Mercurial > repos > bgruening > create_tool_recommendation_model
view optimise_hyperparameters.py @ 0:9bf25dbe00ad draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
author | bgruening |
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date | Wed, 28 Aug 2019 07:19:38 -0400 |
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children | 76251d1ccdcc |
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""" Find the optimal combination of hyperparameters """ import numpy as np from hyperopt import fmin, tpe, hp, STATUS_OK, Trials from keras.models import Sequential from keras.layers import Dense, GRU, Dropout from keras.layers.embeddings import Embedding from keras.layers.core import SpatialDropout1D from keras.optimizers import RMSprop from keras.callbacks import EarlyStopping import utils class HyperparameterOptimisation: @classmethod def __init__(self): """ Init method. """ @classmethod def train_model(self, config, reverse_dictionary, train_data, train_labels, test_data, test_labels, class_weights): """ Train a model and report accuracy """ l_recurrent_activations = config["activation_recurrent"].split(",") l_output_activations = config["activation_output"].split(",") # convert items to integer l_batch_size = list(map(int, config["batch_size"].split(","))) l_embedding_size = list(map(int, config["embedding_size"].split(","))) l_units = list(map(int, config["units"].split(","))) # convert items to float l_learning_rate = list(map(float, config["learning_rate"].split(","))) l_dropout = list(map(float, config["dropout"].split(","))) l_spatial_dropout = list(map(float, config["spatial_dropout"].split(","))) l_recurrent_dropout = list(map(float, config["recurrent_dropout"].split(","))) optimize_n_epochs = int(config["optimize_n_epochs"]) validation_split = float(config["validation_share"]) # get dimensions dimensions = len(reverse_dictionary) + 1 best_model_params = dict() early_stopping = EarlyStopping(monitor='val_loss', mode='min', min_delta=1e-4, verbose=1, patience=1) # specify the search space for finding the best combination of parameters using Bayesian optimisation params = { "embedding_size": hp.quniform("embedding_size", l_embedding_size[0], l_embedding_size[1], 1), "units": hp.quniform("units", l_units[0], l_units[1], 1), "batch_size": hp.quniform("batch_size", l_batch_size[0], l_batch_size[1], 1), "activation_recurrent": hp.choice("activation_recurrent", l_recurrent_activations), "activation_output": hp.choice("activation_output", l_output_activations), "learning_rate": hp.loguniform("learning_rate", np.log(l_learning_rate[0]), np.log(l_learning_rate[1])), "dropout": hp.uniform("dropout", l_dropout[0], l_dropout[1]), "spatial_dropout": hp.uniform("spatial_dropout", l_spatial_dropout[0], l_spatial_dropout[1]), "recurrent_dropout": hp.uniform("recurrent_dropout", l_recurrent_dropout[0], l_recurrent_dropout[1]) } def create_model(params): model = Sequential() model.add(Embedding(dimensions, int(params["embedding_size"]), mask_zero=True)) model.add(SpatialDropout1D(params["spatial_dropout"])) model.add(GRU(int(params["units"]), dropout=params["dropout"], recurrent_dropout=params["recurrent_dropout"], return_sequences=True, activation=params["activation_recurrent"])) model.add(Dropout(params["dropout"])) model.add(GRU(int(params["units"]), dropout=params["dropout"], recurrent_dropout=params["recurrent_dropout"], return_sequences=False, activation=params["activation_recurrent"])) model.add(Dropout(params["dropout"])) model.add(Dense(dimensions, activation=params["activation_output"])) optimizer_rms = RMSprop(lr=params["learning_rate"]) model.compile(loss=utils.weighted_loss(class_weights), optimizer=optimizer_rms) model_fit = model.fit( train_data, train_labels, batch_size=int(params["batch_size"]), epochs=optimize_n_epochs, shuffle="batch", verbose=2, validation_split=validation_split, callbacks=[early_stopping] ) return {'loss': model_fit.history["val_loss"][-1], 'status': STATUS_OK} # minimize the objective function using the set of parameters above4 trials = Trials() learned_params = fmin(create_model, params, trials=trials, algo=tpe.suggest, max_evals=int(config["max_evals"])) print(learned_params) # set the best params with respective values for item in learned_params: item_val = learned_params[item] if item == 'activation_output': best_model_params[item] = l_output_activations[item_val] elif item == 'activation_recurrent': best_model_params[item] = l_recurrent_activations[item_val] else: best_model_params[item] = item_val return best_model_params