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Created with Raphaël 2.2.019Feb18171615127Dec123Nov2019181613121110527Oct14969Sep824Jul20131130Jun2726242316151110985328May26221811643127Apr30Mar2322212019161312118613Feb1075427Jan26252423222120191817161514128765432131Dec26252322212013121110976543230Nov292322211918141130Oct29Results from 4th day of trainingadding training results from day 3adding results from most recent training intervalupdated get_preds.py post testingDebugged get_preds.pyfinished script to run predictions as SLURM jobsmodels from first round of training + some files to enable predictions to be to be run as SLURM jobsfinished debuggin for learned embeddings and began trainingcorrected typo and kicked off all training jobs in ap_models3Debugged new changes and kicked off 1st job of new trainings as testAdjusted sequence preprocessing to work with the ability to learn embeddingsRemoved scripts relating to pssmadjusted some though processes and removed conclusions / experiments that either arent valid or we arent doing anymoremanuscriptmanuscriptUpdated the name of the model / approachadded functionality to model creation that allows for learned embeddings (or combo of learned and hardcoded). Also, adjusted amino_acid.py to make X's index = 0 so that it can be used as a mask.created hyperparameter files and set up training for models with learned embeddingsadded hyperparam options for learned embeddingscreated benchmarking dataset templateadded manuscript latex filesdeleted original mhcflurry and old scriptDeleted mhcflurry/__init__.py, mhcflurry/allele_encoding.py, mhcflurry/amino_acid.py, mhcflurry/calibrate_percentile_ranks_command.py, mhcflurry/class1_affinity_predictor.py, mhcflurry/class1_neural_network.py, mhcflurry/class1_presentation_predictor.py, mhcflurry/class1_processing_neural_network.py, mhcflurry/class1_processing_predictor.py, mhcflurry/cluster_parallelism.py, mhcflurry/common.py, mhcflurry/custom_loss.py, mhcflurry/data_dependent_weights_initialization.py, mhcflurry/downloads.py, mhcflurry/downloads.yml, mhcflurry/downloads_command.py, mhcflurry/encodable_sequences.py, mhcflurry/ensemble_centrality.py, mhcflurry/fasta.py, mhcflurry/flanking_encoding.py, mhcflurry/hyperparameters.py, mhcflurry/local_parallelism.py, mhcflurry/percent_rank_transform.py, mhcflurry/predict_command.py, mhcflurry/predict_scan_command.py, mhcflurry/random_negative_peptides.py, mhcflurry/regression_target.py, mhcflurry/scoring.py, mhcflurry/select_allele_specific_models_command.py, mhcflurry/select_pan_allele_models_command.py, mhcflurry/select_processing_models_command.py, mhcflurry/testing_utils.py, mhcflurry/train_allele_specific_models_command.py, mhcflurry/train_pan_allele_models_command.py, mhcflurry/train_presentation_models_command.py, mhcflurry/train_processing_models_command.py, mhcflurry/version.py, train_APmodels.sh filesremoved original mhcflurry2.0 filesadding training data from ap models with crossentropy lossaltered training init to work with SLURM and corrected typo (BLOSUM --> BLOSUM62) in hyperparameters, specifically encoding optionssplit hyperparams up so that they can be run as separate jobs in OSCfinished debuggingfixed bug in flanking_encodingqsub and CLI training scriptsfixed train AP models scriptaltered training shell script fror qsubfixed nonsensical import of subpackage in middle of script to point to mhc_rank instead of mhcflurryMerge branch 'master' of https://code.osu.edu/skillman-lawrence.1/mhc_rankminor edittrying to figure out why cleave_radius is an unexpected keyword arg in vector_encode even though vector encode has an explicit argument cleave_radisu...debuggingMerge branch 'master' of https://code.osu.edu/skillman-lawrence.1/mhc_rankeditsworking on training scriptsfixed bugsadded training data used to train mhcflurry AP models