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Created with Raphaël 2.2.012Jul24Jun231732121May1918171413111096543229Apr2821201918718Feb171617Dec1313Nov124330Oct2826232221201917151412643216Sep28Jul14132130Jun2928Merge pull request #37 from hammerlab/multi-input-multi-output-modelsdidn't get to multiple outputs but did some experiments on shared embeddingUpdate README.mdforgot that Pandas str helpers are implicitly regexesfilter modified peptides from generated datasetadded missing plotting moduleadded plotting function for w/ & w/out imputationreworking commandline arguments to always perform cartesian product of given options and pick best model for each allelecartesian-produ…cartesian-product-cliif no imputation, return empty DatasetUpdate package_metadata.pyMerge pull request #31 from hammerlab/fix-commandline-predict-peptide-lengthsfixed commandline script for making predictionsfix-commandline…fix-commandline-predict-peptide-lengthsMerge pull request #30 from hammerlab/moving-helpers-from-dataset-to-commonskip imputation in Dataset method if algorithm is 'none'moving-helpers-…moving-helpers-from-dataset-to-commonspecify dropout in Travis setup scriptdefault params -- do they work for training quickly?mysterious xc3 non-ASCII character possibly vanquishedMoving shared functionality from deep within Dataset to helper functions in common.pydon't use batch normalization in small dataset unit testspass dropout to Embedding instead of creating Dropout layerMerge pull request #27 from hammerlab/add-batch-normalizationadded batch normalization between layers and changed default initialization to divide by sum of fan_in + fan_out instead of just fan_inupdates to dataset size sensitivity scriptrun script through Python 3lots of tweaks to dataset size sensitivity scriptusing stratified sampling for dataset size sensitivityuse correct ScoreSetmoved score_set back to experiments since not using itdont' add --max-ic50 to args twiceusing mhcflurry.args in dataset-size-sensitivityadded random shrinkage for right censored affinitiesfaster algorithm for converting Dataset to nested dictionaryadded intersection operator to Datasetadded cross_validation iterator to Datasetadded helpers to Datasetdon't rely on Params.__dict__weirdly some versions of Python don't give __dict__ properties to namedtuplesmoved Params definition downadded Params namedtuple, helper to create all combinations of hyperparams, and simple testadded Dataset tests