- Feb 11, 2017
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Tim O'Donnell authored
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- Feb 10, 2017
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Tim O'Donnell authored
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Tim O'Donnell authored
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- Feb 09, 2017
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Tim O'Donnell authored
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Tim O'Donnell authored
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- Sep 26, 2016
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Tim O'Donnell authored
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Tim O'Donnell authored
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Tim O'Donnell authored
Fixes #54
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Tim O'Donnell authored
Fixes #59
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- Sep 16, 2016
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Tim O'Donnell authored
Return the titin epitope tests back to the original more stringent threshold of 500nm (instead of 700nm)
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Tim O'Donnell authored
Make test_imputation unit test fair by training the model with imputation for the same number of epochs as the model without imputation
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Tim O'Donnell authored
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- Sep 15, 2016
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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
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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
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- Jun 02, 2016
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Alex Rubinsteyn authored
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Alex Rubinsteyn authored
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- Jun 01, 2016
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Alex Rubinsteyn authored
added batch normalization between layers and changed default initialization to divide by sum of fan_in + fan_out instead of just fan_in
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- May 18, 2016
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Alex Rubinsteyn authored
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- May 17, 2016
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Alex Rubinsteyn authored
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- May 14, 2016
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Alex Rubinsteyn authored
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Alex Rubinsteyn authored
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Alex Rubinsteyn authored
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- May 09, 2016
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Alex Rubinsteyn authored
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Alex Rubinsteyn authored
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Alex Rubinsteyn authored
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Alex Rubinsteyn authored
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- May 06, 2016
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Alex Rubinsteyn authored
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Alex Rubinsteyn authored
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Alex Rubinsteyn authored
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Alex Rubinsteyn authored
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Alex Rubinsteyn authored
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Alex Rubinsteyn authored
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Alex Rubinsteyn authored
split up some of the class1_binding_predictor methods, moved code to training_helpers and Dataset, fixing broken unit tests
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- May 05, 2016
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Alex Rubinsteyn authored
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- May 04, 2016
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Alex Rubinsteyn authored
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Alex Rubinsteyn authored
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Alex Rubinsteyn authored
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Alex Rubinsteyn authored
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Alex Rubinsteyn authored
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Alex Rubinsteyn authored
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