def setUp(self):
folder = dirname(__file__)
file_name = folder + "/data/rna.fasta"
self.data = Data(file_name, ("ACGU", "()."))
self.params = {"conv_num":1, "kernel_num":3, "kernel_len":5,
"neuron_num":2, "epochs":3}
self.m1 = Model(self.params, self.data, seed = 2)
self.m2 = Model(self.params, self.data, seed = 13)
self.m3 = Model(self.params, self.data, seed = 2)
def train(self, data, verbose=True):
""" Train all models and return the best one.
Models are evaluated and ranked according to their ROC-AUC on a validation data set.
Parameters
----------
data: pysster.Data
A Data object providing training and validation data sets.
verbose: bool
If True, progress information (train/val loss) will be printed throughout the training.
Returns
-------
results: tuple(pysster.Model, str)
The best performing model and an overview table of all models are returned.
"""
best_model_path = "{}/{}".format(
gettempdir(),
''.join(random.choice(string.ascii_uppercase) for _ in range(20)))
aucs = []
max_auroc = -1
for i, candidate in enumerate(self.candidates):
model = Model(candidate, data)
model.train(data, verbose)
predictions = model.predict(data, "val")
labels = data.get_labels("val")
report = utils.performance_report(labels, predictions)
roc_auc = np.sum(report[:, 0:-1] * report[:, -1, np.newaxis],
axis=0)
roc_auc = (roc_auc / np.sum(report[:, -1]))[3]
aucs.append(roc_auc)
if aucs[-1] > max_auroc:
max_auroc = aucs[-1]
utils.save_model(model, best_model_path)
K.clear_session()
K.reset_uids()
if not verbose: continue
print("\n=== Summary ===")
print("Model {}/{} = {:.5f} weighted avg roc-auc".format(
i + 1, len(self.candidates), aucs[i]))
for param in candidate:
if not param in ["input_shape"]:
print(" - {}: {}".format(param, candidate[param]))
# load the best model (and remove it from disc)
model = utils.load_model(best_model_path)
remove(best_model_path)
remove("{}.h5".format(best_model_path))
# save a formatted summary of all trained models
table = self._grid_search_table(aucs)
return model, table
def test_data_additional(self):
self.assertTrue(len(self.data_pwm.meta) == 2)
self.assertTrue(self.data_pwm.meta[0]['is_categorical'] == False)
self.assertTrue(self.data_pwm.meta[1]['is_categorical'] == True)
self.assertTrue(self.data_pwm.meta[0]['data'] == [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,16,15,14,13,12,11,10,9,8,7,6,5,4,3,2,1])
self.assertTrue(len(self.data_pwm.meta[1]['data']) == 32)
for x in self.data_pwm.meta[1]['data']:
self.assertTrue(sum(x) == 1)
self.assertTrue((self.data_pwm.meta[1]['data'][0] == self.data_pwm.meta[1]['data'][31]).all())
self.assertTrue((self.data_pwm.meta[1]['data'][13] == self.data_pwm.meta[1]['data'][18]).all())
addi = self.data_pwm._get_additional_data([0,1,15,16], 0, 4)
self.assertTrue(len(addi) == 4)
self.assertTrue(np.allclose(addi[0], [1,*self.data_pwm.meta[1]['data'][0]]))
self.assertTrue(np.allclose(addi[1], [2,*self.data_pwm.meta[1]['data'][1]]))
self.assertTrue(np.allclose(addi[2], [16,*self.data_pwm.meta[1]['data'][15]]))
self.assertTrue(np.allclose(addi[3], [16,*self.data_pwm.meta[1]['data'][16]]))
mod = Model({"conv_num":1, "kernel_num":2, "kernel_len":4, "neuron_num":2, "epochs":2}, self.data_pwm)
mod.train(self.data_pwm, verbose=True)
predictions = mod.predict(self.data_pwm, "all")
self.assertTrue(predictions.shape == (32,2))
def load_model(file_path):
""" Load a pysster.Model object.
Parameters
----------
file_path : str
A file containing a pickled pysster.Model object (file_path.h5 must also exist, see save_model()).
Returns
-------
model : pysster.Model
A Model object.
"""
from pysster.Model import Model
if not os.path.exists(file_path):
raise RuntimeError("Path not found.")
if not os.path.exists("{}.h5".format(file_path)):
raise RuntimeError("HDF5 file not found.")
with gzip.open(file_path, "rb") as handle:
params = pickle.load(handle)
model = Model(params, None)
model.model = keras.models.load_model("{}.h5".format(file_path))
return model
def measure_rbp(entry):
import os
from time import time
from pysster import utils
output_folder = entry[4] + "_pysster/"
if not os.path.isdir(output_folder):
os.makedirs(output_folder)
start = time()
# predict secondary structures
utils.predict_structures(entry[0], entry[0] + ".struct", annotate=True)
utils.predict_structures(entry[1], entry[1] + ".struct", annotate=True)
utils.predict_structures(entry[2], entry[2] + ".struct", annotate=True)
utils.predict_structures(entry[3], entry[3] + ".struct", annotate=True)
from pysster.Data import Data
from pysster.Model import Model
# load data
data = Data([entry[0] + ".struct", entry[1] + ".struct"], ("ACGU", "HIMS"))
data.train_val_test_split(
0.8, 0.1999
) # we need to have at least one test sequence, even though we have a separate test object
# training
params = {"kernel_len": 8}
model = Model(params, data)
model.train(data)
# load and predict test data
data_test = Data([entry[2] + ".struct", entry[3] + ".struct"],
("ACGU", "HIMS"))
predictions = model.predict(data_test, "all")
stop = time()
print("{}, time in seconds: {}".format(entry[4], stop - start))
# performance evaluation
labels = data_test.get_labels("all")
utils.plot_roc(labels, predictions, output_folder + "roc.pdf")
utils.plot_prec_recall(labels, predictions, output_folder + "prec.pdf")
# get motifs
activations = model.get_max_activations(data_test, "all")
_ = model.visualize_all_kernels(activations, data_test, output_folder)
# save model to drive
utils.save_model(model, "{}model.pkl".format(output_folder))
def train(self, data, pr_auc=False, verbose=True):
""" Train all models and return the best one.
Models are evaluated and ranked according to their ROC-AUC or PR-AUC (precision-recall)
on a validation data set.
Parameters
----------
data: pysster.Data
A Data object providing training and validation data sets.
pr_auc: bool
If True, the area under the precision-recall curve will be maximized instead of the area under the ROC curve
verbose: bool
If True, progress information (train/val loss) will be printed throughout the training.
Returns
-------
results: tuple(pysster.Model, str)
The best performing model and an overview table of all models are returned.
"""
best_model_path = "{}/{}".format(
gettempdir(),
''.join(random.choice(string.ascii_uppercase) for _ in range(20)))
if True == pr_auc:
metric_idx = 4
metric_name = "pre-auc"
else:
metric_idx = 3
metric_name = "roc-auc"
metric = []
max_metric = -1
for i, candidate in enumerate(self.candidates):
model = Model(candidate, data)
model.train(data, verbose)
predictions = model.predict(data, "val")
labels = data.get_labels("val")
report = utils.performance_report(labels, predictions)
metric_val = np.sum(report[:, 0:-1] * report[:, -1, np.newaxis],
axis=0)
metric_val = (metric_val / np.sum(report[:, -1]))[metric_idx]
metric.append(metric_val)
if metric[-1] > max_metric:
max_metric = metric[-1]
utils.save_model(model, best_model_path)
K.clear_session()
K.reset_uids()
if not verbose: continue
print("\n=== Summary ===")
print("Model {}/{} = {:.5f} weighted avg {}".format(
i + 1, len(self.candidates), metric[i], metric_name))
for param in candidate:
if not param in ["input_shape"]:
print(" - {}: {}".format(param, candidate[param]))
# load the best model (and remove it from disc)
model = utils.load_model(best_model_path)
remove(best_model_path)
remove("{}.h5".format(best_model_path))
# save a formatted summary of all trained models
table = self._grid_search_table(metric, metric_name)
return model, table
class Test_Model(unittest.TestCase):
def setUp(self):
folder = dirname(__file__)
file_name = folder + "/data/rna.fasta"
self.data = Data(file_name, ("ACGU", "()."))
self.params = {
"conv_num": 1,
"kernel_num": 3,
"kernel_len": 5,
"neuron_num": 2,
"epochs": 3
}
self.m1 = Model(self.params, self.data, seed=2)
self.m2 = Model(self.params, self.data, seed=13)
self.m3 = Model(self.params, self.data, seed=2)
def test_model_init(self):
self.assertTrue(self.m1.params["conv_num"] == 1)
self.assertTrue(self.m1.params["kernel_num"] == 3)
self.assertTrue(self.m1.params["kernel_len"] == 5)
self.assertTrue(self.m1.params["neuron_num"] == 2)
self.assertTrue(self.m1.params["activation"] == "sigmoid")
self.assertTrue(self.m1.model.layers[2].get_weights()[0].shape == (5,
12,
3))
self.assertTrue(
np.allclose(self.m1.model.layers[2].get_weights()[0],
self.m3.model.layers[2].get_weights()[0]))
self.assertFalse(
np.allclose(self.m2.model.layers[2].get_weights()[0],
self.m3.model.layers[2].get_weights()[0]))
self.assertTrue(
np.allclose(self.m1.model.layers[6].get_weights()[0],
self.m3.model.layers[6].get_weights()[0]))
self.assertFalse(
np.allclose(self.m2.model.layers[6].get_weights()[0],
self.m3.model.layers[6].get_weights()[0]))
def test_model_train_predict(self):
for obj in [self.m1, self.m2, self.m3]:
obj.train(self.data, verbose=False)
predictions = obj.predict(self.data, "test")
self.assertTrue(predictions.shape == (3, 3))
self.assertTrue((predictions > 0.49).all())
self.assertTrue((predictions < 0.51).all())
predictions = obj.predict(self.data, "all")
self.assertTrue(predictions.shape == (20, 3))
self.assertTrue((predictions > 0.49).all())
self.assertTrue((predictions < 0.51).all())
self.assertTrue(
np.allclose(self.m1.model.layers[2].get_weights()[0],
self.m3.model.layers[2].get_weights()[0],
atol=0.001))
self.assertFalse(
np.allclose(self.m2.model.layers[2].get_weights()[0],
self.m3.model.layers[2].get_weights()[0],
atol=0.001))
self.assertTrue(
np.allclose(self.m1.model.layers[6].get_weights()[0],
self.m3.model.layers[6].get_weights()[0],
atol=0.001))
self.assertFalse(
np.allclose(self.m2.model.layers[6].get_weights()[0],
self.m3.model.layers[6].get_weights()[0],
atol=0.001))
def test_model_get_max_activations(self):
acts = self.m1.get_max_activations(self.data, 'test')
self.assertTrue(acts['activations'].shape == (3, 3))
self.assertTrue(acts['labels'].shape == (3, 3))
self.assertTrue(acts['group'] == 'test')
def test_model_visualize_kernel(self):
acts = self.m1.get_max_activations(self.data, 'all')
folder = gettempdir() + '/'
# individual kernels
for kernel in range(self.params['kernel_num']):
motif, score = self.m1.visualize_kernel(acts, self.data, kernel,
folder)
self.assertTrue(
isfile(folder + "motif_kernel_{}.png".format(kernel)))
self.assertTrue(
isfile(folder + "position_kernel_{}.png".format(kernel)))
self.assertTrue(
isfile(folder + "activations_kernel_{}.png".format(kernel)))
remove(folder + "motif_kernel_{}.png".format(kernel))
remove(folder + "position_kernel_{}.png".format(kernel))
remove(folder + "activations_kernel_{}.png".format(kernel))
self.assertTrue(isinstance(motif, tuple))
self.assertTrue(isinstance(motif[0], Motif))
self.assertTrue(np.isclose(score, 0) or score > 0)
# all kernels
motifs = self.m1.visualize_all_kernels(acts, self.data, folder)
self.assertTrue(len(motifs) == 3)
for x in range(3):
self.assertTrue(isinstance(motifs[x], tuple))
self.assertTrue(isinstance(motifs[x][0], Motif))
for kernel in range(self.params['kernel_num']):
self.assertTrue(
isfile(folder + "motif_kernel_{}.png".format(kernel)))
self.assertTrue(
isfile(folder + "position_kernel_{}.png".format(kernel)))
self.assertTrue(
isfile(folder + "activations_kernel_{}.png".format(kernel)))
remove(folder + "motif_kernel_{}.png".format(kernel))
remove(folder + "position_kernel_{}.png".format(kernel))
remove(folder + "activations_kernel_{}.png".format(kernel))
self.assertTrue(isfile(folder + "summary.html"))
remove(folder + "summary.html")
def test_model_plot_clustering(self):
acts = self.m1.get_max_activations(self.data, 'test')
self.m1.plot_clustering(acts, gettempdir() + "/clust.png")
self.assertFalse(isfile(gettempdir() + "/clust.png"))
def test_model_optimized_inputs(self):
self.m1.visualize_optimized_inputs(self.data,
self.m1.model.layers[2].name,
gettempdir() + "/test.png")
self.m1.visualize_optimized_inputs(self.data,
self.m1.model.layers[2].name,
gettempdir() + "/test2.png",
nodes=[0])
with Image.open(gettempdir() + "/test.png") as img:
self.assertTrue(img.size == (1998, 1128))
with Image.open(gettempdir() + "/test2.png") as img:
self.assertTrue(img.size == (1998, 376))
remove(gettempdir() + "/test.png")
remove(gettempdir() + "/test2.png")
class Test_utils(unittest.TestCase):
def setUp(self):
self.folder = dirname(__file__)
file_name = self.folder + "/data/rna.fasta"
self.data = Data(file_name, ("ACGU", "()."))
self.params = {
"conv_num": 1,
"kernel_num": 3,
"kernel_len": 5,
"neuron_num": 2,
"epochs": 3
}
self.m1 = Model(self.params, self.data, seed=2)
self.m1.train(self.data, verbose=False)
def test_utils_save_load_model(self):
utils.save_model(self.m1, gettempdir() + "/model")
self.assertTrue(isfile(gettempdir() + "/model"))
self.assertTrue(isfile(gettempdir() + "/model.h5"))
model = utils.load_model(gettempdir() + "/model")
self.assertTrue(self.m1.params == model.params)
self.assertTrue(self.m1.model.get_config() == model.model.get_config())
for x in range(6):
self.assertTrue(
np.allclose(self.m1.model.get_weights()[x],
model.model.get_weights()[x]))
remove(gettempdir() + "/model")
remove(gettempdir() + "/model.h5")
def test_utils_save_load_data(self):
utils.save_data(self.data, gettempdir() + "/data")
self.assertTrue(isfile(gettempdir() + "/data"))
data = utils.load_data(gettempdir() + "/data")
self.assertTrue(isinstance(data, Data))
remove(gettempdir() + "/data")
def test_utils_annotate_structures(self):
utils.annotate_structures(self.folder + "/data/rna_annot.fasta",
gettempdir() + "/test.fasta")
with open(self.folder + "/data/rna_annot_ref.fasta", 'rt') as handle:
ref = handle.read()
with open(gettempdir() + "/test.fasta", 'rt') as handle:
comp = handle.read()
self.assertTrue(ref == comp)
remove(gettempdir() + "/test.fasta")
def test_utils_predict_structures(self):
# RNAfold and RNAlib bindings not available
skip = False
try:
from RNA import fold
except:
if which("RNAfold") == None:
try:
utils.predict_structures(
self.folder + "/data/rna_pred.fasta",
gettempdir() + "/test2.fasta", 2, False)
raise RuntimeError(
'predict_structures should have raised an error at this point, but did not'
)
except:
skip = True # we got an error, as expected
#annotate=False
if skip == True:
return
utils.predict_structures(self.folder + "/data/rna_pred.fasta",
gettempdir() + "/test2.fasta", 2, False)
if not isfile(gettempdir() + "/test2.fasta"): return
with open(self.folder + "/data/rna_pred_ref.fasta", 'rt') as handle:
ref = handle.read()
with open(gettempdir() + "/test2.fasta", 'rt') as handle:
comp = handle.read()
self.assertTrue(ref == comp)
remove(gettempdir() + "/test2.fasta")
#annotate=True
utils.predict_structures(self.folder + "/data/rna_pred.fasta",
gettempdir() + "/test2.fasta", 2, True)
if not isfile(gettempdir() + "/test2.fasta"): return
with open(self.folder + "/data/rna_pred_ref_annot.fasta",
'rt') as handle:
ref = handle.read()
with open(gettempdir() + "/test2.fasta", 'rt') as handle:
comp = handle.read()
self.assertTrue(ref == comp)
remove(gettempdir() + "/test2.fasta")
def test_utils_save_as_meme(self):
logos = [Motif('ACGT', ['GATTACA']), Motif('ACGT', ['AAAA'])]
utils.save_as_meme(logos, gettempdir() + "/test.meme")
with open(self.folder + "/data/ref.meme", 'rt') as handle:
ref = handle.read()
with open(gettempdir() + "/test.meme", 'rt') as handle:
comp = handle.read()
self.assertTrue(ref == comp)
remove(gettempdir() + "/test.meme")
def main():
RBPs = [("data/pum2.train.positive.fasta",
"data/pum2.train.negative.fasta",
"data/pum2.test.positive.fasta",
"data/pum2.test.negative.fasta",
"PUM2"),
("data/qki.train.positive.fasta",
"data/qki.train.negative.fasta",
"data/qki.test.positive.fasta",
"data/qki.test.negative.fasta",
"QKI"),
("data/igf2bp123.train.positive.fasta",
"data/igf2bp123.train.negative.fasta",
"data/igf2bp123.test.positive.fasta",
"data/igf2bp123.test.negative.fasta",
"IGF2BP123"),
("data/srsf1.train.positive.fasta",
"data/srsf1.train.negative.fasta",
"data/srsf1.test.positive.fasta",
"data/srsf1.test.negative.fasta",
"SRSF1"),
("data/taf2n.train.positive.fasta",
"data/taf2n.train.negative.fasta",
"data/taf2n.test.positive.fasta",
"data/taf2n.test.negative.fasta",
"TAF2N"),
("data/nova.train.positive.fasta",
"data/nova.train.negative.fasta",
"data/nova.test.positive.fasta",
"data/nova.test.negative.fasta",
"NOVA")]
for entry in RBPs:
output_folder = entry[4] + "_pysster/"
if not os.path.isdir(output_folder):
os.makedirs(output_folder)
start = time()
# predict secondary structures
utils.predict_structures(entry[0], entry[0]+".struct.gz", annotate=True)
utils.predict_structures(entry[1], entry[1]+".struct.gz", annotate=True)
utils.predict_structures(entry[2], entry[2]+".struct.gz", annotate=True)
utils.predict_structures(entry[3], entry[3]+".struct.gz", annotate=True)
# load data
data = Data([entry[0]+".struct.gz", entry[1]+".struct.gz"], ("ACGU", "HIMS"))
data.train_val_test_split(0.8, 0.1999) # we need to have at least one test sequence, even though we don't need it
print(data.get_summary())
# training
params = {"kernel_len": 8}
model = Model(params, data)
model.train(data)
# load and predict test data
data_test = Data([entry[2]+".struct.gz", entry[3]+".struct.gz"], ("ACGU", "HIMS"))
predictions = model.predict(data_test, "all")
stop = time()
print("{}, time in seconds: {}".format(entry[4], stop-start))
# performance evaluation
labels = data_test.get_labels("all")
utils.plot_roc(labels, predictions, output_folder+"roc.pdf")
utils.plot_prec_recall(labels, predictions, output_folder+"prec.pdf")
print(utils.get_performance_report(labels, predictions))
# get motifs
activations = model.get_max_activations(data_test, "all")
logos, scores = [], []
for kernel in range(model.params["kernel_num"]):
logo, score = model.visualize_kernel(activations, data_test, kernel, output_folder)
logos.append(logo)
scores.append(score)
# sort motifs by importance score
sorted_idx = [i[0] for i in sorted(enumerate(scores), key=lambda x:x[1])]
with open(output_folder+"kernel_scores.txt", "wt") as handle:
for x in sorted_idx:
print("kernel {:>3}: {:.3f}".format(x, scores[x]))
handle.write("kernel {:>3}: {:.3f}\n".format(x, scores[x]))
# save model to drive
utils.save_model(model, "{}model.pkl".format(output_folder))
def test_data_additional(self):
self.assertTrue(len(self.data_pwm.meta) == 2)
self.assertTrue(self.data_pwm.meta[0]['is_categorical'] == False)
self.assertTrue(self.data_pwm.meta[1]['is_categorical'] == True)
self.assertTrue(self.data_pwm.meta[0]['data'] == [
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 16, 15, 14,
13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1
])
self.assertTrue(len(self.data_pwm.meta[1]['data']) == 32)
for x in self.data_pwm.meta[1]['data']:
self.assertTrue(sum(x) == 1)
self.assertTrue((self.data_pwm.meta[1]['data'][0] ==
self.data_pwm.meta[1]['data'][31]).all())
self.assertTrue((self.data_pwm.meta[1]['data'][13] ==
self.data_pwm.meta[1]['data'][18]).all())
addi = self.data_pwm._get_additional_data([0, 1, 15, 16], 0, 4)
self.assertTrue(len(addi) == 4)
self.assertTrue(
np.allclose(addi[0], [1, *self.data_pwm.meta[1]['data'][0]]))
self.assertTrue(
np.allclose(addi[1], [2, *self.data_pwm.meta[1]['data'][1]]))
self.assertTrue(
np.allclose(addi[2], [16, *self.data_pwm.meta[1]['data'][15]]))
self.assertTrue(
np.allclose(addi[3], [16, *self.data_pwm.meta[1]['data'][16]]))
# check position-wise additional data
self.assertTrue(len(self.data_pwm.positionwise) == 2)
self.assertTrue(
list(self.data_pwm.positionwise.keys()) == ["feat1", "feat2"])
gen = self.data_pwm._data_generator("all", 32, False, False)
dat = next(gen)
self.assertTrue(dat[1].shape == (32, 17))
self.assertTrue(dat[0].shape == (32, 10, 14))
self.assertTrue(
np.allclose(dat[0][0, :, 12],
[0.9, 0.8, 0.7, 0.9, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]))
self.assertTrue(
np.allclose(dat[0][31, :, 13],
[0.1, 0.2, 0.3, 0.1, 1.0, 1.0, 0.8, 0.3, 0.2, 0.1]))
self.assertTrue(
np.allclose(dat[0][31, :, 12],
[2.1, 2.2, 2.3, 2.1, 2.0, 2.0, 2.8, 2.3, 2.2, 2.1]))
mod = Model(
{
"conv_num": 1,
"kernel_num": 2,
"kernel_len": 4,
"neuron_num": 2,
"epochs": 2
}, self.data_pwm)
mod.train(self.data_pwm, verbose=True)
predictions = mod.predict(self.data_pwm, "all")
self.assertTrue(predictions.shape == (32, 2))
# check kernel output plot for position-wise data
folder = gettempdir() + '/'
acts = mod.get_max_activations(self.data_pwm, 'all')
motif, score = mod.visualize_kernel(acts, self.data_pwm, 0, folder)
with Image.open(folder + "additional_features_kernel_0.png") as img:
self.assertTrue(img.size == (500, 1400))
remove(folder + "additional_features_kernel_0.png")
remove(folder + "motif_kernel_0.png")
remove(folder + "position_kernel_0.png")
remove(folder + "activations_kernel_0.png")