Mercurial > repos > bgruening > create_tool_recommendation_model

annotate predict_tool_usage.py @ 3:98bc44d17561 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 65d36f271296a38deeceb0d0e8d471b2898ee8f4"
author bgruening
date Tue, 07 Jul 2020 07:24:21 +0000
parents 50753817983a
children f0da532be419
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22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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1 """
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2 Predict tool usage to weigh the predicted tools
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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3 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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4
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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5 import os
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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6 import numpy as np
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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7 import warnings
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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8 import csv
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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9 import collections
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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11 from sklearn.svm import SVR
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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12 from sklearn.model_selection import GridSearchCV
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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13 from sklearn.pipeline import Pipeline
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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15 import utils
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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17 warnings.filterwarnings("ignore")
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19 main_path = os.getcwd()
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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22 class ToolPopularity:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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24 def __init__(self):
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25 """ Init method. """
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26
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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27 def extract_tool_usage(self, tool_usage_file, cutoff_date, dictionary):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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28 """
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29 Extract the tool usage over time for each tool
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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30 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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31 tool_usage_dict = dict()
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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32 all_dates = list()
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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33 all_tool_list = list(dictionary.keys())
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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34 with open(tool_usage_file, 'rt') as usage_file:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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35 tool_usage = csv.reader(usage_file, delimiter='\t')
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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36 for index, row in enumerate(tool_usage):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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37 if (str(row[1]) > cutoff_date) is True:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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38 tool_id = utils.format_tool_id(row[0])
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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39 if tool_id in all_tool_list:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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40 all_dates.append(row[1])
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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41 if tool_id not in tool_usage_dict:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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42 tool_usage_dict[tool_id] = dict()
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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43 tool_usage_dict[tool_id][row[1]] = int(row[2])
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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44 else:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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45 curr_date = row[1]
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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46 # merge the usage of different version of tools into one
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47 if curr_date in tool_usage_dict[tool_id]:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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48 tool_usage_dict[tool_id][curr_date] += int(row[2])
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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49 else:
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50 tool_usage_dict[tool_id][curr_date] = int(row[2])
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51 # get unique dates
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52 unique_dates = list(set(all_dates))
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53 for tool in tool_usage_dict:
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54 usage = tool_usage_dict[tool]
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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55 # extract those dates for which tool's usage is not present in raw data
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56 dates_not_present = list(set(unique_dates) ^ set(usage.keys()))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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57 # impute the missing values by 0
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58 for dt in dates_not_present:
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59 tool_usage_dict[tool][dt] = 0
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60 # sort the usage list by date
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61 tool_usage_dict[tool] = collections.OrderedDict(sorted(usage.items()))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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62 return tool_usage_dict
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63
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64 def learn_tool_popularity(self, x_reshaped, y_reshaped):
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65 """
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66 Fit a curve for the tool usage over time to predict future tool usage
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67 """
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68 epsilon = 0.0
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69 cv = 5
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70 s_typ = 'neg_mean_absolute_error'
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71 n_jobs = 4
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72 s_error = 1
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73 iid = True
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74 tr_score = False
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75 try:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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76 pipe = Pipeline(steps=[('regressor', SVR(gamma='scale'))])
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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77 param_grid = {
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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78 'regressor__kernel': ['rbf', 'poly', 'linear'],
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79 'regressor__degree': [2, 3]
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80 }
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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81 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)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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82 search.fit(x_reshaped, y_reshaped.ravel())
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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83 model = search.best_estimator_
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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84 # set the next time point to get prediction for
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85 prediction_point = np.reshape([x_reshaped[-1][0] + 1], (1, 1))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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86 prediction = model.predict(prediction_point)
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87 if prediction < epsilon:
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88 prediction = [epsilon]
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89 return prediction[0]
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90 except Exception:
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91 return epsilon
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92
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93 def get_pupularity_prediction(self, tools_usage):
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94 """
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95 Get the popularity prediction for each tool
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96 """
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97 usage_prediction = dict()
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98 for tool_name, usage in tools_usage.items():
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99 y_val = list()
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100 x_val = list()
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101 for x, y in usage.items():
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102 x_val.append(x)
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103 y_val.append(y)
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104 x_pos = np.arange(len(x_val))
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105 x_reshaped = x_pos.reshape(len(x_pos), 1)
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106 y_reshaped = np.reshape(y_val, (len(x_pos), 1))
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107 prediction = np.round(self.learn_tool_popularity(x_reshaped, y_reshaped), 8)
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108 usage_prediction[tool_name] = prediction
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109 return usage_prediction