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  1. Dec 11, 2016
    • Tim O'Donnell's avatar
      Pin keras version · 5bb1f547
      Tim O'Donnell authored
      Pin keras version. Also add note on KERAS_BACKEND to README.md.
      
      Closes #67. Closes #65.
      5bb1f547
  2. Sep 26, 2016
  3. Sep 17, 2016
  4. Sep 16, 2016
  5. Sep 15, 2016
    • Tim O'Donnell's avatar
      Fix failing test test_class1_allele_specific_cv_and_train_command and switch... · 37b0585f
      Tim O'Donnell authored
      Fix failing test test_class1_allele_specific_cv_and_train_command and switch downloads.yml to point to models without imputation for now
      37b0585f
    • Tim O'Donnell's avatar
    • Tim O'Donnell's avatar
      Big refactor to prepare for release · 942601b3
      Tim O'Donnell authored
      Lazily putting this all in one commit.
      
      * infrastructure for downloading datasets and published trained models (the `mhcflurry-downloads` command)
      * docs and scripts (in `downloads-generation`) to generate the pubilshed datsets and trained models
      * parallelized cross validation and model training implementation, including support for imputation (based on the old mhcflurry-cloud repo, which is now gone)
      * a single front-end script for class1 allele-specific cross validation and model training / testing (`mhcflurry-class1-allele-specific-cv-and-train`)
      * refactor how we deal with hyper-parameters and how we instantiate Class1BindingPredictors
      * make Class1BindingPredictor pickleable and remove old serialization code
      * move code particular to class 1 allele-specific predictors into its own submodule
      * remove unused code including arg parsing, plotting, and ensembles
      * had to bump the binding prediction threshold for the Titin1 epitope from 500 to 700, as this test was sporadically failing for me (see test_known_class1_epitopes.py)
      * Attempt to make tests involving randomness somewhat more reproducible by setting numpy random seed
      * update README
      942601b3
    • Tim O'Donnell's avatar
      Merge pull request #48 from hammerlab/remove-experiements-and-notebooks · 473fe899
      Tim O'Donnell authored
      Remove experiements and notebooks
      473fe899
    • Tim O'Donnell's avatar
      Remove experiements and notebooks · 81697fe0
      Tim O'Donnell authored
      81697fe0
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