Mercurial > repos > bgruening > create_tool_recommendation_model
view predict_tool_usage.py @ 2:76251d1ccdcc draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 6fa2a0294d615c9f267b766337dca0b2d3637219"
author | bgruening |
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date | Fri, 11 Oct 2019 18:24:54 -0400 |
parents | 9bf25dbe00ad |
children | 5b3c08710e47 |
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""" 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