Commits · dbe6a5d707ca48e8f52400039fcc435d60466b1b · Lannoy, Carlos de / baseLess

Oct 24, 2021
- small fixes, update env · dbe6a5d7
  Lannoy, Carlos de authored 3 years ago
  
  dbe6a5d7
- add multi species 16S validation · 68456266
  Carlos de Lannoy authored 3 years ago
  
  68456266
Oct 20, 2021
- misc fixes · 79c33785
  Carlos de Lannoy authored 3 years ago
  
  79c33785
Oct 19, 2021
- fixed 16S validation · 571ffb9c
  Carlos de Lannoy authored 3 years ago
  
  571ffb9c
- fixed 16S validation · 8f6be121
  Carlos de Lannoy authored 3 years ago
  
  8f6be121
- CNN parameter file that was used to train CNNs on initial training data · dd4df0e7
  Noordijk, Ben authored 3 years ago and Lannoy, Carlos de committed 3 years ago
  
  (cherry picked from commit cf2c79f1)
  dd4df0e7
- Merge branch 'cherry-pick-7e059cdf ' into 'master' · 0a21cf23
  Lannoy, Carlos de authored 3 years ago
  
  CNN can now load weights from nn.h5 file See merge request !2
  0a21cf23
- CNN can now load weights from nn.h5 file · 1f1a39be
  Noordijk, Ben authored 3 years ago and Lannoy, Carlos de committed 3 years ago
  
  (cherry picked from commit 7e059cdf)
  1f1a39be
- fixed 16S validation · 89e22487
  Carlos de Lannoy authored 3 years ago
  
  89e22487
- 16S validation scripts added (still bugged) · 3318cb43
  Carlos de Lannoy authored 3 years ago
  
  3318cb43
Oct 14, 2021
- bug fix parallelized optimize_hyperparams · 1f512239
  Carlos de Lannoy authored 3 years ago
  
  1f512239
Oct 13, 2021
- parallelized hyperparameter optimization · beaf5be9
  Carlos de Lannoy authored 3 years ago
  
  beaf5be9
Oct 11, 2021
- training, inference and metrics with logits · 99bfa3a1
  Carlos de Lannoy authored 3 years ago
  
  99bfa3a1
- add inference scripts · 2e5cdaa2
  Lannoy, Carlos de authored 3 years ago
  
  2e5cdaa2
Oct 04, 2021
- Merge branch 'ben_dev' into 'master' · 59a8da4f
  Lannoy, Carlos de authored 3 years ago
  
  All MSc thesis work so far, mainly on CNNs, K-mer design and data preprocessing See merge request !1
  59a8da4f
- Updated yaml environment · eddc8b67
  Noordijk, Ben authored 3 years ago
  
  eddc8b67
- Hyperparameter search bug should be fixed now · db476340
  Noordijk, Ben authored 3 years ago
  
  db476340
Oct 01, 2021
- Added script to only demultiplex reads of target barcode · 73411e8d
  Noordijk, Ben authored 3 years ago
  
  73411e8d
Sep 30, 2021
- Started on class to predict reads with NN · 81906af0
  Noordijk, Ben authored 3 years ago
  
  81906af0
- Added Read superclass to be used for inference of reads · 0fba0ab4
  Noordijk, Ben authored 3 years ago
  
  0fba0ab4
- Fixed bug where not providing --uncenter-kmer would cause snakemake to be... · 619766e5
  Noordijk, Ben authored 3 years ago
  
  Fixed bug where not providing --uncenter-kmer would cause snakemake to be confused (forgot this file)
  619766e5
- Fixed bug where not providing --uncenter-kmer would cause snakemake to be confused · ef3676de
  Noordijk, Ben authored 3 years ago
  
  ef3676de
- Finished 16s extraction function · 24c8fad5
  Noordijk, Ben authored 3 years ago
  
  24c8fad5
Sep 29, 2021
- Started small function to get 16s region from genbank · c9442158
  Noordijk, Ben authored 3 years ago
  
  c9442158
Sep 24, 2021
- Maximum number of k-mers in target sequence now also an option in the false positive simulation · f9f37b3f
  Noordijk, Ben authored 3 years ago
  
  f9f37b3f
Sep 23, 2021
- Cleaned up FPR simulation code · 9bf6131c
  Noordijk, Ben authored 3 years ago
  
  9bf6131c
- Hyperparameter optimalisation now works for uncentered k-mers · b67f54a6
  Noordijk, Ben authored 3 years ago
  
  b67f54a6
Sep 22, 2021
- Hyperparameters added to yaml file, too · 0c315876
  Noordijk, Ben authored 3 years ago
  
  0c315876
- Added more parameters for creating the CNN · 2be783a1
  Noordijk, Ben authored 3 years ago
  
  2be783a1
Sep 15, 2021
- Negative raw read examples now never contain the target kmer · 9c767523
  Noordijk, Ben authored 3 years ago
  
  9c767523
- Added functionality so k-mer is not always in the center of the read · f76ea1e0
  Noordijk, Ben authored 3 years ago
  
  f76ea1e0
- Incorporated hyperparameter optimisation for kernel size, number of filters and pooling size · f545d8e2
  Noordijk, Ben authored 3 years ago
  
  f545d8e2
Sep 14, 2021
- Refactored do_pooling to pool_size, added code for global pooling · dce2590e
  Noordijk, Ben authored 3 years ago
  
  dce2590e
Sep 13, 2021
- Edited CNN so kernel_size and filter_width are no longer the same. Also updated some documentation · 4ce61f17
  Noordijk, Ben authored 3 years ago
  
  4ce61f17
Sep 09, 2021
- Hyperparameter optimilisation appears to work now, too · 464510e6
  Noordijk, Ben authored 3 years ago
  
  464510e6
- CNN now works with production_pipeline. Started on hyperparameter optimisation · 7559e771
  Noordijk, Ben authored 3 years ago
  
  7559e771
Sep 08, 2021
- Implemented predict function, can print confusion matrix and parse... · 653fc08f
  Noordijk, Ben authored 3 years ago
  
  Implemented predict function, can print confusion matrix and parse learning_rate and threshold keywords
  653fc08f
- Fixed bug where CNN couldn't handle the 'quiet' kwarg · b8ada615
  Noordijk, Ben authored 3 years ago
  
  b8ada615
- Some refactoring and CNN parameter improvements also merged master · b4da7db6
  Noordijk, Ben authored 3 years ago
  
  b4da7db6
- Merge branch 'master' into ben_dev · 4ae91e05
  Noordijk, Ben authored 3 years ago
  
  # Conflicts: # nns/Rnn_keras.py
  4ae91e05