diff --git a/downloads-generation/models_class1_pan_unselected/GENERATE.sh b/downloads-generation/models_class1_pan_unselected/GENERATE.sh new file mode 100755 index 0000000000000000000000000000000000000000..569677daec5dc1bee8c2cc4b345e7c0e8285cef4 --- /dev/null +++ b/downloads-generation/models_class1_pan_unselected/GENERATE.sh @@ -0,0 +1,54 @@ +#!/bin/bash +# +# Train pan-allele MHCflurry Class I models. +# +set -e +set -x + +DOWNLOAD_NAME=models_class1_unselected +SCRATCH_DIR=${TMPDIR-/tmp}/mhcflurry-downloads-generation +SCRIPT_ABSOLUTE_PATH="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/$(basename "${BASH_SOURCE[0]}")" +SCRIPT_DIR=$(dirname "$SCRIPT_ABSOLUTE_PATH") + +mkdir -p "$SCRATCH_DIR" +rm -rf "$SCRATCH_DIR/$DOWNLOAD_NAME" +mkdir "$SCRATCH_DIR/$DOWNLOAD_NAME" + +# Send stdout and stderr to a logfile included with the archive. +#exec > >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt") +#exec 2> >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt" >&2) + +# Log some environment info +date +pip freeze +git status + +cd $SCRATCH_DIR/$DOWNLOAD_NAME + +mkdir models + +python $SCRIPT_DIR/generate_hyperparameters.py > hyperparameters.yaml + +GPUS=$(nvidia-smi -L 2> /dev/null | wc -l) || GPUS=0 +echo "Detected GPUS: $GPUS" + +PROCESSORS=$(getconf _NPROCESSORS_ONLN) +echo "Detected processors: $PROCESSORS" + +time mhcflurry-class1-train-pan-allele-models \ + --data "$(mhcflurry-downloads path data_curated)/curated_training_data.with_mass_spec.csv.bz2" \ + --allele-sequences "$(mhcflurry-downloads path allele_sequences)/allele_sequences.csv" \ + --pretrain-data "$(mhcflurry-downloads path random_peptide_predictions)/predictions.csv.bz2" \ + --held-out-measurements-per-allele-fraction-and-max 0.25 100 \ + --ensemble-size 4 \ + --hyperparameters hyperparameters.yaml \ + --out-models-dir models \ + + + #--num-jobs $(expr $PROCESSORS \* 2) --gpus $GPUS --max-workers-per-gpu 2 --max-tasks-per-worker 50 + +cp $SCRIPT_ABSOLUTE_PATH . +bzip2 LOG.txt +tar -cjf "../${DOWNLOAD_NAME}.tar.bz2" * + +echo "Created archive: $SCRATCH_DIR/$DOWNLOAD_NAME.tar.bz2" diff --git a/downloads-generation/models_class1_pan_unselected/README.md b/downloads-generation/models_class1_pan_unselected/README.md new file mode 100644 index 0000000000000000000000000000000000000000..add1df33bd2c70557485846ba141668706043fc6 --- /dev/null +++ b/downloads-generation/models_class1_pan_unselected/README.md @@ -0,0 +1,9 @@ +# Class I pan-allele models (ensemble) + +This download contains trained MHC Class I MHCflurry models. + +To generate this download run: + +``` +./GENERATE.sh +``` diff --git a/downloads-generation/models_class1_pan_unselected/generate_hyperparameters.py b/downloads-generation/models_class1_pan_unselected/generate_hyperparameters.py new file mode 100644 index 0000000000000000000000000000000000000000..6a9c2782873be030b070fbffc777e34927ccb9c1 --- /dev/null +++ b/downloads-generation/models_class1_pan_unselected/generate_hyperparameters.py @@ -0,0 +1,55 @@ +""" +Generate grid of hyperparameters +""" + +from sys import stdout +from copy import deepcopy +from yaml import dump + +base_hyperparameters = { + 'activation': 'tanh', + 'allele_dense_layer_sizes': [], + 'batch_normalization': False, + 'dense_layer_l1_regularization': 0.0, + 'dense_layer_l2_regularization': 0.0, + 'dropout_probability': 0.5, + 'early_stopping': True, + 'init': 'glorot_uniform', + 'layer_sizes': [1024, 512], + 'learning_rate': None, + 'locally_connected_layers': [], + 'loss': 'custom:mse_with_inequalities', + 'max_epochs': 5000, + 'minibatch_size': 128, + 'optimizer': 'rmsprop', + 'output_activation': 'sigmoid', + "patience": 20, + 'peptide_encoding': { + 'vector_encoding_name': 'BLOSUM62', + 'alignment_method': 'left_pad_centered_right_pad', + 'max_length': 15, + }, + 'peptide_allele_merge_activation': '', + 'peptide_allele_merge_method': 'concatenate', + 'peptide_amino_acid_encoding': 'BLOSUM62', + 'peptide_dense_layer_sizes': [], + 'random_negative_affinity_max': 50000.0, + 'random_negative_affinity_min': 20000.0, + 'random_negative_constant': 25, + 'random_negative_distribution_smoothing': 0.0, + 'random_negative_match_distribution': True, + 'random_negative_rate': 0.2, + 'train_data': {}, + 'validation_split': 0.1, +} + +grid = [] +for layer_sizes in [[1024], [1024 * 10], [1024, 512], [512, 512], [1024, 1024]]: + for l1 in [0.0, 0.0001, 0.001, 0.01]: + new = deepcopy(base_hyperparameters) + new["layer_sizes"] = layer_sizes + new["dense_layer_l1_regularization"] = l1 + if not grid or new not in grid: + grid.append(new) + +dump(grid, stdout)