noordijk, Ben authored 3 years ago
  
  b9049d1d
Nov 02, 2021
- Opens path object properly now · 86393885
  Noordijk, Ben authored 3 years ago
  
  86393885
- Run time analysis now parses all steps of the tools and saves figure to a file · c11af51a
  Noordijk, Ben authored 3 years ago
  
  c11af51a
- Added basic script that plots runtime of benchmark · 5378f7bc
  Noordijk, Ben authored 3 years ago
  
  5378f7bc
Nov 01, 2021
- lock-safe sql read/writes · 533d0c9c
  Carlos de Lannoy authored 3 years ago
  
  533d0c9c
- Added script to assess quality of ground truth data · b0e5ed2f
  Noordijk, Ben authored 3 years ago
  
  b0e5ed2f
- Removed superfluous dataframe processing · 12a14a66
  Noordijk, Ben authored 3 years ago
  
  12a14a66
- Ground truth parser now includes query length · cadda6a4
  Noordijk, Ben authored 3 years ago
  
  cadda6a4
- Ground truth parser now includes percent identity and alignment length · 535c250f
  Noordijk, Ben authored 3 years ago
  
  535c250f
Oct 29, 2021
- Now takes command line arguments · 8e404a0b
  Noordijk, Ben authored 3 years ago
  
  8e404a0b
- Hots hots, better plots · 9f44976b
  Noordijk, Ben authored 3 years ago
  
  9f44976b
- compare_accuracy.py now also parses guppy output and makes proper plots · 9cbec9d2
  Noordijk, Ben authored 3 years ago
  
  9cbec9d2
Oct 28, 2021
- Merge remote-tracking branch 'origin/master' into ben_dev · 8bae9293
  Noordijk, Ben authored 3 years ago
  
  8bae9293
- squigglenet_data_preparation.py can now be run from command line · c19ccdf6
  Noordijk, Ben authored 3 years ago
  
  c19ccdf6
- Added more documentation and basic plotting to accuracy evaluation · b1ce900a
  Noordijk, Ben authored 3 years ago
  
  b1ce900a