Commits · 86a1badb698daf884bbf3533f9a7d12f8cafbb20 · Patrick Skillman-Lawrence / mhc_rank

Jul 12, 2016
- didn't get to multiple outputs but did some experiments on shared embedding · 86a1badb
  Alex Rubinsteyn authored 8 years ago
  
  86a1badb
Jun 24, 2016
- forgot that Pandas str helpers are implicitly regexes · 3fe18db1
  Alex Rubinsteyn authored 8 years ago
  
  3fe18db1
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
- added plotting function for w/ & w/out imputation · 7416de5d
  Alex Rubinsteyn authored 8 years ago
  
  7416de5d
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
- Merge pull request #31 from hammerlab/fix-commandline-predict-peptide-lengths · 9af676dd
  Alex Rubinsteyn authored 8 years ago
  
  fixed commandline script for making predictions
  9af676dd
- fixed commandline script for making predictions · 4f026cf9
  Alex Rubinsteyn authored 8 years ago
  
  4f026cf9
- Merge pull request #30 from hammerlab/moving-helpers-from-dataset-to-common · 2b0df761
  Alex Rubinsteyn authored 8 years ago
  
  Stratified cross-validation
  2b0df761
Jun 02, 2016
- skip imputation in Dataset method if algorithm is 'none' · fc1e981a
  Alex Rubinsteyn authored 8 years ago
  
  fc1e981a
- specify dropout in Travis setup script · f2f2f039
  Alex Rubinsteyn authored 8 years ago
  
  f2f2f039
- 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
- don't use batch normalization in small dataset unit tests · 9896944c
  Alex Rubinsteyn authored 8 years ago
  
  9896944c
- pass dropout to Embedding instead of creating Dropout layer · 53496d26
  Alex Rubinsteyn authored 8 years ago
  
  53496d26
- Merge pull request #27 from hammerlab/add-batch-normalization · 837d7b54
  Alex Rubinsteyn authored 8 years ago
  
  added batch normalization between layers, changed default weight initialization
  837d7b54
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
- run script through Python 3 · f0fdbc98
  Alex Rubinsteyn authored 8 years ago
  
  f0fdbc98
- 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
- use correct ScoreSet · 91a7ed7d
  Alex Rubinsteyn authored 8 years ago
  
  91a7ed7d
- moved score_set back to experiments since not using it · 499420cc
  Alex Rubinsteyn authored 8 years ago
  
  499420cc
- 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
- don't rely on Params.__dict__ · 361dc375
  Alex Rubinsteyn authored 8 years ago
  
  361dc375
- 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
- Merge pull request #26 from hammerlab/dataset · c894b11f
  Alex Rubinsteyn authored 8 years ago
  
  Generalizing AlleleData into Dataset
  c894b11f
- added min_ arguments to to_dense_pMHC_matrix · a2e339d5
  Alex Rubinsteyn authored 8 years ago
  
  a2e339d5
- use Dataset.from_csv in matrix-completion-accuracy · ca7f46de
  Alex Rubinsteyn authored 8 years ago
  
  ca7f46de