Commits · 3b83c2bdc90e64d8b6e311cc0ffcedd876f71cee · Patrick Skillman-Lawrence / mhc_rank

Jun 23, 2016
- filter modified peptides from generated dataset · 3b83c2bd
  Alex Rubinsteyn authored 8 years ago
  
  3b83c2bd
- added missing plotting module · 5976e85e
  Alex Rubinsteyn authored 8 years ago
  
  5976e85e
Jun 03, 2016
- if no imputation, return empty Dataset · 274d769a
  Alex Rubinsteyn authored 8 years ago
  
  274d769a
- Update package_metadata.py · ba9a8c79
  Alex Rubinsteyn authored 8 years ago
  
  ba9a8c79
- fixed commandline script for making predictions · 4f026cf9
  Alex Rubinsteyn authored 8 years ago
  
  4f026cf9
Jun 02, 2016
- skip imputation in Dataset method if algorithm is 'none' · fc1e981a
  Alex Rubinsteyn authored 8 years ago
  
  fc1e981a
- default params -- do they work for training quickly? · 474383af
  Alex Rubinsteyn authored 8 years ago
  
  474383af
- mysterious xc3 non-ASCII character possibly vanquished · ab08abf7
  Alex Rubinsteyn authored 8 years ago
  
  ab08abf7
- Moving shared functionality from deep within Dataset to helper functions in common.py · 9508c208
  Alex Rubinsteyn authored 8 years ago
  
  9508c208
- pass dropout to Embedding instead of creating Dropout layer · 53496d26
  Alex Rubinsteyn authored 8 years ago
  
  53496d26
Jun 01, 2016

added batch normalization between layers and changed default initialization to... · 3bc225c0

Alex Rubinsteyn authored 8 years ago

added batch normalization between layers and changed default initialization to divide by sum of fan_in + fan_out instead of just fan_in

3bc225c0

May 21, 2016
- updates to dataset size sensitivity script · 52a88ace
  Alex Rubinsteyn authored 8 years ago
  
  52a88ace
- lots of tweaks to dataset size sensitivity script · 328d2c12
  Alex Rubinsteyn authored 8 years ago
  
  328d2c12
May 19, 2016
- using stratified sampling for dataset size sensitivity · d122c743
  Alex Rubinsteyn authored 8 years ago
  
  d122c743
- dont' add --max-ic50 to args twice · 95de1b69
  Alex Rubinsteyn authored 8 years ago
  
  95de1b69
- using mhcflurry.args in dataset-size-sensitivity · f7039fb4
  Alex Rubinsteyn authored 8 years ago
  
  f7039fb4
- added random shrinkage for right censored affinities · 5e820f66
  Alex Rubinsteyn authored 8 years ago
  
  5e820f66
- faster algorithm for converting Dataset to nested dictionary · 8c5a4ca5
  Alex Rubinsteyn authored 8 years ago
  
  8c5a4ca5
May 18, 2016
- added intersection operator to Dataset · 180575f6
  Alex Rubinsteyn authored 8 years ago
  
  180575f6
May 17, 2016
- added cross_validation iterator to Dataset · 4b337b22
  Alex Rubinsteyn authored 8 years ago
  
  4b337b22
- added helpers to Dataset · 37e0372b
  Alex Rubinsteyn authored 8 years ago
  
  37e0372b
May 14, 2016
- weirdly some versions of Python don't give __dict__ properties to namedtuples · b42fbf1d
  Alex Rubinsteyn authored 8 years ago
  
  b42fbf1d
- moved Params definition down · e766e86a
  Alex Rubinsteyn authored 8 years ago
  
  e766e86a
- added Params namedtuple, helper to create all combinations of hyperparams, and simple test · f13a6c26
  Alex Rubinsteyn authored 8 years ago
  
  f13a6c26
- added Dataset tests · 2c380b44
  Alex Rubinsteyn authored 8 years ago
  
  2c380b44
May 13, 2016
- added min_ arguments to to_dense_pMHC_matrix · a2e339d5
  Alex Rubinsteyn authored 8 years ago
  
  a2e339d5
- always return parser from args helpers · c6e1410f
  Alex Rubinsteyn authored 8 years ago
  
  c6e1410f
- added random negative samples to training · ce1bbda1
  Alex Rubinsteyn authored 8 years ago
  
  ce1bbda1
- added dataset-size-sensitivity script · 7fef98d0
  Alex Rubinsteyn authored 8 years ago
  
  7fef98d0
May 11, 2016
- small fixes · 629baf60
  Alex Rubinsteyn authored 8 years ago
  
  629baf60
May 10, 2016
- working on liberating the titration script from the experiments directory · d1aa3d76
  Alex Rubinsteyn authored 8 years ago
  
  d1aa3d76
- fixed obscure shape bug on empty arrays · fa353a34
  Alex Rubinsteyn authored 8 years ago
  
  fa353a34
May 09, 2016
- fixing training script · 345869a0
  Alex Rubinsteyn authored 8 years ago
  
  345869a0
- imputation seems to be better than not for A0205 · f661d99f
  Alex Rubinsteyn authored 8 years ago
  
  f661d99f
- added back imputation helpers · d9c37838
  Alex Rubinsteyn authored 8 years ago
  
  d9c37838
- moved main impute method onto Dataset · 294f70ee
  Alex Rubinsteyn authored 8 years ago
  
  294f70ee
- debugging imputation with Dataset · bb35d247
  Alex Rubinsteyn authored 8 years ago
  
  bb35d247
May 06, 2016
- changed load_allele_datasets test to work on Datatset, added quality over datasets · 14705f3f
  Alex Rubinsteyn authored 8 years ago
  
  14705f3f
- changing imputation logic to use Dataset · ec233b8c
  Alex Rubinsteyn authored 8 years ago
  
  ec233b8c
- moving encoding to dataset · 9e3c4c8b
  Alex Rubinsteyn authored 8 years ago
  
  9e3c4c8b