comparison utils.py @ 3:98bc44d17561 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 65d36f271296a38deeceb0d0e8d471b2898ee8f4"

2:50753817983a

import os
import numpy as np
import json
import h5py
import random

from keras import backend as K


def read_file(file_path):

    Create a weighted loss function. Penalise the misclassification
    of classes more with the higher usage
    """
    weight_values = list(class_weights.values())
    weight_values.extend(weight_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 balanced_sample_generator(train_data, train_labels, batch_size, l_tool_tr_samples):
    while True:
        dimension = train_data.shape[1]
        n_classes = train_labels.shape[1]
        tool_ids = list(l_tool_tr_samples.keys())
        generator_batch_data = np.zeros([batch_size, dimension])
        generator_batch_labels = np.zeros([batch_size, n_classes])
        for i in range(batch_size):
            random_toolid_index = random.sample(range(0, len(tool_ids)), 1)[0]
            random_toolid = tool_ids[random_toolid_index]
            sample_indices = l_tool_tr_samples[str(random_toolid)]
            random_index = random.sample(range(0, len(sample_indices)), 1)[0]
            random_tr_index = sample_indices[random_index]
            generator_batch_data[i] = train_data[random_tr_index]
            generator_batch_labels[i] = train_labels[random_tr_index]

    # compute scores for published recommendations
    if standard_topk_prediction_pos in reverse_data_dictionary:
        pred_t_name = reverse_data_dictionary[int(standard_topk_prediction_pos)]
        if last_tool_name in standard_conn:
            pub_tools = standard_conn[last_tool_name]
        if pred_t_name in pub_tools:
            pub_precision = 1.0
            if last_tool_id in lowest_tool_ids:
                lowest_pub_prec = 1.0
            if standard_topk_prediction_pos in usage_scores:
                usage_wt_score.append(np.log(usage_scores[standard_topk_prediction_pos] + 1.0))
    # compute scores for normal recommendations
    if normal_topk_prediction_pos in reverse_data_dictionary:
        pred_t_name = reverse_data_dictionary[int(normal_topk_prediction_pos)]
        if pred_t_name in actual_next_tool_names:
            if normal_topk_prediction_pos in usage_scores:
                usage_wt_score.append(np.log(usage_scores[normal_topk_prediction_pos] + 1.0))
            top_precision = 1.0
            if last_tool_id in lowest_tool_ids:
                lowest_norm_prec = 1.0
    if len(usage_wt_score) > 0:
        mean_usage = np.mean(usage_wt_score)
    return mean_usage, top_precision, pub_precision, lowest_pub_prec, lowest_norm_prec

    precision = np.zeros([len(y), len(topk_list)])
    usage_weights = np.zeros([len(y), len(topk_list)])
    epo_pub_prec = np.zeros([len(y), len(topk_list)])
    epo_lowest_tools_pub_prec = list()
    epo_lowest_tools_norm_prec = list()

    # loop over all the test samples and find prediction precision
    for i in range(size):
        lowest_pub_topk = list()
        lowest_norm_topk = list()
        actual_classes_pos = np.where(y[i] > 0)[0]

        for index, abs_topk in enumerate(topk_list):
            usg_wt_score, absolute_precision, pub_prec, lowest_p_prec, lowest_n_prec = compute_precision(model, test_sample, y, reverse_data_dictionary, usage_scores, actual_classes_pos, abs_topk, standard_conn, last_tool_id, lowest_tool_ids)
            precision[i][index] = absolute_precision
            usage_weights[i][index] = usg_wt_score
            epo_pub_prec[i][index] = pub_prec
            if last_tool_id in lowest_tool_ids:
                lowest_pub_topk.append(lowest_p_prec)
                lowest_norm_topk.append(lowest_n_prec)
        if last_tool_id in lowest_tool_ids:
            epo_lowest_tools_pub_prec.append(lowest_pub_topk)
            epo_lowest_tools_norm_prec.append(lowest_norm_topk)
    mean_precision = np.mean(precision, axis=0)
    mean_usage = np.mean(usage_weights, axis=0)
    mean_pub_prec = np.mean(epo_pub_prec, axis=0)
    mean_lowest_pub_prec = np.mean(epo_lowest_tools_pub_prec, axis=0)
    mean_lowest_norm_prec = np.mean(epo_lowest_tools_norm_prec, axis=0)
    return mean_usage, mean_precision, mean_pub_prec, mean_lowest_pub_prec, mean_lowest_norm_prec, len(epo_lowest_tools_pub_prec)


def save_model(results, data_dictionary, compatible_next_tools, trained_model_path, class_weights, standard_connections):
    # save files
    trained_model = results["model"]

3:98bc44d17561

import numpy as np
import json
import h5py
import random
from numpy.random import choice

from keras import backend as K


def read_file(file_path):

    Create a weighted loss function. Penalise the misclassification
    of classes more with the higher usage
    """
    weight_values = list(class_weights.values())
    weight_values.extend(weight_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 balanced_sample_generator(train_data, train_labels, batch_size, l_tool_tr_samples, reverse_dictionary):
    while True:
        dimension = train_data.shape[1]
        n_classes = train_labels.shape[1]
        tool_ids = list(l_tool_tr_samples.keys())
        random.shuffle(tool_ids)
        generator_batch_data = np.zeros([batch_size, dimension])
        generator_batch_labels = np.zeros([batch_size, n_classes])
        generated_tool_ids = choice(tool_ids, batch_size)
        for i in range(batch_size):
            random_toolid = generated_tool_ids[i]
            sample_indices = l_tool_tr_samples[str(random_toolid)]
            random_index = random.sample(range(0, len(sample_indices)), 1)[0]
            random_tr_index = sample_indices[random_index]
            generator_batch_data[i] = train_data[random_tr_index]
            generator_batch_labels[i] = train_labels[random_tr_index]

    # compute scores for published recommendations
    if standard_topk_prediction_pos in reverse_data_dictionary:
        pred_t_name = reverse_data_dictionary[int(standard_topk_prediction_pos)]
        if last_tool_name in standard_conn:
            pub_tools = standard_conn[last_tool_name]
            if pred_t_name in pub_tools:
                pub_precision = 1.0
                # count precision only when there is actually true published tools
                if last_tool_id in lowest_tool_ids:
                    lowest_pub_prec = 1.0
                else:
                    lowest_pub_prec = np.nan
                if standard_topk_prediction_pos in usage_scores:
                    usage_wt_score.append(np.log(usage_scores[standard_topk_prediction_pos] + 1.0))
        else:
            # count precision only when there is actually true published tools
            # else set to np.nan. Set to 0 only when there is wrong prediction
            pub_precision = np.nan
            lowest_pub_prec = np.nan
    # compute scores for normal recommendations
    if normal_topk_prediction_pos in reverse_data_dictionary:
        pred_t_name = reverse_data_dictionary[int(normal_topk_prediction_pos)]
        if pred_t_name in actual_next_tool_names:
            if normal_topk_prediction_pos in usage_scores:
                usage_wt_score.append(np.log(usage_scores[normal_topk_prediction_pos] + 1.0))
            top_precision = 1.0
            if last_tool_id in lowest_tool_ids:
                lowest_norm_prec = 1.0
            else:
                lowest_norm_prec = np.nan
    if len(usage_wt_score) > 0:
        mean_usage = np.mean(usage_wt_score)
    return mean_usage, top_precision, pub_precision, lowest_pub_prec, lowest_norm_prec

    precision = np.zeros([len(y), len(topk_list)])
    usage_weights = np.zeros([len(y), len(topk_list)])
    epo_pub_prec = np.zeros([len(y), len(topk_list)])
    epo_lowest_tools_pub_prec = list()
    epo_lowest_tools_norm_prec = list()
    lowest_counter = 0
    # loop over all the test samples and find prediction precision
    for i in range(size):
        lowest_pub_topk = list()
        lowest_norm_topk = list()
        actual_classes_pos = np.where(y[i] > 0)[0]

        for index, abs_topk in enumerate(topk_list):
            usg_wt_score, absolute_precision, pub_prec, lowest_p_prec, lowest_n_prec = compute_precision(model, test_sample, y, reverse_data_dictionary, usage_scores, actual_classes_pos, abs_topk, standard_conn, last_tool_id, lowest_tool_ids)
            precision[i][index] = absolute_precision
            usage_weights[i][index] = usg_wt_score
            epo_pub_prec[i][index] = pub_prec
            lowest_pub_topk.append(lowest_p_prec)
            lowest_norm_topk.append(lowest_n_prec)
        epo_lowest_tools_pub_prec.append(lowest_pub_topk)
        epo_lowest_tools_norm_prec.append(lowest_norm_topk)
        if last_tool_id in lowest_tool_ids:
            lowest_counter += 1
    mean_precision = np.mean(precision, axis=0)
    mean_usage = np.mean(usage_weights, axis=0)
    mean_pub_prec = np.nanmean(epo_pub_prec, axis=0)
    mean_lowest_pub_prec = np.nanmean(epo_lowest_tools_pub_prec, axis=0)
    mean_lowest_norm_prec = np.nanmean(epo_lowest_tools_norm_prec, axis=0)
    return mean_usage, mean_precision, mean_pub_prec, mean_lowest_pub_prec, mean_lowest_norm_prec, lowest_counter


def save_model(results, data_dictionary, compatible_next_tools, trained_model_path, class_weights, standard_connections):
    # save files
    trained_model = results["model"]