def main(args):
target_dir = os.path.join(args.root, args.target_dir)
test_split_file = os.path.join(args.root, 'test.txt')
lattice_path_list, target_path_list = pred_ref_lists(test_split_file, target_dir)
preds, refs = load_eval_data(lattice_path_list, target_path_list)
assert len(preds) == len(refs), \
'Predictions and references must be sequences of the same length'
nce = evaluation.nce(refs, preds)
precision, recall, area = evaluation.pr(refs, preds)
precision_bl, recall_bl, area_bl = evaluation.pr(refs, preds)
utils.print_color_msg(
"".ljust(7) + "NCE: %.4f. AUC(PR): %.4f. AUC(BL): %.4f" \
%(nce, area, area_bl)
)
print('NCE: %f\nAUC(PR): %f\n' %(nce, area))
evaluation.plot_pr(
[precision, precision_bl], [recall, recall_bl],
[area, area_bl], ['BiRNN', 'posterior']
)
def main():
"""Main function for training and testing."""
# Parse command line arguments and cache
opt = opts.Opts().args
utils.savecmd(opt.resume, sys.argv)
utils.print_color_msg("==> Setting up data loader")
train_loader, val_loader, test_loader = dataloader.create(opt)
# Load checkpoint if specified, None otherwise
utils.print_color_msg("==> Checking checkpoints")
checkpoint = checkpoints.load(opt)
utils.print_color_msg("==> Setting up model and criterion")
model, optim_state = init.setup(opt, checkpoint)
loss_fn = criterion.setup(opt, checkpoint)
utils.print_color_msg("==> Loading trainer")
trainer = train.create_trainer(model, loss_fn, opt, optim_state)
best_loss = float('Inf')
val_loss = float('Inf')
start_epoch = max([1, opt.epochNum])
if checkpoint is not None:
start_epoch = checkpoint['epoch'] + 1
best_loss = checkpoint['loss']
print("".ljust(4) + "Previous best loss: " +
utils.color_msg('%.5f' % best_loss))
if opt.valOnly:
assert start_epoch > 1, "There must be at least one epoch"
utils.print_color_msg("==> Validation:")
print("".ljust(4) + "=> Epoch %i" % (start_epoch - 1))
trainer.val(val_loader, start_epoch - 1)
sys.exit()
if opt.testOnly:
assert start_epoch > 1, "There must be at least one epoch"
utils.print_color_msg("==> Testing:")
print("".ljust(4) + "=> Epoch %i" % (start_epoch - 1))
_, prediction, reference, post = trainer.test(test_loader,
start_epoch - 1)
if opt.loss == 'BCELogit':
prediction = F.sigmoid(torch.Tensor(prediction)).numpy()
nce = evaluation.nce(reference, prediction)
precision, recall, area = evaluation.pr(reference, prediction)
precision_bl, recall_bl, area_bl = evaluation.pr(reference, post)
utils.print_color_msg(
"".ljust(7) + "NCE: %.4f. AUC(PR): %.4f. AUC(BL): %.4f" \
%(nce, area, area_bl))
trainer.logger['test'].write('NCE: %f\nAUC(PR): %f\n' % (nce, area))
evaluation.plot_pr([precision, precision_bl], [recall, recall_bl],
[area, area_bl], ['BiRNN', 'posterior'], opt.resume)
np.savez(os.path.join(opt.resume, 'result.npz'),
prediction=prediction,
reference=reference,
posteriors=post)
sys.exit()
utils.print_color_msg("==> Training:")
for epoch in range(start_epoch, opt.nEpochs + 1):
print("".ljust(4) + "=> Epoch %i" % epoch)
best_model = False
_ = trainer.train(train_loader, epoch, val_loss)
if not opt.debug:
val_loss = trainer.val(val_loader, epoch)
if val_loss < best_loss:
best_model = True
print("".ljust(4) + "** Best model: " +
utils.color_msg('%.4f' % val_loss))
best_loss = val_loss
checkpoints.save(epoch, trainer.model, loss_fn,
trainer.optim_state, best_model, val_loss, opt)
if not opt.debug:
utils.print_color_msg("==> Testing:")
_, prediction, reference, _ = trainer.test(test_loader, opt.nEpochs)
prediction = F.sigmoid(torch.Tensor(prediction)).numpy()
nce = evaluation.nce(reference, prediction)
precision, recall, area = evaluation.pr(reference, prediction)
utils.print_color_msg("".ljust(7) + "NCE: %.4f. AUC(PR): %.4f" %
(nce, area))
trainer.logger['test'].write('NCE: %f\nAUC(PR): %f\n' % (nce, area))
evaluation.plot_pr([precision], [recall], [area], ['BiRNN'],
opt.resume)
# Flush write out and reset pointer
for open_file in trainer.logger.values():
open_file.flush()
open_file.seek(0)
plot.plot(opt.resume, opt.onebest)
def main():
"""Main function for training and testing."""
# Parse command line arguments and cache
opt = opts.Opts().args
utils.savecmd(opt.resume, sys.argv)
utils.print_color_msg("==> Setting up data loader")
train_loader, val_loader, test_loader = dataloader.create(opt)
# Load checkpoint if specified, None otherwise
utils.print_color_msg("==> Checking checkpoints")
checkpoint = checkpoints.load(opt)
utils.print_color_msg("==> Setting up model and criterion")
model, optim_state = init.setup(opt, checkpoint)
loss_fn = criterion.setup(opt, checkpoint)
utils.print_color_msg("==> Loading trainer")
trainer = train.create_trainer(model, loss_fn, opt, optim_state)
best_loss = float('Inf')
val_loss = float('Inf')
start_epoch = max([1, opt.epochNum])
if checkpoint is not None:
start_epoch = checkpoint['epoch'] + 1
best_loss = checkpoint['loss']
print("".ljust(4) + "Previous best loss: " +
utils.color_msg('%.5f' % best_loss))
if opt.valOnly:
assert start_epoch > 1, "There must be at least one epoch"
utils.print_color_msg("==> Validation:")
print("".ljust(4) + "=> Epoch %i" % (start_epoch - 1))
trainer.val(val_loader, start_epoch - 1)
sys.exit()
if opt.testOnly:
assert start_epoch > 1, "There must be at least one epoch"
utils.print_color_msg("==> Testing:")
print("".ljust(4) + "=> Epoch %i" % (start_epoch - 1))
_, prediction, reference, post, seq_length = trainer.test(
test_loader, start_epoch - 1)
prediction = F.sigmoid(torch.Tensor(prediction)).numpy()
nce = evaluation.nce(reference, prediction)
precision, recall, area, threshold = evaluation.pr(
reference, prediction)
precision_bl, recall_bl, area_bl, _ = evaluation.pr(reference, post)
f1, f1_precision, f1_recall, f1_threshold = evaluation.f1(
precision, recall, threshold)
tpr, fpr, roc_area = evaluation.roc(reference, prediction)
# Calculate stats for sequences binned by the posterior
limits = np.linspace(0, 1, 11).tolist()
utils.print_color_msg('\n\nEffect of Input Posterior on Performance')
for i in range(len(limits) - 1):
ref, pred, p = evaluation.bin_results(reference, prediction, post, measure=post, \
lower_limit=limits[i], upper_limit=limits[i+1])
if ref.size:
nce_post = evaluation.nce(ref, pred)
nce_post_bl = evaluation.nce(ref, p)
precision_post, recall_post, area_post, threshold_post = evaluation.pr(
ref, pred)
precision_post_bl, recall_post_bl, area_post_bl, threshold_post_bl = evaluation.pr(
ref, p)
f1_post, _, _, _ = evaluation.f1(precision_post, recall_post,
threshold_post)
f1_post_bl, _, _, _ = evaluation.f1(precision_post_bl,
recall_post_bl,
threshold_post_bl)
_, _, roc_area_post = evaluation.roc(ref, pred)
print('%.1f. - %.1f. %d Results (model/bl) NCE: %.4f. , %.4f. AUC(PR): %.4f. , %.4f. F-1: %.4f. , %.4f. AUC(ROC): %.4f.'\
%(limits[i], limits[i+1], int(ref.size), nce_post, nce_post_bl, area_post, area_post_bl, f1_post, f1_post_bl, roc_area_post))
else:
print('%.1f. - %.1f. Empty' % (limits[i], limits[i + 1]))
# Caluclate stats for sequences binned by sequence length
limits = [0, 2, 3, 6, 10, 20, 40]
utils.print_color_msg('\n\nEffect of Sequence Length on Performance')
for i in range(len(limits) - 1):
ref, pred, p = evaluation.bin_results(reference, prediction, post, measure=seq_length, \
lower_limit=limits[i], upper_limit=limits[i+1])
if ref.size:
nce_len = evaluation.nce(ref, pred)
nce_len_bl = evaluation.nce(ref, p)
precision_len, recall_len, area_len, threshold_len = evaluation.pr(
ref, pred)
precision_len_bl, recall_len_bl, area_len_bl, threshold_len_bl = evaluation.pr(
ref, p)
f1_len, _, _, _ = evaluation.f1(precision_len, recall_len,
threshold_len)
f1_len_bl, _, _, _ = evaluation.f1(precision_len_bl,
recall_len_bl,
threshold_len_bl)
_, _, roc_area_len = evaluation.roc(ref, pred)
print(f'%d - %d %d Results (model/bl) NCE: %.4f. , %.4f. AUC: %.4f. , %.4f. F-1: %.4f. , %.4f. AUC(ROC): %.4f.'\
%(limits[i], limits[i+1], int(ref.size), nce_len, nce_len_bl, area_len, area_len_bl, f1_len, f1_len_bl, roc_area_len))
else:
print('%d - %d Empty' % (limits[i], limits[i + 1]))
# Calulate calibration stats
limits = np.linspace(0, 1, 11).tolist()
print('\n\nCalibration Stats')
ece = 0
for i in range(len(limits) - 1):
ref, pred, p = evaluation.bin_results(reference, prediction, post, measure=prediction, \
lower_limit=limits[i], upper_limit=limits[i+1])
if ref.size:
accuracy_bin = np.mean(ref)
confidence_bin = np.mean(pred)
posterior_bin = np.mean(p)
ece += abs(accuracy_bin -
confidence_bin) * len(ref) / len(reference)
print(
f'%.1f. - %.1f. %d Reference: %.4f. , Prediction: %.4f. , Posterior: %.4f.'
% (limits[i], limits[i + 1], int(ref.size), accuracy_bin,
confidence_bin, posterior_bin))
else:
print('%.1f. - %.1f. Empty' % (limits[i], limits[i + 1]))
# Print Test Stats
print('\n\nTest Stats')
print(
"".ljust(7) + "\nNCE: %.4f. \nAUC(PR): %.4f. \nF-1: %.4f. p: %.4f. r: %.4f. t: %.4f. \nAUC(ROC): %.4f. \nECE: %.4f. " \
%(nce, area, f1, f1_precision, f1_recall, f1_threshold, roc_area, nce))
trainer.logger['test'].write('NCE: %f\nAUC(PR): %f\n' % (nce, area))
evaluation.plot_pr([precision, precision_bl], [recall, recall_bl],
[area, area_bl], ['BiLatticeRNN', 'posterior'],
opt.resume)
np.savez(os.path.join(opt.resume, 'result.npz'),
prediction=prediction,
reference=reference,
posteriors=post)
sys.exit()
utils.print_color_msg("==> Training:")
for epoch in range(start_epoch, opt.nEpochs + 1):
print("".ljust(4) + "=> Epoch %i" % epoch)
best_model = False
_ = trainer.train(train_loader, epoch, val_loss)
if not opt.debug:
val_loss = trainer.val(val_loader, epoch)
if val_loss < best_loss:
best_model = True
print("".ljust(4) + "** Best model: " +
utils.color_msg('%.4f' % val_loss))
best_loss = val_loss
checkpoints.save(epoch, trainer.model, loss_fn,
trainer.optim_state, best_model, val_loss, opt)
if not opt.debug:
utils.print_color_msg("==> Testing:")
_, prediction, reference, _, _ = trainer.test(test_loader, opt.nEpochs)
prediction = F.sigmoid(torch.Tensor(prediction)).numpy()
nce = evaluation.nce(reference, prediction)
precision, recall, area, _ = evaluation.pr(reference, prediction)
utils.print_color_msg("".ljust(7) + "NCE: %.4f. AUC(PR): %.4f" %
(nce, area))
trainer.logger['test'].write('NCE: %f\nAUC(PR): %f\n' % (nce, area))
evaluation.plot_pr([precision], [recall], [area], ['BiLatticeRNN'],
opt.resume)
# Flush write out and reset pointer
for open_file in trainer.logger.values():
open_file.flush()
open_file.seek(0)
plot.plot(opt.resume, opt.onebest)