diff prepare_data.py @ 0:9bf25dbe00ad draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"

--- /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