comparison utils.py @ 3:5b3c08710e47 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit c635df659fe1835679438589ded43136b0e515c6"

2:76251d1ccdcc

import os
import numpy as np
import json
import h5py

from keras import backend as K


def read_file(file_path):

    Read a file
    """
    with open(file_path, "r") as json_file:
        file_content = json.loads(json_file.read())
    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 format_tool_id(tool_link):
    """
    Extract tool id from tool link

            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 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 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)

3:5b3c08710e47

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

from keras import backend as K


def read_file(file_path):

    Read a file
    """
    with open(file_path, "r") as json_file:
        file_content = json.loads(json_file.read())
    return file_content


def format_tool_id(tool_link):
    """
    Extract tool id from tool link

            else:
                hf_file.create_dataset(key, data=json.dumps(value))
    hf_file.close()


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())
    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]
        yield generator_batch_data, generator_batch_labels


def compute_precision(model, x, y, reverse_data_dictionary, usage_scores, actual_classes_pos, topk, standard_conn, last_tool_id, lowest_tool_ids):
    """
    Compute absolute and compatible precision
    """
    pred_t_name = ""
    top_precision = 0.0
    mean_usage = 0.0
    usage_wt_score = list()
    pub_precision = 0.0
    lowest_pub_prec = 0.0
    lowest_norm_prec = 0.0
    pub_tools = list()
    actual_next_tool_names = list()
    test_sample = np.reshape(x, (1, len(x)))

    # predict next tools for a test path
    prediction = model.predict(test_sample, verbose=0)

    # divide the predicted vector into two halves - one for published and
    # another for normal workflows
    nw_dimension = prediction.shape[1]
    half_len = int(nw_dimension / 2)

    # predict tools
    prediction = np.reshape(prediction, (nw_dimension,))
    # get predictions of tools from published workflows
    standard_pred = prediction[:half_len]
    # get predictions of tools from normal workflows
    normal_pred = prediction[half_len:]

    standard_prediction_pos = np.argsort(standard_pred, axis=-1)
    standard_topk_prediction_pos = standard_prediction_pos[-topk]

    normal_prediction_pos = np.argsort(normal_pred, axis=-1)
    normal_topk_prediction_pos = normal_prediction_pos[-topk]

    # get true tools names
    for a_t_pos in actual_classes_pos:
        if a_t_pos > half_len:
            t_name = reverse_data_dictionary[int(a_t_pos - half_len)]
        else:
            t_name = reverse_data_dictionary[int(a_t_pos)]
        actual_next_tool_names.append(t_name)
    last_tool_name = reverse_data_dictionary[x[-1]]
    # 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


def get_lowest_tools(l_tool_freq, fraction=0.25):
    l_tool_freq = dict(sorted(l_tool_freq.items(), key=lambda kv: kv[1], reverse=True))
    tool_ids = list(l_tool_freq.keys())
    lowest_ids = tool_ids[-int(len(tool_ids) * fraction):]
    return lowest_ids


def verify_model(model, x, y, reverse_data_dictionary, usage_scores, standard_conn, lowest_tool_ids, 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)])
    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]
        test_sample = x[i, :]
        last_tool_id = str(int(test_sample[-1]))
        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"]
    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,
        "standard_connections": standard_connections
    }
    set_trained_model(trained_model_path, model_values)