Skip to content
Snippets Groups Projects
Select Git revision
  • 1.7.0
  • 1.7.0b
  • 1.7.0c
  • 2017-11-13
  • 20180114
  • 201911
  • 20200121_pre_presentation_refactor
  • 202010-phospho
  • 3-flank-variant
  • add-class1-ensemble
  • add-class1-ensemble-rebased
  • add-hyperparameters-base
  • antigen-presentation-updates
  • arch2
  • cartesian-product-cli
  • dataset-object
  • docs-pan-motifs
  • fix-commandline-predict-peptide-lengths
  • gh-pages
  • improved-allele-parsing
  • pre-2.1
  • v2.0.1
  • v2.0.0
  • pre-2.0
  • 1.6.1
  • pre-1.7.0
  • pre_presentation_refactor
  • 1.6.0
  • 1.4.0
  • pre-1.4.0
  • pan-dev1
  • 1.2.2
  • 1.2.0
  • pre-1.2.1
  • pre-1.2
  • pre-1.1
  • 1.0.0
  • pre-1.0
  • 0.9.2
  • 0.9.1
40 results
You can move around the graph by using the arrow keys.
Created with Raphaël 2.2.012Feb7Dec123Nov2019181613121110527Oct14969Sep824Jul20131130Jun2726242316151110985328May26221811643127Apr30Mar2322212019161312118613Feb1075427Jan26252423222120191817161514128765432131Dec26252322212013121110976543230Nov292322211918141130Oct292726181615Adjusted 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 modelsFixed big in argparse for make_architectures.py script. Created file with architecture options (1296) and saved as hyperparameters.json to ap_models dirdebugged architecture / training & created script to make models fitting all combinations of varied hyperparameters for tuningAdjusted hyperparams and processing architectureRemoved print functions that had been used for debuggingdebugged encoding processadjusted when cleave radius is supplied to produce flank encoding.fixed import error for other scripts in mhc_rank dirfixed bug in pssm retreival for flanking encodingadded feature to flank_encoding.py, enabling pssm scores to be added as first position in residue encoding vectorsextract cleavage site, converted pssm from pd.Series and pd.DataFrames to np.ndarrays, enabled pssm calculation.