Commits · eec10d07541b6874e06622f6d0e91355e03958c7 · Patrick Skillman-Lawrence / mhc_rank · GitLab

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Apr 19, 2016
- added scripts to download data and train models to Travis · eec10d07
  Alex Rubinsteyn authored 8 years ago
  
  eec10d07
- train very limited models on travis · de4615fa
  Alex Rubinsteyn authored 8 years ago
  
  de4615fa
- added back some basic imports into __init__ · cadc5480
  Alex Rubinsteyn authored 8 years ago
  
  cadc5480
- moved script directory, added scripts to setup.py · bd589e3e
  Alex Rubinsteyn authored 8 years ago
  
  bd589e3e
- added requirements.txt · 42425311
  Alex Rubinsteyn authored 8 years ago
  
  42425311
- don't try to install requirements on travis · ac8c408c
  Alex Rubinsteyn authored 8 years ago
  
  ac8c408c
- added known epitope tests · a59fe505
  Alex Rubinsteyn authored 8 years ago
  
  a59fe505
- training script seems to work · eee968c9
  Alex Rubinsteyn authored 8 years ago
  
  eee968c9
Apr 18, 2016
- added LR to hypeparameters · 79b04065
  Alex Rubinsteyn authored 8 years ago
  
  79b04065
- adding options to training script and updating to work with new predictor class · 6d52392f
  Alex Rubinsteyn authored 8 years ago
  
  6d52392f
- added prediction data from NetMHC dataset paper · 7cb4b493
  Alex Rubinsteyn authored 8 years ago
  
  7cb4b493
- renamed travis file · 7fc70ec6
  Alex Rubinsteyn authored 8 years ago
  
  7fc70ec6
- added travis config and lint script · 6595436f
  Alex Rubinsteyn authored 8 years ago
  
  6595436f
Apr 07, 2016
- Merge pull request #13 from hammerlab/ensembles-of-predictors · e4d6ae74
  Alex Rubinsteyn authored 8 years ago
  
  Ensembles of predictors
  e4d6ae74
- fixed unit test import name · b6107213
  Alex Rubinsteyn authored 8 years ago
  
  b6107213
Feb 18, 2016
- added missing serialization_helpers module · 32c5fa3e
  Alex Rubinsteyn authored 9 years ago
  
  32c5fa3e
Feb 17, 2016
- Merge pull request #12 from hammerlab/soft-pretraining · bb4701a0
  Alex Rubinsteyn authored 9 years ago
  
  Soft-pretraining and lots of other changes
  bb4701a0
- write to log file without ScoreSet · d2989115
  Alex Rubinsteyn authored 9 years ago
  
  d2989115
- moved ScoreSet out of experiments · f110ea6e
  Alex Rubinsteyn authored 9 years ago
  
  f110ea6e
- reorganizing predictor to allow Ensemble as replacement for single predictor · deb4e546
  Alex Rubinsteyn authored 9 years ago
  
  deb4e546
- no pretrain as an option · 9f081ed9
  Alex Rubinsteyn authored 9 years ago
  
  9f081ed9
- args.alleles should be prefix arguments · 10606b65
  Alex Rubinsteyn authored 9 years ago
  
  10606b65
- run each fold of data over every possible predictor, should be faster · 80d8c161
  Alex Rubinsteyn authored 9 years ago
  
  80d8c161
- skip alleles with less than n_folds positive examples · 8308c397
  Alex Rubinsteyn authored 9 years ago
  
  8308c397
- moved the copy to use of weights · a9ab62f8
  Alex Rubinsteyn authored 9 years ago
  
  a9ab62f8
- copy weights before setting them to model & opt · 93dc75b5
  Alex Rubinsteyn authored 9 years ago
  
  93dc75b5
- results weren't being split by allele · 5618cf96
  Alex Rubinsteyn authored 9 years ago
  
  5618cf96
- add batch size as an argument, use nanmean for pretraining if allele gets... · 19c16cc8
  Alex Rubinsteyn authored 9 years ago
  
  add batch size as an argument, use nanmean for pretraining if allele gets pruned from the completed matrix
  19c16cc8
- formatting · 870f0cd0
  Alex Rubinsteyn authored 9 years ago
  
  870f0cd0
- added 2nd layer · a1483f10
  Alex Rubinsteyn authored 9 years ago
  
  a1483f10
- added back dropout to training loop · 9b0dff97
  Alex Rubinsteyn authored 9 years ago
  
  9b0dff97
- get optimizer from model, not predictor · 47454c13
  Alex Rubinsteyn authored 9 years ago
  
  47454c13
- reset optimizer state · 84d5ba84
  Alex Rubinsteyn authored 9 years ago
  
  84d5ba84
- don't print while predicting · 72898f9f
  Alex Rubinsteyn authored 9 years ago
  
  72898f9f
- create all predictors up front · 31f8cedf
  Alex Rubinsteyn authored 9 years ago
  
  31f8cedf
- rearranged peptide encoding, fixed unit tests · c528b372
  Alex Rubinsteyn authored 9 years ago
  
  c528b372
- limit range of values with MICE · 9972264f
  Alex Rubinsteyn authored 9 years ago
  
  9972264f
- reducing search space · 31ef8118
  Alex Rubinsteyn authored 9 years ago
  
  31ef8118
- moved fit code over to Class1BindingPredictor · 6055e465
  Alex Rubinsteyn authored 9 years ago
  
  6055e465
- filter out rows of matrix with only one observation · 68dd95d9
  Alex Rubinsteyn authored 9 years ago
  
  68dd95d9