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Delete 'conditional_new_nn_hirearchical_seq.py'

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Seyyede Fateme Seyyedsalehi 4 years ago
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conditional_new_nn_hirearchical_seq.py View File

#!/usr/bin/env python

"""
parts of codes are based on the work in https://github.com/bio-ontology-research-group/deepgo.

"""
from __future__ import division

import logging
import sys
import time
from collections import deque
from multiprocessing import Pool

import click as ck
import numpy as np
import pandas as pd
import tensorflow as tf
from keras import backend as K
from keras.callbacks import EarlyStopping, ModelCheckpoint
from keras.layers import (
Dense, Input, SpatialDropout1D, Conv1D, MaxPooling1D,
Flatten, Concatenate, Add, Maximum, Embedding, BatchNormalization, Activation, Dropout)
from keras.losses import binary_crossentropy
from keras.models import Sequential, Model, load_model
from keras.preprocessing import sequence
from scipy.spatial import distance
from sklearn.metrics import log_loss
from sklearn.metrics import roc_curve, auc, matthews_corrcoef
from keras.layers import Lambda
from sklearn.metrics import precision_recall_curve

from utils import (
get_gene_ontology,
get_go_set,
get_anchestors,
get_parents,
DataGenerator,
FUNC_DICT,
get_height,
get_ipro)
from conditional_wgan_wrapper_post import WGAN_wrapper, wasserstein_loss, generator_recunstruction_loss_new

config = tf.ConfigProto()
config.gpu_options.allow_growth = True
sess = tf.Session(config=config)
K.set_session(sess)

logging.basicConfig(format='%(levelname)s:%(message)s', level=logging.INFO)
sys.setrecursionlimit(100000)

DATA_ROOT = 'data/swiss/'
MAXLEN = 1000
REPLEN = 256
ind = 0


@ck.command()
@ck.option(
'--function',
default='bp',
help='Ontology id (mf, bp, cc)')
@ck.option(
'--device',
default='gpu:0',
help='GPU or CPU device id')
@ck.option(
'--org',
default= None,
help='Organism id for filtering test set')
@ck.option('--train',default = True, is_flag=True)
@ck.option('--param', default=0, help='Param index 0-7')
def main(function, device, org, train, param):
global FUNCTION
FUNCTION = function
global GO_ID
GO_ID = FUNC_DICT[FUNCTION]
global go
go = get_gene_ontology('go.obo')
global ORG
ORG = org
func_df = pd.read_pickle(DATA_ROOT + FUNCTION + '.pkl')
global functions
functions = func_df['functions'].values
global func_set
func_set = set(functions)
global all_functions
all_functions = get_go_set(go, GO_ID)
logging.info('Functions: %s %d' % (FUNCTION, len(functions)))
if ORG is not None:
logging.info('Organism %s' % ORG)
global go_indexes
go_indexes = dict()
for ind, go_id in enumerate(functions):
go_indexes[go_id] = ind
global node_names
node_names = set()
with tf.device('/' + device):
params = {
'fc_output': 1024,
'learning_rate': 0.001,
'embedding_dims': 128,
'embedding_dropout': 0.2,
'nb_conv': 1,
'nb_dense': 1,
'filter_length': 128,
'nb_filter': 32,
'pool_length': 64,
'stride': 32
}
model(params, is_train=train)

def load_data():

df = pd.read_pickle(DATA_ROOT + 'train' + '-' + FUNCTION + '.pkl')
n = len(df)
index = df.index.values
valid_n = int(n * 0.8)
train_df = df.loc[index[:valid_n]]
valid_df = df.loc[index[valid_n:]]
test_df = pd.read_pickle(DATA_ROOT + 'test' + '-' + FUNCTION + '.pkl')
print( test_df['orgs'] )
if ORG is not None:
logging.info('Unfiltered test size: %d' % len(test_df))
test_df = test_df[test_df['orgs'] == ORG]
logging.info('Filtered test size: %d' % len(test_df))

# Filter by type
# org_df = pd.read_pickle('data/prokaryotes.pkl')
# orgs = org_df['orgs']
# test_df = test_df[test_df['orgs'].isin(orgs)]

def reshape(values):
values = np.hstack(values).reshape(
len(values), len(values[0]))
return values

def normalize_minmax(values):
mn = np.min(values)
mx = np.max(values)
if mx - mn != 0.0:
return (values - mn) / (mx - mn)
return values - mn

def get_values(data_frame):
print(data_frame['labels'].values.shape)
labels = reshape(data_frame['labels'].values)
ngrams = sequence.pad_sequences(
data_frame['ngrams'].values, maxlen=MAXLEN)
ngrams = reshape(ngrams)
rep = reshape(data_frame['embeddings'].values)
data = ngrams
return data, labels

train = get_values(train_df)
valid = get_values(valid_df)
test = get_values(test_df)

return train, valid, test, train_df, valid_df, test_df


def get_feature_model(params):
embedding_dims = params['embedding_dims']
max_features = 8001
model = Sequential()
model.add(Embedding(
max_features,
embedding_dims,
input_length=MAXLEN))
model.add(SpatialDropout1D(0.4))
for i in range(params['nb_conv']):
model.add(Conv1D(
activation="relu",
padding="valid",
strides=1,
filters=params['nb_filter'],
kernel_size=params['filter_length']))
model.add(MaxPooling1D(strides=params['stride'], pool_size=params['pool_length']))
model.add(Flatten())
return model

def merge_outputs(outputs, name):
if len(outputs) == 1:
return outputs[0]
## return merge(outputs, mode='concat', name=name, concat_axis=1)
return Concatenate(axis=1, name=name)(outputs)


def merge_nets(nets, name):
if len(nets) == 1:
return nets[0]
## return merge(nets, mode='sum', name=name)
return Add(name=name)(nets)

def get_node_name(go_id, unique=False):
name = go_id.split(':')[1]
if not unique:
return name
if name not in node_names:
node_names.add(name)
return name
i = 1
while (name + '_' + str(i)) in node_names:
i += 1
name = name + '_' + str(i)
node_names.add(name)
return name


def get_layers(inputs):
q = deque()
layers = {}
name = get_node_name(GO_ID)
layers[GO_ID] = {'net': inputs}
for node_id in go[GO_ID]['children']:
if node_id in func_set:
q.append((node_id, inputs))
while len(q) > 0:
node_id, net = q.popleft()
parent_nets = [inputs]
# for p_id in get_parents(go, node_id):
# if p_id in func_set:
# parent_nets.append(layers[p_id]['net'])
# if len(parent_nets) > 1:
# name = get_node_name(node_id) + '_parents'
# net = merge(
# parent_nets, mode='concat', concat_axis=1, name=name)
name = get_node_name(node_id)
net, output = get_function_node(name, inputs)
if node_id not in layers:
layers[node_id] = {'net': net, 'output': output}
for n_id in go[node_id]['children']:
if n_id in func_set and n_id not in layers:
ok = True
for p_id in get_parents(go, n_id):
if p_id in func_set and p_id not in layers:
ok = False
if ok:
q.append((n_id, net))

for node_id in functions:
childs = set(go[node_id]['children']).intersection(func_set)
if len(childs) > 0:
outputs = [layers[node_id]['output']]
for ch_id in childs:
outputs.append(layers[ch_id]['output'])
name = get_node_name(node_id) + '_max'
## layers[node_id]['output'] = merge(
## outputs, mode='max', name=name)
layers[node_id]['output'] = Maximum(name=name)(outputs)
return layers

def get_function_node(name, inputs):
output_name = name + '_out'
# net = Dense(256, name=name, activation='relu')(inputs)
output = Dense(1, name=output_name, activation='sigmoid')(inputs)
return output, output




def get_generator(params, n_classes):
inputs = Input(shape=(MAXLEN,), dtype='int32', name='input1')
feature_model = get_feature_model(params)(inputs)
net = Dense(300, activation='relu')(feature_model)
net = BatchNormalization()(net)
layers = get_layers(net)
output_models = []
for i in range(len(functions)):
output_models.append(layers[functions[i]]['output'])
net = Concatenate(axis=1)(output_models)
output = Dense(n_classes, activation='sigmoid')(net)
model = Model(inputs=inputs, outputs=output)

return model




def get_discriminator(params, n_classes, dropout_rate=0.5):
inputs = Input(shape=(n_classes, ))
inputs2 = Input(shape =(MAXLEN,), dtype ='int32', name='d_input2')
x2 = Embedding(8001,128, input_length=MAXLEN)(inputs2)
x2 = Conv1D(filters =1 , kernel_size= 1, padding = 'valid', activation ='relu', strides=1)(x2)
x2 = Lambda(lambda x: K.squeeze(x, 2))(x2)

#for i in range(params['nb_conv']):
# x2 = Conv1D ( activation="relu", padding="valid", strides=1, filters=params['nb_filter'],kernel_size=params['filter_length'])(x2)

#x2 =MaxPooling1D(strides=params['stride'], pool_size=params['pool_length'])(x2)
#x2 = Flatten()(x2)
size = 40
x = inputs
x = Dropout(dropout_rate)(x)
x = Dense(size)(x)
x = BatchNormalization()(x)
x = Activation('relu')(x)


size = 40
x2 = Dropout(dropout_rate)(x2)
x2 = Dense(size)(x2)
x2 = BatchNormalization()(x2)
x2 = Activation('relu')(x2)


x = Concatenate(axis =1 , name = 'merged2')([x, x2])
layer_sizes = [80, 40,30]
for size in layer_sizes:
x = Dropout(dropout_rate)(x)
x = Dense(size)(x)
x = BatchNormalization()(x)
x = Activation('relu')(x)


outputs = Dense(1)(x)
model = Model(inputs = [inputs ,inputs2], outputs=outputs, name='Discriminator')

return model



def get_model(params,nb_classes, batch_size, GRADIENT_PENALTY_WEIGHT=10):
generator = get_generator(params, nb_classes)
discriminator = get_discriminator(params, nb_classes)

generator_model, discriminator_model = \
WGAN_wrapper(generator=generator,
discriminator=discriminator,
generator_input_shape=(MAXLEN,),
discriminator_input_shape=(nb_classes,),
discriminator_input_shape2 = (MAXLEN, ),
batch_size=batch_size,
gradient_penalty_weight=GRADIENT_PENALTY_WEIGHT)

logging.info('Compilation finished')
return generator_model, discriminator_model


def train_wgan(generator_model, discriminator_model, batch_size, epochs,
x_train, y_train, x_val, y_val, generator_model_path, discriminator_model_path,
TRAINING_RATIO=10, N_WARM_UP=0):
BATCH_SIZE = batch_size
N_EPOCH = epochs
positive_y = np.ones((batch_size, 1), dtype=np.float32)
zero_y = positive_y * 0
negative_y = -positive_y
positive_full_y = np.ones((BATCH_SIZE * TRAINING_RATIO, 1), dtype=np.float32)
dummy_y = np.zeros((BATCH_SIZE, 1), dtype=np.float32)
positive_full_enable_train = np.ones((len(x_train), 1), dtype = np.float32 )
positive_full_enable_val = np.ones((len(x_val), 1), dtype =np.float32 )
#positive_enable_train = np.ones((1, batch_size),dtype = np.float32 )
#positive_full_train_enable = np.ones((1,BATCH_SIZE * TRAINING_RATIO ), dtype=np.float32 )
best_validation_loss = None

for epoch in range(N_EPOCH):
# np.random.shuffle(X_train)
print("Epoch: ", epoch)
print("Number of batches: ", int(y_train.shape[0] // BATCH_SIZE))
discriminator_loss = []
generator_loss = []
minibatches_size = BATCH_SIZE * TRAINING_RATIO

shuffled_indexes = np.random.permutation(x_train.shape[0])
shuffled_indexes_2 = np.random.permutation(x_train.shape[0])

for i in range(int(y_train.shape[0] // (BATCH_SIZE * TRAINING_RATIO))):
batch_indexes = shuffled_indexes[i * minibatches_size:(i + 1) * minibatches_size]
batch_indexes_2 = shuffled_indexes_2[i * minibatches_size:(i + 1) * minibatches_size]
x = x_train[batch_indexes]
y = y_train[batch_indexes]
y_2 = y_train[batch_indexes_2]
x_2 = x_train[batch_indexes_2]
if epoch < N_WARM_UP:
for j in range(TRAINING_RATIO):
x_batch = x[j * BATCH_SIZE:(j + 1) * BATCH_SIZE]
y_batch = y[j * BATCH_SIZE:(j + 1) * BATCH_SIZE]

generator_loss.append(generator_model.train_on_batch([x_batch, positive_y], [y_batch, zero_y]))
else:
for j in range(TRAINING_RATIO):
x_batch = x[j * BATCH_SIZE:(j + 1) * BATCH_SIZE]
y_batch_2 = y_2[j * BATCH_SIZE:(j + 1) * BATCH_SIZE]
x_batch_2 = x_2[j * BATCH_SIZE:(j + 1) * BATCH_SIZE]
# noise = np.random.rand(BATCH_SIZE, 100).astype(np.float32)
noise = x_batch
#print(sum(y_batch_2))
discriminator_loss.append(discriminator_model.train_on_batch(
[y_batch_2, noise, x_batch_2 ],
[positive_y, negative_y, dummy_y]))

generator_loss.append(generator_model.train_on_batch([x,positive_full_y], [y, positive_full_y]))
# Still needs some code to display losses from the generator and discriminator, progress bars, etc.
predicted_y_train, _ = generator_model.predict([x_train , positive_full_enable_train], batch_size=BATCH_SIZE)
predicted_y_val, _ = generator_model.predict([ x_val , positive_full_enable_val ], batch_size=BATCH_SIZE)
#print(sum(sum(positive_full_enable_train)))
#print(predicted_y_train)
train_loss = log_loss(y_train, predicted_y_train)
val_loss = log_loss(y_val, predicted_y_val)

print("train loss: {:.4f}, validation loss: {:.4f}, discriminator loss: {:.4f}".format(
train_loss, val_loss,
(np.sum(np.asarray(discriminator_loss)) if discriminator_loss else -1) / x_train.shape[0]))

if best_validation_loss is None or best_validation_loss > val_loss:
print('\nEpoch %05d: improved from %0.5f,'
' saving model to %s and %s'
% (epoch + 1, val_loss, generator_model_path, discriminator_model_path))

best_validation_loss = val_loss
generator_model.save(generator_model_path, overwrite=True)
discriminator_model.save(discriminator_model_path, overwrite=True)


def model(params, batch_size=20, nb_epoch=40, is_train=True):
# set parameters:
nb_classes = len(functions)
start_time = time.time()
logging.info("Loading Data")

train, val, test, train_df, valid_df, test_df = load_data()
train_df = pd.concat([train_df, valid_df])
test_gos = test_df['gos'].values
train_data, train_labels = train
val_data, val_labels = val
test_data, test_labels = test


logging.info("Data loaded in %d sec" % (time.time() - start_time))
logging.info("Training data size: %d" % len(train_data))
logging.info("Validation data size: %d" % len(val_data))
logging.info("Test data size: %d" % len(test_data))
generator_model_path = DATA_ROOT + 'models/new_model_seq_' + FUNCTION + '.h5'
discriminator_model_path = DATA_ROOT + 'models/new_model_disc_seq_' + FUNCTION + '.h5'


logging.info('Starting training the model')

train_generator = DataGenerator(batch_size, nb_classes)
train_generator.fit(train_data, train_labels)
valid_generator = DataGenerator(batch_size, nb_classes)
valid_generator.fit(val_data, val_labels)
test_generator = DataGenerator(batch_size, nb_classes)
test_generator.fit(test_data, test_labels)

if is_train:
generator_model, discriminator_model = get_model(params, nb_classes, batch_size)
train_wgan(generator_model, discriminator_model, batch_size=batch_size, epochs=nb_epoch,
x_train=train_data, y_train=train_labels, x_val=val_data, y_val=val_labels,
generator_model_path=generator_model_path,
discriminator_model_path=discriminator_model_path)

logging.info('Loading best model')
model = load_model(generator_model_path,
custom_objects={'generator_recunstruction_loss_new': generator_recunstruction_loss_new,
'wasserstein_loss': wasserstein_loss})

logging.info('Predicting')
preds = model.predict_generator(test_generator, steps=len(test_data) / batch_size)[0]

logging.info('Computing performance')
f, p, r, t, preds_max = compute_performance(preds, test_labels) #, test_gos)
roc_auc = compute_roc(preds, test_labels)
mcc = compute_mcc(preds_max, test_labels)
aupr , _ = compute_aupr(preds, test_labels)
m_pr_max, m_rc_max, m_f1_max, M_pr_max, M_rc_max, M_f1_max = micro_macro_function_centric_f1(preds.T, test_labels.T)

logging.info('Protein centric macro Th, PR, RC, F1: \t %f %f %f %f' % (t, p, r, f))
logging.info('ROC AUC: \t %f ' % (roc_auc, ))
logging.info('MCC: \t %f ' % (mcc, ))
logging.info('AUPR: \t %f ' % (aupr, ))
logging.info('Function centric macro PR, RC, F1: \t %f %f %f' % (M_pr_max, M_rc_max, M_f1_max) )
logging.info('Function centric micro PR, RC, F1: \t %f %f %f' % (m_pr_max, m_rc_max, m_f1_max) )

function_centric_performance(functions, preds.T, test_labels.T, train_labels.T)



def load_prot_ipro():
proteins = list()
ipros = list()
with open(DATA_ROOT + 'swissprot_ipro.tab') as f:
for line in f:
it = line.strip().split('\t')
if len(it) != 3:
continue
prot = it[1]
iprs = it[2].split(';')
proteins.append(prot)
ipros.append(iprs)
return pd.DataFrame({'proteins': proteins, 'ipros': ipros})


def performanc_by_interpro():
pred_df = pd.read_pickle(DATA_ROOT + 'test-' + FUNCTION + '-preds.pkl')
ipro_df = load_prot_ipro()
df = pred_df.merge(ipro_df, on='proteins', how='left')
ipro = get_ipro()

def reshape(values):
values = np.hstack(values).reshape(
len(values), len(values[0]))
return values

for ipro_id in ipro:
if len(ipro[ipro_id]['parents']) > 0:
continue
labels = list()
predictions = list()
gos = list()
for i, row in df.iterrows():
if not isinstance(row['ipros'], list):
continue
if ipro_id in row['ipros']:
labels.append(row['labels'])
predictions.append(row['predictions'])
gos.append(row['gos'])
pr = 0
rc = 0
total = 0
p_total = 0
for i in range(len(labels)):
tp = np.sum(labels[i] * predictions[i])
fp = np.sum(predictions[i]) - tp
fn = np.sum(labels[i]) - tp
all_gos = set()
for go_id in gos[i]:
if go_id in all_functions:
all_gos |= get_anchestors(go, go_id)
all_gos.discard(GO_ID)
all_gos -= func_set
fn += len(all_gos)
if tp == 0 and fp == 0 and fn == 0:
continue
total += 1
if tp != 0:
p_total += 1
precision = tp / (1.0 * (tp + fp))
recall = tp / (1.0 * (tp + fn))
pr += precision
rc += recall
if total > 0 and p_total > 0:
rc /= total
pr /= p_total
if pr + rc > 0:
f = 2 * pr * rc / (pr + rc)
logging.info('%s\t%d\t%f\t%f\t%f' % (
ipro_id, len(labels), f, pr, rc))


def function_centric_performance(functions, preds, labels, labels_train):
results = []
preds = np.round(preds, 2)
for i in range(preds.shape[0]):
f_max = 0
p_max = 0
r_max = 0
for t in range(1, 100):
threshold = t / 100.0
predictions = (preds[i, :] > threshold).astype(np.int32)
tp = np.sum(predictions * labels[i, :])
fp = np.sum(predictions) - tp
fn = np.sum(labels[i, :]) - tp
if tp > 0:
precision = tp / (1.0 * (tp + fp))
recall = tp / (1.0 * (tp + fn))
f = 2 * precision * recall / (precision + recall)
else:
if fp == 0 and fn == 0:
precision = 1
recall = 1
f = 1
else:
precision = 0
recall = 0
f = 0

if f_max < f:
f_max = f
p_max = precision
r_max = recall
num_prots_train = np.sum(labels_train[i, :])
height = get_height(go, functions[i])
results.append([functions[i], num_prots_train, height, f_max, p_max, r_max])
results = pd.DataFrame(results)
results.to_csv('Con_GodGanSeq_results_' + FUNCTION + '.txt', sep='\t', index=False)



def function_centric_performance_backup(functions, preds, labels, labels_train):
results = []
preds = np.round(preds, 2)
for i in range(len(functions)):
f_max = 0
p_max = 0
r_max = 0
x = list()
y = list()
total = 0
for t in range(1, 100):
threshold = t / 100.0
predictions = (preds[i, :] > threshold).astype(np.int32)
tp = np.sum(predictions * labels[i, :])
fp = np.sum(predictions) - tp
fn = np.sum(labels[i, :]) - tp
if tp >0:
sn = tp / (1.0 * np.sum(labels[i, :]))
sp = np.sum((predictions ^ 1) * (labels[i, :] ^ 1))
sp /= 1.0 * np.sum(labels[i, :] ^ 1)
fpr = 1 - sp
x.append(fpr)
y.append(sn)
precision = tp / (1.0 * (tp + fp))
recall = tp / (1.0 * (tp + fn))
f = 2 * precision * recall / (precision + recall)
total +=1
if f_max < f:
f_max = f
p_max = precision
r_max = recall
num_prots = np.sum(labels[i, :])
num_prots_train = np.sum(labels_train[i,:])
if total >1 :
roc_auc = auc(x, y)
else:
roc_auc =0
height = get_height(go , functions[i])
results.append([functions[i], f_max, p_max, r_max, num_prots, num_prots_train, height,roc_auc])
results = pd.DataFrame(results)
#results.to_csv('new_results.txt' , sep='\t' , index = False)
results.to_csv('Con_GodGanSeq_results_'+FUNCTION +'.txt', sep='\t', index=False)
#results = np.array(results)
#p_mean = (np.sum(results[:,2])) / len(functions)
#r_mean = (np.sum(results[:,3])) / len(functions)
#f_mean = (2*p_mean*r_mean)/(p_mean+r_mean)
#roc_auc_mean = (np.sum(results[:,7])) / len(functions)
#print('Function centric performance (macro) ' '%f %f %f %f' % (f_mean, p_mean, r_mean, roc_auc_mean))



def micro_macro_function_centric_f1_backup(preds, labels):
preds = np.round(preds, 2)
m_f1_max = 0
M_f1_max = 0
for t in range(1, 100):
threshold = t / 100.0
predictions = (preds > threshold).astype(np.int32)
m_tp = 0
m_fp = 0
m_fn = 0
M_pr = 0
M_rc = 0
total = 0
p_total = 0
for i in range(len(preds)):
tp = np.sum(predictions[i, :] * labels[i, :])
fp = np.sum(predictions[i, :]) - tp
fn = np.sum(labels[i, :]) - tp
if tp == 0 and fp == 0 and fn == 0:
continue
total += 1
if tp > 0:
pr = tp / (1.0 * (tp + fp))
rc = tp / (1.0 * (tp + fn))
m_tp += tp
m_fp += fp
m_fn += fn
M_pr += pr
M_rc += rc
p_total += 1

if p_total == 0:
continue
if total > 0:
m_tp /= total
m_fn /= total
m_fp /= total
m_pr = m_tp / (1.0 * (m_tp + m_fp))
m_rc = m_tp / (1.0 * (m_tp + m_fn))
M_pr /= p_total
M_rc /= total
m_f1 = 2 * m_pr * m_rc / (m_pr + m_rc)
M_f1 = 2 * M_pr * M_rc / (M_pr + M_rc)

if m_f1 > m_f1_max:
m_f1_max = m_f1
m_pr_max = m_pr
m_rc_max = m_rc

if M_f1 > M_f1_max:
M_f1_max = M_f1
M_pr_max = M_pr
M_rc_max = M_rc

return m_pr_max, m_rc_max, m_f1_max, M_pr_max, M_rc_max, M_f1_max





def micro_macro_function_centric_f1(preds, labels):
preds = np.round(preds, 2)
m_f1_max = 0
M_f1_max = 0
for t in range(1, 200):
threshold = t / 200.0
predictions = (preds > threshold).astype(np.int32)
m_tp = 0
m_fp = 0
m_fn = 0
M_pr = 0
M_rc = 0
for i in range(preds.shape[0]):
tp = np.sum(predictions[i, :] * labels[i, :])
fp = np.sum(predictions[i, :]) - tp
fn = np.sum(labels[i, :]) - tp
m_tp += tp
m_fp += fp
m_fn += fn
if tp > 0:
pr = 1.0 * tp / (1.0 * (tp + fp))
rc = 1.0 * tp / (1.0 * (tp + fn))
else:
if fp == 0 and fn == 0:
pr = 1
rc = 1
else:
pr = 0
rc = 0
M_pr += pr
M_rc += rc

if m_tp > 0:
m_pr = 1.0 * m_tp / (1.0 * (m_tp + m_fp))
m_rc = 1.0 * m_tp / (1.0 * (m_tp + m_fn))
m_f1 = 2.0 * m_pr * m_rc / (m_pr + m_rc)
else:
if m_fp == 0 and m_fn == 0:
m_pr = 1
m_rc = 1
m_f1 = 1
else:
m_pr = 0
m_rc = 0
m_f1 = 0

M_pr /= preds.shape[0]
M_rc /= preds.shape[0]
if M_pr == 0 and M_rc == 0:
M_f1 = 0
else:
M_f1 = 2.0 * M_pr * M_rc / (M_pr + M_rc)
if m_f1 > m_f1_max:
m_f1_max = m_f1
m_pr_max = m_pr
m_rc_max = m_rc

if M_f1 > M_f1_max:
M_f1_max = M_f1
M_pr_max = M_pr
M_rc_max = M_rc

return m_pr_max, m_rc_max, m_f1_max, M_pr_max, M_rc_max, M_f1_max


def compute_roc(preds, labels):
# Compute ROC curve and ROC area for each class
fpr, tpr, _ = roc_curve(labels.flatten(), preds.flatten())
roc_auc = auc(fpr, tpr)
return roc_auc


def compute_aupr(preds, labels):
# Compute ROC curve and ROC area for each class
pr, rc, threshold =precision_recall_curve(labels.flatten(), preds.flatten())
pr_auc = auc(rc, pr)
#pr, rc, threshold =precision_recall_curve(labels.flatten(), preds.flatten(),average ='macro' )
M_pr_auc = 0
return pr_auc, M_pr_auc



def compute_mcc(preds, labels):
# Compute ROC curve and ROC area for each class
mcc = matthews_corrcoef(labels.flatten(), preds.flatten())
return mcc


def compute_performance(preds, labels): #, gos):
preds = np.round(preds, 2)
f_max = 0
p_max = 0
r_max = 0
t_max = 0
for t in range(1, 100):
threshold = t / 100.0
predictions = (preds > threshold).astype(np.int32)
total = 0
f = 0.0
p = 0.0
r = 0.0
p_total = 0
for i in range(labels.shape[0]):
tp = np.sum(predictions[i, :] * labels[i, :])
fp = np.sum(predictions[i, :]) - tp
fn = np.sum(labels[i, :]) - tp
all_gos = set()
#for go_id in gos[i]:
# if go_id in all_functions:
# all_gos |= get_anchestors(go, go_id)
#all_gos.discard(GO_ID)
#all_gos -= func_set
#fn += len(all_gos)
if tp == 0 and fp == 0 and fn == 0:
continue
total += 1
if tp != 0:
p_total += 1
precision = tp / (1.0 * (tp + fp))
recall = tp / (1.0 * (tp + fn))
p += precision
r += recall
if p_total == 0:
continue
r /= total
p /= p_total
if p + r > 0:
f = 2 * p * r / (p + r)
if f_max < f:
f_max = f
p_max = p
r_max = r
t_max = threshold
predictions_max = predictions
return f_max, p_max, r_max, t_max, predictions_max


def get_gos(pred):
mdist = 1.0
mgos = None
for i in range(len(labels_gos)):
labels, gos = labels_gos[i]
dist = distance.cosine(pred, labels)
if mdist > dist:
mdist = dist
mgos = gos
return mgos


def compute_similarity_performance(train_df, test_df, preds):
logging.info("Computing similarity performance")
logging.info("Training data size %d" % len(train_df))
train_labels = train_df['labels'].values
train_gos = train_df['gos'].values
global labels_gos
labels_gos = zip(train_labels, train_gos)
p = Pool(64)
pred_gos = p.map(get_gos, preds)
total = 0
p = 0.0
r = 0.0
f = 0.0
test_gos = test_df['gos'].values
for gos, tgos in zip(pred_gos, test_gos):
preds = set()
test = set()
for go_id in gos:
if go_id in all_functions:
preds |= get_anchestors(go, go_id)
for go_id in tgos:
if go_id in all_functions:
test |= get_anchestors(go, go_id)
tp = len(preds.intersection(test))
fp = len(preds - test)
fn = len(test - preds)
if tp == 0 and fp == 0 and fn == 0:
continue
total += 1
if tp != 0:
precision = tp / (1.0 * (tp + fp))
recall = tp / (1.0 * (tp + fn))
p += precision
r += recall
f += 2 * precision * recall / (precision + recall)
return f / total, p / total, r / total


def print_report(report, go_id):
with open(DATA_ROOT + 'reports.txt', 'a') as f:
f.write('Classification report for ' + go_id + '\n')
f.write(report + '\n')


if __name__ == '__main__':
main()

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