# HG changeset patch # User bgruening # Date 1566991178 14400 # Node ID 9bf25dbe00adb261f3dac74da53430ae94e840ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad" diff -r 000000000000 -r 9bf25dbe00ad create_tool_recommendation_model.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/create_tool_recommendation_model.xml Wed Aug 28 07:19:38 2019 -0400 @@ -0,0 +1,164 @@ + + using deep learning + + python + tensorflow + keras + scikit-learn + h5py + csvkit + hyperopt + + echo "@VERSION@" + + + + + + +
+ + +
+
+ + + + + +
+
+ + + + + + + + + + +
+ + + + + + + + + + + + + + + + + 0). This data helps to know the usage pattern of a tool i.e. if a tool is being used often (high frequency in recent months) in the last one year or not being used at all (low frequency in recent months). This frequency is then used as weights for these tools in the neural network learning. The tools with high frequency in recent months is more important than tools with low frequency in recent months. This constraint allows to phase-out those tools from predictions which are not being used recently. + +----- + + +**Parameters** + +There are multiple parameters which can be set. They are divided into 3 categories: + +1. Data parameters + - "input_cutoff_date": It is used to set the earliest date from which the usage frequencies of tools should be considered. The format of the date is YYYY-MM-DD. This date should be in the past. + - "input_maximum_path_length": This takes an integer and specifies the maximum size of a tool sequence extracted from any workflow. Any tool sequence of length larger than this number is not included in the dataset for training. + +2. Training parameters + - "max_evals": The hyperparameters of the neural network are tuned using a Bayesian optimisation approach and multiple configurations are sampled from different ranges of parameters. The number specified in this parameter is the number of configurations of hyperparameters evaluated to optimise them. Higher the number, the longer is the running time of the tool. + - "optimize_n_epochs": This number specifies how many iterations would the neural network executes to evaluate each sampled configuration. + - "n_epochs": Once the best configuration of hyperparameters has been found, the neural network takes this configuration and runs for "n_epochs" number of times minimising the error to produce a model at the end. + - "test_share": It specifies the size of the test set. For example, if it is 0.5, then the test set is half of the entire data available. It should not be set to more than 0.5. This set is used for evaluating the precision on an unseen set. + - "validation_share": It specifies the size of the validation set. For example, if it is 0.5, then the validation set is half of the entire data available. It should not be set to more than 0.5. This set is used for computing error while training on the best configuration. + +3. Neural network parameters: + - "batch_size": The training of the neural network is done using batch learning in this work. The training data is divided into equal batches and for each epoch (a training iteration), all batches of data are trained one after another. A higher or lower value can unsettle the training. Therefore, this parameter should be optimised. + - "units": This number is the number of hidden recurrent units. A higher number means stronger learning (may lead to overfitting) and a lower number means weaker learning (may lead to underfitting). Therefore, this number should be optimised. + - "embedding_size": For each tool, a fixed-size vector is learned and this fixed-size is known as the embedding size. This size remains same for all the tools. A lower number may underfit and a higher number may overfit. This parameter should be optimised as well. + - "dropout": A neural network tends to overfit (especially when it is stronger). Therefore, to avoid or minimize overfitting, dropout is used. The fraction specified by dropout is the fraction of units "deleted" randomly from the network to impose randomness which helps in avoiding overfitting. This parameter should be optimised as well. + - "spatial_dropout": Similar to dropout, this is used to reduce overfitting in the embedding layer. This parameter should be optimised as well. + - "recurrent_dropout": Similar to dropout and spatial dropout, this is used to reduce overfitting in the recurrent layers (hidden). This parameter should be optimised as well. + - "learning_rate": The learning rate specifies the speed of learning. A higher value ensures fast learning (the optimiser may diverge) and a lower value causes slow learning (may not reach the optimum). This parameter should be optimised as well. + - "activation_recurrent": Activations are mathematical functions to transform input into output. This takes the name of an activation function from the list of Keras activations (https://keras.io/activations/) for recurrent layers. + - "activation_output": This takes the activation for transforming the input of the last layer to the output of the neural network. It is also taken from Keras activations (https://keras.io/activations/). + - "loss_type": This is also a mathematical function which computes the error between true and predicted outputs. An optimizer uses this loss function to compute error and minimize it. It is taken from the list of Keras optimisers (https://keras.io/optimizers/). + +----- + +**Output file** + +The output file (model) is an HDF5 file (http://docs.h5py.org/en/latest/high/file.html) containing multiple attributes like a dictionary of tools, neural network configuration and weights for each layer, weights of all tools and so on. After the tool has finished executing, it can be downloaded and placed at "/galaxy/database/" inside a Galaxy instance codebase. To see the recommended tools (enable the UI integrations) in Galaxy, the following changes should be made to "galaxy.yml" file: + + - Enable and then set the property "enable_tool_recommendation" to "true". + - Enable and then set the property "model_path" to "database/<>". + + ]]> + + + + @ARTICLE{anuprulez_galaxytools, + Author = {Anup Kumar and Björn Grüning}, + keywords = {bioinformatics, recommendation system, deep learning}, + title = {{Tool recommendation system for Galaxy workflows}}, + url = {https://github.com/anuprulez/galaxytools} + } + + + diff -r 000000000000 -r 9bf25dbe00ad extract_workflow_connections.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_workflow_connections.py Wed Aug 28 07:19:38 2019 -0400 @@ -0,0 +1,140 @@ +""" +Extract workflow paths from the tabular file containing +input and output tools +""" + +import csv +import random + +import utils + + +class ExtractWorkflowConnections: + + @classmethod + def __init__(self): + """ Init method. """ + + @classmethod + def read_tabular_file(self, raw_file_path): + """ + Read tabular file and extract workflow connections + """ + print("Reading workflows...") + workflows = {} + workflow_paths_dup = "" + workflow_parents = dict() + workflow_paths = list() + unique_paths = list() + with open(raw_file_path, 'rt') as workflow_connections_file: + workflow_connections = csv.reader(workflow_connections_file, delimiter='\t') + for index, row in enumerate(workflow_connections): + wf_id = str(row[0]) + in_tool = row[3] + out_tool = row[6] + if wf_id not in workflows: + workflows[wf_id] = list() + if out_tool and in_tool and out_tool != in_tool: + workflows[wf_id].append((in_tool, out_tool)) + print("Processing workflows...") + wf_ctr = 0 + for wf_id in workflows: + wf_ctr += 1 + workflow_parents[wf_id] = self.read_workflow(wf_id, workflows[wf_id]) + + for wf_id in workflow_parents: + flow_paths = list() + parents_graph = workflow_parents[wf_id] + roots, leaves = self.get_roots_leaves(parents_graph) + for root in roots: + for leaf in leaves: + paths = self.find_tool_paths_workflow(parents_graph, root, leaf) + # reverse the paths as they are computed from leaves to roots leaf + paths = [tool_path for tool_path in paths] + if len(paths) > 0: + flow_paths.extend(paths) + workflow_paths.extend(flow_paths) + + print("Workflows processed: %d" % wf_ctr) + + # remove slashes from the tool ids + wf_paths_no_slash = list() + for path in workflow_paths: + path_no_slash = [utils.format_tool_id(tool_id) for tool_id in path] + wf_paths_no_slash.append(path_no_slash) + + # collect duplicate paths + for path in wf_paths_no_slash: + workflow_paths_dup += ",".join(path) + "\n" + + # collect unique paths + unique_paths = list(workflow_paths_dup.split("\n")) + unique_paths = list(filter(None, unique_paths)) + random.shuffle(unique_paths) + no_dup_paths = list(set(unique_paths)) + + print("Finding compatible next tools...") + compatible_next_tools = self.set_compatible_next_tools(no_dup_paths) + return unique_paths, compatible_next_tools + + @classmethod + def set_compatible_next_tools(self, workflow_paths): + """ + Find next tools for each tool + """ + next_tools = dict() + for path in workflow_paths: + path_split = path.split(",") + for window in range(0, len(path_split) - 1): + current_next_tools = path_split[window: window + 2] + current_tool = current_next_tools[0] + next_tool = current_next_tools[1] + try: + next_tools[current_tool] += "," + next_tool + except Exception: + next_tools[current_tool] = next_tool + for tool in next_tools: + next_tools[tool] = ",".join(list(set(next_tools[tool].split(",")))) + return next_tools + + @classmethod + def read_workflow(self, wf_id, workflow_rows): + """ + Read all connections for a workflow + """ + tool_parents = dict() + for connection in workflow_rows: + in_tool = connection[0] + out_tool = connection[1] + if out_tool not in tool_parents: + tool_parents[out_tool] = list() + if in_tool not in tool_parents[out_tool]: + tool_parents[out_tool].append(in_tool) + return tool_parents + + @classmethod + def get_roots_leaves(self, graph): + roots = list() + leaves = list() + all_parents = list() + for item in graph: + all_parents.extend(graph[item]) + all_parents = list(set(all_parents)) + children = graph.keys() + roots = list(set(all_parents).difference(set(children))) + leaves = list(set(children).difference(set(all_parents))) + return roots, leaves + + @classmethod + def find_tool_paths_workflow(self, graph, start, end, path=[]): + path = path + [end] + if start == end: + return [path] + path_list = list() + if end in graph: + for node in graph[end]: + if node not in path: + new_tools_paths = self.find_tool_paths_workflow(graph, start, node, path) + for tool_path in new_tools_paths: + path_list.append(tool_path) + return path_list diff -r 000000000000 -r 9bf25dbe00ad main.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/main.py Wed Aug 28 07:19:38 2019 -0400 @@ -0,0 +1,178 @@ +""" +Predict next tools in the Galaxy workflows +using machine learning (recurrent neural network) +""" + +import numpy as np +import argparse +import time + +# machine learning library +import keras.callbacks as callbacks + +import extract_workflow_connections +import prepare_data +import optimise_hyperparameters +import utils + + +class PredictTool: + + @classmethod + def __init__(self): + """ Init method. """ + + @classmethod + def find_train_best_network(self, network_config, reverse_dictionary, train_data, train_labels, test_data, test_labels, n_epochs, class_weights, usage_pred, compatible_next_tools): + """ + Define recurrent neural network and train sequential data + """ + print("Start hyperparameter optimisation...") + hyper_opt = optimise_hyperparameters.HyperparameterOptimisation() + best_params = hyper_opt.train_model(network_config, reverse_dictionary, train_data, train_labels, test_data, test_labels, class_weights) + + # retrieve the model and train on complete dataset without validation set + model, best_params = utils.set_recurrent_network(best_params, reverse_dictionary, class_weights) + + # define callbacks + predict_callback_test = PredictCallback(test_data, test_labels, reverse_dictionary, n_epochs, compatible_next_tools, usage_pred) + # tensor_board = callbacks.TensorBoard(log_dir=log_directory, histogram_freq=0, write_graph=True, write_images=True) + callbacks_list = [predict_callback_test] + + print("Start training on the best model...") + model_fit = model.fit( + train_data, + train_labels, + batch_size=int(best_params["batch_size"]), + epochs=n_epochs, + verbose=2, + callbacks=callbacks_list, + shuffle="batch", + validation_data=(test_data, test_labels) + ) + + train_performance = { + "train_loss": np.array(model_fit.history["loss"]), + "model": model, + "best_parameters": best_params + } + + # if there is test data, add more information + if len(test_data) > 0: + train_performance["validation_loss"] = np.array(model_fit.history["val_loss"]) + train_performance["precision"] = predict_callback_test.precision + train_performance["usage_weights"] = predict_callback_test.usage_weights + return train_performance + + +class PredictCallback(callbacks.Callback): + def __init__(self, test_data, test_labels, reverse_data_dictionary, n_epochs, next_compatible_tools, usg_scores): + self.test_data = test_data + self.test_labels = test_labels + self.reverse_data_dictionary = reverse_data_dictionary + self.precision = list() + self.usage_weights = list() + self.n_epochs = n_epochs + self.next_compatible_tools = next_compatible_tools + self.pred_usage_scores = usg_scores + + def on_epoch_end(self, epoch, logs={}): + """ + Compute absolute and compatible precision for test data + """ + if len(self.test_data) > 0: + precision, usage_weights = utils.verify_model(self.model, self.test_data, self.test_labels, self.reverse_data_dictionary, self.next_compatible_tools, self.pred_usage_scores) + self.precision.append(precision) + self.usage_weights.append(usage_weights) + print("Epoch %d precision: %s" % (epoch + 1, precision)) + print("Epoch %d usage weights: %s" % (epoch + 1, usage_weights)) + + +if __name__ == "__main__": + start_time = time.time() + arg_parser = argparse.ArgumentParser() + arg_parser.add_argument("-wf", "--workflow_file", required=True, help="workflows tabular file") + arg_parser.add_argument("-tu", "--tool_usage_file", required=True, help="tool usage file") + arg_parser.add_argument("-om", "--output_model", required=True, help="trained model file") + # data parameters + arg_parser.add_argument("-cd", "--cutoff_date", required=True, help="earliest date for taking tool usage") + arg_parser.add_argument("-pl", "--maximum_path_length", required=True, help="maximum length of tool path") + arg_parser.add_argument("-ep", "--n_epochs", required=True, help="number of iterations to run to create model") + arg_parser.add_argument("-oe", "--optimize_n_epochs", required=True, help="number of iterations to run to find best model parameters") + arg_parser.add_argument("-me", "--max_evals", required=True, help="maximum number of configuration evaluations") + arg_parser.add_argument("-ts", "--test_share", required=True, help="share of data to be used for testing") + arg_parser.add_argument("-vs", "--validation_share", required=True, help="share of data to be used for validation") + # neural network parameters + arg_parser.add_argument("-bs", "--batch_size", required=True, help="size of the tranining batch i.e. the number of samples per batch") + arg_parser.add_argument("-ut", "--units", required=True, help="number of hidden recurrent units") + arg_parser.add_argument("-es", "--embedding_size", required=True, help="size of the fixed vector learned for each tool") + arg_parser.add_argument("-dt", "--dropout", required=True, help="percentage of neurons to be dropped") + arg_parser.add_argument("-sd", "--spatial_dropout", required=True, help="1d dropout used for embedding layer") + arg_parser.add_argument("-rd", "--recurrent_dropout", required=True, help="dropout for the recurrent layers") + arg_parser.add_argument("-lr", "--learning_rate", required=True, help="learning rate") + arg_parser.add_argument("-ar", "--activation_recurrent", required=True, help="activation function for recurrent layers") + arg_parser.add_argument("-ao", "--activation_output", required=True, help="activation function for output layers") + arg_parser.add_argument("-lt", "--loss_type", required=True, help="type of the loss/error function") + # get argument values + args = vars(arg_parser.parse_args()) + tool_usage_path = args["tool_usage_file"] + workflows_path = args["workflow_file"] + cutoff_date = args["cutoff_date"] + maximum_path_length = int(args["maximum_path_length"]) + trained_model_path = args["output_model"] + n_epochs = int(args["n_epochs"]) + optimize_n_epochs = int(args["optimize_n_epochs"]) + max_evals = int(args["max_evals"]) + test_share = float(args["test_share"]) + validation_share = float(args["validation_share"]) + batch_size = args["batch_size"] + units = args["units"] + embedding_size = args["embedding_size"] + dropout = args["dropout"] + spatial_dropout = args["spatial_dropout"] + recurrent_dropout = args["recurrent_dropout"] + learning_rate = args["learning_rate"] + activation_recurrent = args["activation_recurrent"] + activation_output = args["activation_output"] + loss_type = args["loss_type"] + + config = { + 'cutoff_date': cutoff_date, + 'maximum_path_length': maximum_path_length, + 'n_epochs': n_epochs, + 'optimize_n_epochs': optimize_n_epochs, + 'max_evals': max_evals, + 'test_share': test_share, + 'validation_share': validation_share, + 'batch_size': batch_size, + 'units': units, + 'embedding_size': embedding_size, + 'dropout': dropout, + 'spatial_dropout': spatial_dropout, + 'recurrent_dropout': recurrent_dropout, + 'learning_rate': learning_rate, + 'activation_recurrent': activation_recurrent, + 'activation_output': activation_output, + 'loss_type': loss_type + } + + # Extract and process workflows + connections = extract_workflow_connections.ExtractWorkflowConnections() + workflow_paths, compatible_next_tools = connections.read_tabular_file(workflows_path) + # Process the paths from workflows + print("Dividing data...") + data = prepare_data.PrepareData(maximum_path_length, test_share) + train_data, train_labels, test_data, test_labels, data_dictionary, reverse_dictionary, class_weights, usage_pred = data.get_data_labels_matrices(workflow_paths, tool_usage_path, cutoff_date, compatible_next_tools) + # find the best model and start training + predict_tool = PredictTool() + # start training with weighted classes + print("Training with weighted classes and samples ...") + results_weighted = predict_tool.find_train_best_network(config, reverse_dictionary, train_data, train_labels, test_data, test_labels, n_epochs, class_weights, usage_pred, compatible_next_tools) + print() + print("Best parameters \n") + print(results_weighted["best_parameters"]) + print() + utils.save_model(results_weighted, data_dictionary, compatible_next_tools, trained_model_path, class_weights) + end_time = time.time() + print() + print("Program finished in %s seconds" % str(end_time - start_time)) diff -r 000000000000 -r 9bf25dbe00ad optimise_hyperparameters.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/optimise_hyperparameters.py Wed Aug 28 07:19:38 2019 -0400 @@ -0,0 +1,99 @@ +""" +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 diff -r 000000000000 -r 9bf25dbe00ad predict_tool_usage.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/predict_tool_usage.py Wed Aug 28 07:19:38 2019 -0400 @@ -0,0 +1,113 @@ +""" +Predict tool usage to weigh the predicted tools +""" + +import os +import numpy as np +import warnings +import csv +import collections + +from sklearn.svm import SVR +from sklearn.model_selection import GridSearchCV +from sklearn.pipeline import Pipeline + +import utils + +warnings.filterwarnings("ignore") + +main_path = os.getcwd() + + +class ToolPopularity: + + @classmethod + def __init__(self): + """ Init method. """ + + @classmethod + def extract_tool_usage(self, tool_usage_file, cutoff_date, dictionary): + """ + Extract the tool usage over time for each tool + """ + tool_usage_dict = dict() + all_dates = list() + all_tool_list = list(dictionary.keys()) + with open(tool_usage_file, 'rt') as usage_file: + tool_usage = csv.reader(usage_file, delimiter='\t') + for index, row in enumerate(tool_usage): + if (str(row[1]) > cutoff_date) is True: + tool_id = utils.format_tool_id(row[0]) + if tool_id in all_tool_list: + all_dates.append(row[1]) + if tool_id not in tool_usage_dict: + tool_usage_dict[tool_id] = dict() + tool_usage_dict[tool_id][row[1]] = int(row[2]) + else: + curr_date = row[1] + # merge the usage of different version of tools into one + if curr_date in tool_usage_dict[tool_id]: + tool_usage_dict[tool_id][curr_date] += int(row[2]) + else: + tool_usage_dict[tool_id][curr_date] = int(row[2]) + # get unique dates + unique_dates = list(set(all_dates)) + for tool in tool_usage_dict: + usage = tool_usage_dict[tool] + # extract those dates for which tool's usage is not present in raw data + dates_not_present = list(set(unique_dates) ^ set(usage.keys())) + # impute the missing values by 0 + for dt in dates_not_present: + tool_usage_dict[tool][dt] = 0 + # sort the usage list by date + tool_usage_dict[tool] = collections.OrderedDict(sorted(usage.items())) + return tool_usage_dict + + @classmethod + def learn_tool_popularity(self, x_reshaped, y_reshaped): + """ + Fit a curve for the tool usage over time to predict future tool usage + """ + epsilon = 0.0 + cv = 5 + s_typ = 'neg_mean_absolute_error' + n_jobs = 4 + s_error = 1 + iid = True + tr_score = False + try: + pipe = Pipeline(steps=[('regressor', SVR(gamma='scale'))]) + param_grid = { + 'regressor__kernel': ['rbf', 'poly', 'linear'], + 'regressor__degree': [2, 3] + } + search = GridSearchCV(pipe, param_grid, iid=iid, cv=cv, scoring=s_typ, n_jobs=n_jobs, error_score=s_error, return_train_score=tr_score) + search.fit(x_reshaped, y_reshaped.ravel()) + model = search.best_estimator_ + # set the next time point to get prediction for + prediction_point = np.reshape([x_reshaped[-1][0] + 1], (1, 1)) + prediction = model.predict(prediction_point) + if prediction < epsilon: + prediction = [epsilon] + return prediction[0] + except Exception: + return epsilon + + @classmethod + def get_pupularity_prediction(self, tools_usage): + """ + Get the popularity prediction for each tool + """ + usage_prediction = dict() + for tool_name, usage in tools_usage.items(): + y_val = list() + x_val = list() + for x, y in usage.items(): + x_val.append(x) + y_val.append(y) + x_pos = np.arange(len(x_val)) + x_reshaped = x_pos.reshape(len(x_pos), 1) + y_reshaped = np.reshape(y_val, (len(x_pos), 1)) + prediction = np.round(self.learn_tool_popularity(x_reshaped, y_reshaped), 8) + usage_prediction[tool_name] = prediction + return usage_prediction diff -r 000000000000 -r 9bf25dbe00ad prepare_data.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prepare_data.py Wed Aug 28 07:19:38 2019 -0400 @@ -0,0 +1,251 @@ +""" +Prepare the workflow paths to be used by downstream +machine learning algorithm. The paths are divided +into the test and training sets +""" + +import os +import collections +import numpy as np +import random + +import predict_tool_usage + +main_path = os.getcwd() + + +class PrepareData: + + @classmethod + def __init__(self, max_seq_length, test_data_share): + """ Init method. """ + self.max_tool_sequence_len = max_seq_length + self.test_share = test_data_share + + @classmethod + def process_workflow_paths(self, workflow_paths): + """ + Get all the tools and complete set of individual paths for each workflow + """ + tokens = list() + raw_paths = workflow_paths + raw_paths = [x.replace("\n", '') for x in raw_paths] + for item in raw_paths: + split_items = item.split(",") + for token in split_items: + if token is not "": + tokens.append(token) + tokens = list(set(tokens)) + tokens = np.array(tokens) + tokens = np.reshape(tokens, [-1, ]) + return tokens, raw_paths + + @classmethod + def create_new_dict(self, new_data_dict): + """ + Create new data dictionary + """ + reverse_dict = dict((v, k) for k, v in new_data_dict.items()) + return new_data_dict, reverse_dict + + @classmethod + def assemble_dictionary(self, new_data_dict, old_data_dictionary={}): + """ + Create/update tools indices in the forward and backward dictionary + """ + new_data_dict, reverse_dict = self.create_new_dict(new_data_dict) + return new_data_dict, reverse_dict + + @classmethod + def create_data_dictionary(self, words, old_data_dictionary={}): + """ + Create two dictionaries having tools names and their indexes + """ + count = collections.Counter(words).most_common() + dictionary = dict() + for word, _ in count: + dictionary[word] = len(dictionary) + 1 + dictionary, reverse_dictionary = self.assemble_dictionary(dictionary, old_data_dictionary) + return dictionary, reverse_dictionary + + @classmethod + def decompose_paths(self, paths, dictionary): + """ + Decompose the paths to variable length sub-paths keeping the first tool fixed + """ + sub_paths_pos = list() + for index, item in enumerate(paths): + tools = item.split(",") + len_tools = len(tools) + if len_tools <= self.max_tool_sequence_len: + for window in range(1, len_tools): + sequence = tools[0: window + 1] + tools_pos = [str(dictionary[str(tool_item)]) for tool_item in sequence] + if len(tools_pos) > 1: + sub_paths_pos.append(",".join(tools_pos)) + sub_paths_pos = list(set(sub_paths_pos)) + return sub_paths_pos + + @classmethod + def prepare_paths_labels_dictionary(self, dictionary, reverse_dictionary, paths, compatible_next_tools): + """ + Create a dictionary of sequences with their labels for training and test paths + """ + paths_labels = dict() + random.shuffle(paths) + for item in paths: + if item and item not in "": + tools = item.split(",") + label = tools[-1] + train_tools = tools[:len(tools) - 1] + last_but_one_name = reverse_dictionary[int(train_tools[-1])] + try: + compatible_tools = compatible_next_tools[last_but_one_name].split(",") + except Exception: + continue + if len(compatible_tools) > 0: + compatible_tools_ids = [str(dictionary[x]) for x in compatible_tools] + compatible_tools_ids.append(label) + composite_labels = ",".join(compatible_tools_ids) + train_tools = ",".join(train_tools) + if train_tools in paths_labels: + paths_labels[train_tools] += "," + composite_labels + else: + paths_labels[train_tools] = composite_labels + for item in paths_labels: + paths_labels[item] = ",".join(list(set(paths_labels[item].split(",")))) + return paths_labels + + @classmethod + def pad_paths(self, paths_dictionary, num_classes): + """ + Add padding to the tools sequences and create multi-hot encoded labels + """ + size_data = len(paths_dictionary) + data_mat = np.zeros([size_data, self.max_tool_sequence_len]) + label_mat = np.zeros([size_data, num_classes + 1]) + train_counter = 0 + for train_seq, train_label in list(paths_dictionary.items()): + positions = train_seq.split(",") + start_pos = self.max_tool_sequence_len - len(positions) + for id_pos, pos in enumerate(positions): + data_mat[train_counter][start_pos + id_pos] = int(pos) + for label_item in train_label.split(","): + label_mat[train_counter][int(label_item)] = 1.0 + train_counter += 1 + return data_mat, label_mat + + @classmethod + def split_test_train_data(self, multilabels_paths): + """ + Split into test and train data randomly for each run + """ + train_dict = dict() + test_dict = dict() + all_paths = multilabels_paths.keys() + random.shuffle(list(all_paths)) + split_number = int(self.test_share * len(all_paths)) + for index, path in enumerate(list(all_paths)): + if index < split_number: + test_dict[path] = multilabels_paths[path] + else: + train_dict[path] = multilabels_paths[path] + return train_dict, test_dict + + @classmethod + def verify_overlap(self, train_paths, test_paths): + """ + Verify the overlapping of samples in train and test data + """ + intersection = list(set(train_paths).intersection(set(test_paths))) + print("Overlap in train and test: %d" % len(intersection)) + + @classmethod + def get_predicted_usage(self, data_dictionary, predicted_usage): + """ + Get predicted usage for tools + """ + usage = dict() + epsilon = 0.0 + # index 0 does not belong to any tool + usage[0] = epsilon + for k, v in data_dictionary.items(): + try: + usg = predicted_usage[k] + if usg < epsilon: + usg = epsilon + usage[v] = usg + except Exception: + usage[v] = epsilon + continue + return usage + + @classmethod + def assign_class_weights(self, n_classes, predicted_usage): + """ + Compute class weights using usage + """ + class_weights = dict() + class_weights[str(0)] = 0.0 + for key in range(1, n_classes): + u_score = predicted_usage[key] + if u_score < 1.0: + u_score += 1.0 + class_weights[key] = np.log(u_score) + return class_weights + + @classmethod + def get_sample_weights(self, train_data, reverse_dictionary, paths_frequency): + """ + Compute the frequency of paths in training data + """ + path_weights = np.zeros(len(train_data)) + for path_index, path in enumerate(train_data): + sample_pos = np.where(path > 0)[0] + sample_tool_pos = path[sample_pos[0]:] + path_name = ",".join([reverse_dictionary[int(tool_pos)] for tool_pos in sample_tool_pos]) + try: + path_weights[path_index] = int(paths_frequency[path_name]) + except Exception: + path_weights[path_index] = 1 + return path_weights + + @classmethod + def get_data_labels_matrices(self, workflow_paths, tool_usage_path, cutoff_date, compatible_next_tools, old_data_dictionary={}): + """ + Convert the training and test paths into corresponding numpy matrices + """ + processed_data, raw_paths = self.process_workflow_paths(workflow_paths) + dictionary, reverse_dictionary = self.create_data_dictionary(processed_data, old_data_dictionary) + num_classes = len(dictionary) + + print("Raw paths: %d" % len(raw_paths)) + random.shuffle(raw_paths) + + print("Decomposing paths...") + all_unique_paths = self.decompose_paths(raw_paths, dictionary) + random.shuffle(all_unique_paths) + + print("Creating dictionaries...") + multilabels_paths = self.prepare_paths_labels_dictionary(dictionary, reverse_dictionary, all_unique_paths, compatible_next_tools) + + print("Complete data: %d" % len(multilabels_paths)) + train_paths_dict, test_paths_dict = self.split_test_train_data(multilabels_paths) + + print("Train data: %d" % len(train_paths_dict)) + print("Test data: %d" % len(test_paths_dict)) + + test_data, test_labels = self.pad_paths(test_paths_dict, num_classes) + train_data, train_labels = self.pad_paths(train_paths_dict, num_classes) + + # Predict tools usage + print("Predicting tools' usage...") + usage_pred = predict_tool_usage.ToolPopularity() + usage = usage_pred.extract_tool_usage(tool_usage_path, cutoff_date, dictionary) + tool_usage_prediction = usage_pred.get_pupularity_prediction(usage) + tool_predicted_usage = self.get_predicted_usage(dictionary, tool_usage_prediction) + + # get class weights using the predicted usage for each tool + class_weights = self.assign_class_weights(train_labels.shape[1], tool_predicted_usage) + + return train_data, train_labels, test_data, test_labels, dictionary, reverse_dictionary, class_weights, tool_predicted_usage diff -r 000000000000 -r 9bf25dbe00ad test-data/test_tool_usage --- 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Remove beginning1 1.0.0 11300 heatmapper 1.3 +577 2013-10-21 10:42:00 11439 Remove_ending 1.0.0 11305 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11422 Remove beginning1 1.0.0 11306 heatmapper 1.3 +577 2013-10-21 10:42:00 11294 heatmapper 1.3 11307 Filter1 1.1.0 +577 2013-10-21 10:42:00 11293 heatmapper 1.3 11308 Filter1 1.1.0 +577 2013-10-21 10:42:00 11459 heatmapper 1.3 11309 Filter1 1.1.0 +577 2013-10-21 10:42:00 11290 heatmapper 1.3 11311 Filter1 1.1.0 +577 2013-10-21 10:42:00 11306 heatmapper 1.3 11312 Filter1 1.1.0 +577 2013-10-21 10:42:00 11337 heatmapper 1.3 11313 Filter1 1.1.0 +577 2013-10-21 10:42:00 11342 heatmapper 1.3 11314 Filter1 1.1.0 +577 2013-10-21 10:42:00 11523 cat1 1.0.0 11317 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11318 Paste1 1.0.0 11320 Paste1 1.0.0 +577 2013-10-21 10:42:00 11356 Remove_ending 1.0.0 11323 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11526 Remove_ending 1.0.0 11324 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11370 Remove_ending 1.0.0 11326 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11354 Remove_ending 1.0.0 11329 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11371 Remove_ending 1.0.0 11331 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11364 Remove_ending 1.0.0 11334 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11359 Remove beginning1 1.0.0 11336 heatmapper 1.3 +577 2013-10-21 10:42:00 11514 Remove beginning1 1.0.0 11338 heatmapper 1.3 +577 2013-10-21 10:42:00 11466 Remove beginning1 1.0.0 11339 heatmapper 1.3 +577 2013-10-21 10:42:00 11411 Remove beginning1 1.0.0 11340 heatmapper 1.3 +577 2013-10-21 10:42:00 11409 heatmapper 1.3 11343 heatmapper 1.3 +577 2013-10-21 10:42:00 11505 heatmapper 1.3 11344 Filter1 1.1.0 +577 2013-10-21 10:42:00 11506 heatmapper 1.3 11345 Filter1 1.1.0 +577 2013-10-21 10:42:00 11507 heatmapper 1.3 11346 Filter1 1.1.0 +577 2013-10-21 10:42:00 11508 heatmapper 1.3 11347 Filter1 1.1.0 +577 2013-10-21 10:42:00 11503 heatmapper 1.3 11350 Filter1 1.1.0 +577 2013-10-21 10:42:00 11475 cat1 1.0.0 11352 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11523 cat1 1.0.0 11354 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11363 cat1 1.0.0 11356 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11523 cat1 1.0.0 11357 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11478 Remove_ending 1.0.0 11359 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11475 cat1 1.0.0 11360 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11454 Cut1 1.0.2 11361 Filter1 1.1.0 +577 2013-10-21 10:42:00 11475 cat1 1.0.0 11362 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11533 heatmapper 1.3 11362 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11489 Cut1 1.0.2 11363 cat1 1.0.0 +577 2013-10-21 10:42:00 11523 cat1 1.0.0 11364 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11363 cat1 1.0.0 11365 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11438 Remove beginning1 1.0.0 11368 heatmapper 1.3 +577 2013-10-21 10:42:00 11285 Remove beginning1 1.0.0 11374 heatmapper 1.3 +577 2013-10-21 10:42:00 11423 Remove beginning1 1.0.0 11377 heatmapper 1.3 +577 2013-10-21 10:42:00 11252 Remove beginning1 1.0.0 11380 heatmapper 1.3 +577 2013-10-21 10:42:00 11267 Remove beginning1 1.0.0 11381 heatmapper 1.3 +577 2013-10-21 10:42:00 11374 heatmapper 1.3 11382 Filter1 1.1.0 +577 2013-10-21 10:42:00 11377 heatmapper 1.3 11383 Filter1 1.1.0 +577 2013-10-21 10:42:00 11448 heatmapper 1.3 11384 Filter1 1.1.0 +577 2013-10-21 10:42:00 11445 heatmapper 1.3 11385 Filter1 1.1.0 +577 2013-10-21 10:42:00 11376 heatmapper 1.3 11388 Filter1 1.1.0 +577 2013-10-21 10:42:00 11435 heatmapper 1.3 11389 Filter1 1.1.0 +577 2013-10-21 10:42:00 11447 heatmapper 1.3 11391 Filter1 1.1.0 +577 2013-10-21 10:42:00 11475 cat1 1.0.0 11392 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11280 Paste1 1.0.0 11393 Cut1 1.0.2 +577 2013-10-21 10:42:00 11475 cat1 1.0.0 11394 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11363 cat1 1.0.0 11396 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11300 heatmapper 1.3 11403 Filter1 1.1.0 +577 2013-10-21 10:42:00 11301 heatmapper 1.3 11404 Filter1 1.1.0 +577 2013-10-21 10:42:00 11302 heatmapper 1.3 11405 Filter1 1.1.0 +577 2013-10-21 10:42:00 11259 heatmapper 1.3 11407 Filter1 1.1.0 +577 2013-10-21 10:42:00 11482 Remove beginning1 1.0.0 11409 heatmapper 1.3 +577 2013-10-21 10:42:00 11487 Remove_ending 1.0.0 11412 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11254 Remove_ending 1.0.0 11414 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11363 cat1 1.0.0 11415 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11475 cat1 1.0.0 11418 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11475 cat1 1.0.0 11419 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11367 Remove_ending 1.0.0 11420 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11366 Remove_ending 1.0.0 11421 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11488 Remove_ending 1.0.0 11423 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11392 Remove_ending 1.0.0 11425 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11363 cat1 1.0.0 11427 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11253 Remove_ending 1.0.0 11431 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11292 Remove_ending 1.0.0 11432 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11363 cat1 1.0.0 11433 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11362 Remove_ending 1.0.0 11434 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11473 Remove beginning1 1.0.0 11436 heatmapper 1.3 +577 2013-10-21 10:42:00 11484 Remove_ending 1.0.0 11437 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11485 Remove_ending 1.0.0 11438 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11464 cat1 1.0.0 11439 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11464 cat1 1.0.0 11440 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11468 Remove beginning1 1.0.0 11441 heatmapper 1.3 +577 2013-10-21 10:42:00 11471 Remove beginning1 1.0.0 11448 heatmapper 1.3 +577 2013-10-21 10:42:00 11455 cshl_word_list_grep 1.0.0 11450 Cut1 1.0.2 +577 2013-10-21 10:42:00 11457 cshl_word_list_grep 1.0.0 11452 Cut1 1.0.2 +577 2013-10-21 10:42:00 11270 Filter1 1.1.0 11455 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11271 Filter1 1.1.0 11455 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11277 Filter1 1.1.0 11455 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11385 Filter1 1.1.0 11455 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11386 Filter1 1.1.0 11455 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11275 cshl_word_list_grep 1.0.0 11456 Cut1 1.0.2 +577 2013-10-21 10:42:00 11490 Filter1 1.1.0 11457 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11491 Filter1 1.1.0 11457 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11492 Filter1 1.1.0 11457 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11493 Filter1 1.1.0 11457 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11494 Filter1 1.1.0 11457 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11495 Filter1 1.1.0 11457 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11496 Filter1 1.1.0 11457 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11497 Filter1 1.1.0 11457 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11382 Filter1 1.1.0 11458 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11383 Filter1 1.1.0 11458 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11384 Filter1 1.1.0 11458 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11389 Filter1 1.1.0 11458 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11391 Filter1 1.1.0 11458 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11498 Filter1 1.1.0 11458 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11499 Filter1 1.1.0 11458 cshl_word_list_grep 1.0.0 +577 2013-10-21 10:42:00 11475 cat1 1.0.0 11460 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11393 Cut1 1.0.2 11464 cat1 1.0.0 +577 2013-10-21 10:42:00 11249 Remove_ending 1.0.0 11465 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11248 Remove_ending 1.0.0 11466 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11247 Remove_ending 1.0.0 11467 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11246 Remove_ending 1.0.0 11468 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11245 Remove_ending 1.0.0 11469 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11244 Remove_ending 1.0.0 11470 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11256 Remove_ending 1.0.0 11471 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11433 Remove_ending 1.0.0 11473 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11427 Remove_ending 1.0.0 11474 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11287 Cut1 1.0.2 11475 cat1 1.0.0 +577 2013-10-21 10:42:00 11464 cat1 1.0.0 11476 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11303 Remove_ending 1.0.0 11480 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11464 cat1 1.0.0 11481 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11464 cat1 1.0.0 11483 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11464 cat1 1.0.0 11484 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11464 cat1 1.0.0 11485 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11464 cat1 1.0.0 11486 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11464 cat1 1.0.0 11487 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11363 cat1 1.0.0 11488 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11343 heatmapper 1.3 11491 Filter1 1.1.0 +577 2013-10-21 10:42:00 11369 heatmapper 1.3 11492 Filter1 1.1.0 +577 2013-10-21 10:42:00 11341 heatmapper 1.3 11493 Filter1 1.1.0 +577 2013-10-21 10:42:00 11379 heatmapper 1.3 11494 Filter1 1.1.0 +577 2013-10-21 10:42:00 11368 heatmapper 1.3 11495 Filter1 1.1.0 +577 2013-10-21 10:42:00 11381 heatmapper 1.3 11496 Filter1 1.1.0 +577 2013-10-21 10:42:00 11378 heatmapper 1.3 11497 Filter1 1.1.0 +577 2013-10-21 10:42:00 11375 heatmapper 1.3 11498 Filter1 1.1.0 +577 2013-10-21 10:42:00 11479 Cut1 1.0.2 11502 cat1 1.0.0 +577 2013-10-21 10:42:00 11511 Remove beginning1 1.0.0 11504 heatmapper 1.3 +577 2013-10-21 10:42:00 11480 Remove beginning1 1.0.0 11506 heatmapper 1.3 +577 2013-10-21 10:42:00 11395 Remove beginning1 1.0.0 11508 heatmapper 1.3 +577 2013-10-21 10:42:00 11414 Remove beginning1 1.0.0 11510 heatmapper 1.3 +577 2013-10-21 10:42:00 11291 Remove_ending 1.0.0 11511 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11531 Remove_ending 1.0.0 11512 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11251 Remove_ending 1.0.0 11514 Remove beginning1 1.0.0 +577 2013-10-21 10:42:00 11265 heatmapper 1.3 11515 Filter1 1.1.0 +577 2013-10-21 10:42:00 11266 heatmapper 1.3 11516 Filter1 1.1.0 +577 2013-10-21 10:42:00 11261 heatmapper 1.3 11517 Filter1 1.1.0 +577 2013-10-21 10:42:00 11262 heatmapper 1.3 11518 Filter1 1.1.0 +577 2013-10-21 10:42:00 11263 heatmapper 1.3 11519 Filter1 1.1.0 +577 2013-10-21 10:42:00 11264 heatmapper 1.3 11520 Filter1 1.1.0 +577 2013-10-21 10:42:00 11257 heatmapper 1.3 11521 Filter1 1.1.0 +577 2013-10-21 10:42:00 11258 heatmapper 1.3 11522 Filter1 1.1.0 +577 2013-10-21 10:42:00 11510 heatmapper 1.3 11524 Filter1 1.1.0 +577 2013-10-21 10:42:00 11523 cat1 1.0.0 11526 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11475 cat1 1.0.0 11527 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11523 cat1 1.0.0 11528 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11363 cat1 1.0.0 11529 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11523 cat1 1.0.0 11530 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11523 cat1 1.0.0 11532 Remove_ending 1.0.0 +577 2013-10-21 10:42:00 11257 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11258 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11259 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11261 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11262 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11263 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11264 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11265 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11266 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11290 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11293 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11294 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11300 heatmapper 1.3 11536 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2013-10-21 10:42:00 11444 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11445 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11447 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11448 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11459 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11503 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11505 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11506 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11507 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11508 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11510 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11533 heatmapper 1.3 11536 +577 2013-10-21 10:42:00 11275 cshl_word_list_grep 1.0.0 11537 +577 2013-10-21 10:42:00 11455 cshl_word_list_grep 1.0.0 11537 +577 2013-10-21 10:42:00 11457 cshl_word_list_grep 1.0.0 11537 +577 2013-10-21 10:42:00 11281 Filter1 1.1.0 11538 +577 2013-10-21 10:42:00 11283 Filter1 1.1.0 11538 +577 2013-10-21 10:42:00 11361 Filter1 1.1.0 11538 +577 2013-10-21 10:42:00 11426 Filter1 1.1.0 11538 +578 2013-10-21 10:57:00 11798 cat1 1.0.0 11540 Remove_ending 1.0.0 +578 2013-10-21 10:57:00 11798 cat1 1.0.0 11541 Remove_ending 1.0.0 +578 2013-10-21 10:57:00 11798 cat1 1.0.0 11542 Remove_ending 1.0.0 +578 2013-10-21 10:57:00 11798 cat1 1.0.0 11543 Remove_ending 1.0.0 +578 2013-10-21 10:57:00 11798 cat1 1.0.0 11544 Remove_ending 1.0.0 +578 2013-10-21 10:57:00 11798 cat1 1.0.0 11545 Remove_ending 1.0.0 +578 2013-10-21 10:57:00 11798 cat1 1.0.0 11546 Remove_ending 1.0.0 +578 2013-10-21 10:57:00 11798 cat1 1.0.0 11547 Remove_ending 1.0.0 +578 2013-10-21 10:57:00 11617 cat1 1.0.0 11549 Remove_ending 1.0.0 +578 2013-10-21 10:57:00 11617 cat1 1.0.0 11550 Remove_ending 1.0.0 +578 2013-10-21 10:57:00 11798 cat1 1.0.0 11551 Remove_ending 1.0.0 +578 2013-10-21 10:57:00 11659 cat1 1.0.0 11552 Remove_ending 1.0.0 +578 2013-10-21 10:57:00 11625 Remove beginning1 1.0.0 11554 heatmapper 1.3 +578 2013-10-21 10:57:00 11631 Remove beginning1 1.0.0 11556 heatmapper 1.3 +578 2013-10-21 10:57:00 11621 Remove beginning1 1.0.0 11557 heatmapper 1.3 +578 2013-10-21 10:57:00 11634 heatmapper 1.3 11565 Filter1 1.1.0 +578 2013-10-21 10:57:00 11635 heatmapper 1.3 11566 Filter1 1.1.0 +578 2013-10-21 10:57:00 11603 Filter1 1.1.0 11568 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11604 Filter1 1.1.0 11568 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11605 Filter1 1.1.0 11568 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11607 Filter1 1.1.0 11568 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11611 Filter1 1.1.0 11568 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11612 Filter1 1.1.0 11568 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11695 Filter1 1.1.0 11569 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11697 Filter1 1.1.0 11569 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11698 Filter1 1.1.0 11569 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11699 Filter1 1.1.0 11569 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11700 Filter1 1.1.0 11569 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11701 Filter1 1.1.0 11569 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11703 Filter1 1.1.0 11570 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11811 Filter1 1.1.0 11570 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11812 Filter1 1.1.0 11570 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11813 Filter1 1.1.0 11570 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11816 Filter1 1.1.0 11570 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11643 Filter1 1.1.0 11571 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11820 Filter1 1.1.0 11571 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11821 Filter1 1.1.0 11571 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11711 Remove_ending 1.0.0 11572 Remove beginning1 1.0.0 +578 2013-10-21 10:57:00 11618 Paste1 1.0.0 11576 Paste1 1.0.0 +578 2013-10-21 10:57:00 11712 Remove_ending 1.0.0 11580 Remove beginning1 1.0.0 +578 2013-10-21 10:57:00 11661 Remove_ending 1.0.0 11581 Remove beginning1 1.0.0 +578 2013-10-21 10:57:00 11616 Paste1 1.0.0 11583 Cut1 1.0.2 +578 2013-10-21 10:57:00 11618 Paste1 1.0.0 11584 Cut1 1.0.2 +578 2013-10-21 10:57:00 11576 Paste1 1.0.0 11585 Paste1 1.0.0 +578 2013-10-21 10:57:00 11713 Remove beginning1 1.0.0 11586 heatmapper 1.3 +578 2013-10-21 10:57:00 11617 cat1 1.0.0 11587 Remove_ending 1.0.0 +578 2013-10-21 10:57:00 11716 Remove beginning1 1.0.0 11589 heatmapper 1.3 +578 2013-10-21 10:57:00 11724 Remove beginning1 1.0.0 11593 heatmapper 1.3 +578 2013-10-21 10:57:00 11720 Remove beginning1 1.0.0 11594 heatmapper 1.3 +578 2013-10-21 10:57:00 11628 Remove beginning1 1.0.0 11598 heatmapper 1.3 +578 2013-10-21 10:57:00 11617 cat1 1.0.0 11599 Remove_ending 1.0.0 +578 2013-10-21 10:57:00 11617 cat1 1.0.0 11600 Remove_ending 1.0.0 +578 2013-10-21 10:57:00 11735 Remove_ending 1.0.0 11601 Remove beginning1 1.0.0 +578 2013-10-21 10:57:00 11602 heatmapper 1.3 11608 Filter1 1.1.0 +578 2013-10-21 10:57:00 11633 heatmapper 1.3 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2013-10-21 10:57:00 11732 heatmapper 1.3 11686 Filter1 1.1.0 +578 2013-10-21 10:57:00 11743 heatmapper 1.3 11687 Filter1 1.1.0 +578 2013-10-21 10:57:00 11576 Paste1 1.0.0 11689 Cut1 1.0.2 +578 2013-10-21 10:57:00 11659 cat1 1.0.0 11692 Remove_ending 1.0.0 +578 2013-10-21 10:57:00 11773 Remove_ending 1.0.0 11693 Remove beginning1 1.0.0 +578 2013-10-21 10:57:00 11592 heatmapper 1.3 11695 Filter1 1.1.0 +578 2013-10-21 10:57:00 11598 heatmapper 1.3 11701 Filter1 1.1.0 +578 2013-10-21 10:57:00 11556 heatmapper 1.3 11702 Filter1 1.1.0 +578 2013-10-21 10:57:00 11555 heatmapper 1.3 11703 Filter1 1.1.0 +578 2013-10-21 10:57:00 11779 Remove_ending 1.0.0 11704 Remove beginning1 1.0.0 +578 2013-10-21 10:57:00 11777 Remove_ending 1.0.0 11706 Remove beginning1 1.0.0 +578 2013-10-21 10:57:00 11550 Remove_ending 1.0.0 11710 Remove beginning1 1.0.0 +578 2013-10-21 10:57:00 11659 cat1 1.0.0 11711 Remove_ending 1.0.0 +578 2013-10-21 10:57:00 11617 cat1 1.0.0 11712 Remove_ending 1.0.0 +578 2013-10-21 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2013-10-21 10:57:00 11767 Remove beginning1 1.0.0 11744 heatmapper 1.3 +578 2013-10-21 10:57:00 11751 cshl_word_list_grep 1.0.0 11746 Cut1 1.0.2 +578 2013-10-21 10:57:00 11753 cshl_word_list_grep 1.0.0 11748 Cut1 1.0.2 +578 2013-10-21 10:57:00 11569 cshl_word_list_grep 1.0.0 11750 Cut1 1.0.2 +578 2013-10-21 10:57:00 11564 Filter1 1.1.0 11751 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11681 Filter1 1.1.0 11751 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11682 Filter1 1.1.0 11751 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11683 Filter1 1.1.0 11751 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11610 Filter1 1.1.0 11753 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11788 Filter1 1.1.0 11753 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11790 Filter1 1.1.0 11753 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11791 Filter1 1.1.0 11753 cshl_word_list_grep 1.0.0 +578 2013-10-21 10:57:00 11793 Filter1 1.1.0 11753 cshl_word_list_grep 1.0.0 +578 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return file_content + + +def write_file(file_path, content): + """ + Write a file + """ + remove_file(file_path) + with open(file_path, "w") as json_file: + json_file.write(json.dumps(content)) + + +def save_processed_workflows(file_path, unique_paths): + workflow_paths_unique = "" + for path in unique_paths: + workflow_paths_unique += path + "\n" + with open(file_path, "w") as workflows_file: + workflows_file.write(workflow_paths_unique) + + +def load_saved_model(model_config, model_weights): + """ + Load the saved trained model using the saved network and its weights + """ + # load the network + loaded_model = model_from_json(model_config) + # load the saved weights into the model + loaded_model.set_weights(model_weights) + return loaded_model + + +def format_tool_id(tool_link): + """ + Extract tool id from tool link + """ + tool_id_split = tool_link.split("/") + tool_id = tool_id_split[-2] if len(tool_id_split) > 1 else tool_link + return tool_id + + +def get_HDF5(hf, d_key): + """ + Read h5 file to get train and test data + """ + return hf.get(d_key).value + + +def save_HDF5(hf_file, d_key, data, d_type=""): + """ + Save datasets as h5 file + """ + if (d_type == 'json'): + data = json.dumps(data) + hf_file.create_dataset(d_key, data=data) + + +def set_trained_model(dump_file, model_values): + """ + Create an h5 file with the trained weights and associated dicts + """ + hf_file = h5py.File(dump_file, 'w') + for key in model_values: + value = model_values[key] + if key == 'model_weights': + for idx, item in enumerate(value): + w_key = "weight_" + str(idx) + if w_key in hf_file: + hf_file.modify(w_key, item) + else: + hf_file.create_dataset(w_key, data=item) + else: + if key in hf_file: + hf_file.modify(key, json.dumps(value)) + else: + hf_file.create_dataset(key, data=json.dumps(value)) + hf_file.close() + + +def remove_file(file_path): + if os.path.exists(file_path): + os.remove(file_path) + + +def extract_configuration(config_object): + config_loss = dict() + for index, item in enumerate(config_object): + config_loss[index] = list() + d_config = dict() + d_config['loss'] = item['result']['loss'] + d_config['params_config'] = item['misc']['vals'] + config_loss[index].append(d_config) + return config_loss + + +def get_best_parameters(mdl_dict): + """ + Get param values (defaults as well) + """ + lr = float(mdl_dict.get("learning_rate", "0.001")) + embedding_size = int(mdl_dict.get("embedding_size", "512")) + dropout = float(mdl_dict.get("dropout", "0.2")) + recurrent_dropout = float(mdl_dict.get("recurrent_dropout", "0.2")) + spatial_dropout = float(mdl_dict.get("spatial_dropout", "0.2")) + units = int(mdl_dict.get("units", "512")) + batch_size = int(mdl_dict.get("batch_size", "512")) + activation_recurrent = mdl_dict.get("activation_recurrent", "elu") + activation_output = mdl_dict.get("activation_output", "sigmoid") + + return { + "lr": lr, + "embedding_size": embedding_size, + "dropout": dropout, + "recurrent_dropout": recurrent_dropout, + "spatial_dropout": spatial_dropout, + "units": units, + "batch_size": batch_size, + "activation_recurrent": activation_recurrent, + "activation_output": activation_output, + } + + +def weighted_loss(class_weights): + """ + Create a weighted loss function. Penalise the misclassification + of classes more with the higher usage + """ + weight_values = list(class_weights.values()) + + def weighted_binary_crossentropy(y_true, y_pred): + # add another dimension to compute dot product + expanded_weights = K.expand_dims(weight_values, axis=-1) + return K.dot(K.binary_crossentropy(y_true, y_pred), expanded_weights) + return weighted_binary_crossentropy + + +def set_recurrent_network(mdl_dict, reverse_dictionary, class_weights): + """ + Create a RNN network and set its parameters + """ + dimensions = len(reverse_dictionary) + 1 + model_params = get_best_parameters(mdl_dict) + + # define the architecture of the neural network + model = Sequential() + model.add(Embedding(dimensions, model_params["embedding_size"], mask_zero=True)) + model.add(SpatialDropout1D(model_params["spatial_dropout"])) + model.add(GRU(model_params["units"], dropout=model_params["spatial_dropout"], recurrent_dropout=model_params["recurrent_dropout"], activation=model_params["activation_recurrent"], return_sequences=True)) + model.add(Dropout(model_params["dropout"])) + model.add(GRU(model_params["units"], dropout=model_params["spatial_dropout"], recurrent_dropout=model_params["recurrent_dropout"], activation=model_params["activation_recurrent"], return_sequences=False)) + model.add(Dropout(model_params["dropout"])) + model.add(Dense(dimensions, activation=model_params["activation_output"])) + optimizer = RMSprop(lr=model_params["lr"]) + model.compile(loss=weighted_loss(class_weights), optimizer=optimizer) + return model, model_params + + +def compute_precision(model, x, y, reverse_data_dictionary, next_compatible_tools, usage_scores, actual_classes_pos, topk): + """ + Compute absolute and compatible precision + """ + absolute_precision = 0.0 + test_sample = np.reshape(x, (1, len(x))) + + # predict next tools for a test path + prediction = model.predict(test_sample, verbose=0) + + nw_dimension = prediction.shape[1] + + # remove the 0th position as there is no tool at this index + prediction = np.reshape(prediction, (nw_dimension,)) + + prediction_pos = np.argsort(prediction, axis=-1) + topk_prediction_pos = prediction_pos[-topk:] + + # remove the wrong tool position from the predicted list of tool positions + topk_prediction_pos = [x for x in topk_prediction_pos if x > 0] + + # read tool names using reverse dictionary + actual_next_tool_names = [reverse_data_dictionary[int(tool_pos)] for tool_pos in actual_classes_pos] + top_predicted_next_tool_names = [reverse_data_dictionary[int(tool_pos)] for tool_pos in topk_prediction_pos] + + # compute the class weights of predicted tools + mean_usg_score = 0 + usg_wt_scores = list() + for t_id in topk_prediction_pos: + t_name = reverse_data_dictionary[int(t_id)] + if t_id in usage_scores and t_name in actual_next_tool_names: + usg_wt_scores.append(np.log(usage_scores[t_id] + 1.0)) + if len(usg_wt_scores) > 0: + mean_usg_score = np.sum(usg_wt_scores) / float(topk) + false_positives = [tool_name for tool_name in top_predicted_next_tool_names if tool_name not in actual_next_tool_names] + absolute_precision = 1 - (len(false_positives) / float(topk)) + return mean_usg_score, absolute_precision + + +def verify_model(model, x, y, reverse_data_dictionary, next_compatible_tools, usage_scores, topk_list=[1, 2, 3]): + """ + Verify the model on test data + """ + print("Evaluating performance on test data...") + print("Test data size: %d" % len(y)) + size = y.shape[0] + precision = np.zeros([len(y), len(topk_list)]) + usage_weights = np.zeros([len(y), len(topk_list)]) + # loop over all the test samples and find prediction precision + for i in range(size): + actual_classes_pos = np.where(y[i] > 0)[0] + for index, abs_topk in enumerate(topk_list): + abs_mean_usg_score, absolute_precision = compute_precision(model, x[i, :], y, reverse_data_dictionary, next_compatible_tools, usage_scores, actual_classes_pos, abs_topk) + precision[i][index] = absolute_precision + usage_weights[i][index] = abs_mean_usg_score + mean_precision = np.mean(precision, axis=0) + mean_usage = np.mean(usage_weights, axis=0) + return mean_precision, mean_usage + + +def save_model(results, data_dictionary, compatible_next_tools, trained_model_path, class_weights): + # save files + trained_model = results["model"] + best_model_parameters = results["best_parameters"] + model_config = trained_model.to_json() + model_weights = trained_model.get_weights() + + model_values = { + 'data_dictionary': data_dictionary, + 'model_config': model_config, + 'best_parameters': best_model_parameters, + 'model_weights': model_weights, + "compatible_tools": compatible_next_tools, + "class_weights": class_weights + } + set_trained_model(trained_model_path, model_values)