def cluster_analysis(dim, k_cls):
X_dim_red = {}
print "Reducing dimensions..."
util.tic()
svd_cls = TruncatedSVD(n_components=dim, algorithm='arpack')
svd = make_pipeline(normalizer_svd, svd_cls)
X_dim_red['SVD'] = svd.fit_transform(X_tfidf)
nmf_cls = NMF(n_components=dim, init='random', random_state=random_state)
nmf = make_pipeline(normalizer_nmf, nmf_cls)
X_dim_red['NMF'] = nmf.fit_transform(X_tfidf)
util.toc()
# transform
#X_dim_red['SVD'] += np.max(X_dim_red['SVD'])
#X_dim_red['SVD'] = X_dim_red['SVD'] ** 2
X_dim_red['NMF'] = util.clamp(-10, np.log(X_dim_red['NMF']), 10)
# clustering
print "Clustering..."
util.tic()
kmeans = {}
kmeans['SVD'] = KMeans(n_clusters=k_cls,
random_state=random_state).fit(X_dim_red['SVD'])
kmeans['NMF'] = KMeans(n_clusters=k_cls,
random_state=random_state).fit(X_dim_red['NMF'])
util.toc()
#--------------------------------
### Evaluation
# Purity statistics
if k_cls == 6:
y_true = group6_true
elif k_cls == 20:
y_true = group20_true
print "Purity stats report:"
print "Dimension = %d" % dim
print "No. of groups = {}".format(k_cls)
for method in ['SVD', 'NMF']:
conf_mat = metrics.confusion_matrix(y_true, kmeans[method].labels_)
print "======== Method: %s ========" % method
print "Confusion Matrix:"
print conf_mat
#print "Confusion Matrix (w/ best permutation):"
#print util.sort_matrix_diagonally(conf_mat)
print "Homogeneity_score = {:4f}".format(
homogeneity_score(y_true, kmeans[method].labels_))
print "Completeness_score = {:4f}".format(
completeness_score(y_true, kmeans[method].labels_))
print "Adjusted_rand_score = {:4f}".format(
adjusted_rand_score(y_true, kmeans[method].labels_))
print "Adjusted_mutual_info_score = {:4f}".format(
adjusted_mutual_info_score(y_true, kmeans[method].labels_))
return
def propagate(self, image, superpixels, pairwise):
elapsed = tic()
nLayers = 1 + len(self.layers)
act = [ActiveLayer() for i in range(nLayers)]
act[0].x = image.reshape(image.shape + tuple([1]))
mi = ModelInputs(superpixels, pairwise)
for i in range(nLayers - 1):
lyr = self.layers[i]
when = tic()
if lyr.type in ['conv', 'logistic', 'pool', 'relu', 'custom']:
act[i + 1].x = lyr.propagate(act[i].x, mi)
elif lyr.type == 'structured_loss':
act[i + 1].labels = self.structured_loss(act[i].x, lyr, mi)
else:
error('Unknown layer type %s', lyr.type)
act[i].x = None # Recover memory.
act[i].time = toc(when) # Save time elapsed processing the layer.
if act[i + 1].x is not None:
print(
"L[%d]: %s layer '%s'\t produced a %s\t output in %f seconds."
% (i, str(lyr.type), str(lyr.name), str(
act[i + 1].x.shape), act[i].time))
else:
print(
"L[%d]: %s layer '%s'\t produced a %s\t output in %f seconds."
% (i, str(lyr.type), str(
lyr.name), str(act[i + 1].labels.shape), act[i].time))
print("NN forward propagation completed in %f seconds." %
(toc(elapsed)))
return act
def _solve(m):
"""Solve instance of switch model, using the specified objective, then load the results"""
tic()
results = opt.solve(m, keepfiles=False, tee=True,
symbolic_solver_labels=True, suffixes=['dual', 'iis'])
log("Solver finished; "); toc()
# results.write()
log("loading solution... "); tic()
# Pyomo changed their interface for loading results somewhere
# between 4.0.x and 4.1.x in a way that was not backwards compatible.
# Make the code accept either version
if hasattr(m, 'solutions'):
# Works in Pyomo version 4.1.x
m.solutions.load_from(results)
else:
# Works in Pyomo version 4.0.9682
m.load(results)
toc()
return results
def prCOut(nRep):
"""
Stop a propmter for counting.
Input
nRep - #steps
"""
# variables defined in "prSet.m"
global lPr, nmPrs, ticPrs, ticPr0s, nRepPrs, scaPrs
lPr = lPr - 1
# time
t = toc(ticPr0s[lPr])
# print
pr('%s: %d iters, %.2f secs' %(nmPrs[lPr], nRep, t))
def prC(iRep):
"""
Prompt information of a counter.
Input
iRep - current step
"""
# variables defined in "prSet()"
global lPr, nmPrs, ticPrs, nRepPrs, scaPrs
lPr = lPr - 1
if (iRep != 0 and iRep % scaPrs[lPr] == 0) or (iRep == nRepPrs[lPr]):
# time
t = toc(ticPrs[lPr])
# print
pr('%s: %d/%d, %.2f secs' %(nmPrs[lPr], iRep, nRepPrs[lPr], t))
# re-start a timer
ticPrs[lPr] = tic()
lPr = lPr + 1
def go(arg):
global repeats
repeats = arg.repeats
tbdir = arg.tb_dir if arg.tb_dir is not None else os.path.join(
'./runs', get_slug(arg))[:250]
tbw = SummaryWriter(log_dir=tbdir)
dev = 'cuda' if torch.cuda.is_available() else 'cpu'
train_mrrs = []
test_mrrs = []
train, val, test, (n2i, i2n), (r2i, i2r) = \
kgmodels.load_lp(arg.name)
print(len(i2n), 'nodes')
print(len(i2r), 'relations')
print(train.size(0), 'training triples')
print(test.size(0), 'test triples')
print(train.size(0) + test.size(0), 'total triples')
# print(train)
# print(test)
# sys.exit()
# set of all triples (for filtering)
alltriples = set()
for s, p, o in torch.cat([train, test], dim=0):
s, p, o = s.item(), p.item(), o.item()
alltriples.add((s, p, o))
if arg.final:
train, test = torch.cat([train, val], dim=0), test
else:
train, test = train, val
if arg.decomp == 'block':
# -- pad the node list to make it divisible by the nr. of blocks
added = 0
while len(i2n) % arg.num_blocks != 0:
label = 'null' + str(added)
i2n.append(label)
n2i[label] = len(i2n) - 1
added += 1
print(
f'nodes padded to {len(i2n)} to make it divisible by {arg.num_blocks} (added {added} null nodes).'
)
if repeats > 1:
RP, EP = trange, range
else:
RP, EP = range, trange
for r in RP(repeats):
"""
Define model
"""
if arg.model == 'classic':
model = kgmodels.LinkPrediction(triples=train,
n=len(i2n),
r=len(i2r),
hidden=arg.emb,
out=arg.emb,
decomp=arg.decomp,
numbases=arg.num_bases,
numblocks=arg.num_blocks,
depth=arg.depth,
do=arg.do,
biases=arg.biases,
prune=arg.prune,
dropout=arg.edge_dropout)
elif arg.model == 'narrow':
model = kgmodels.LPNarrow(triples=train,
n=len(i2n),
r=len(i2r),
emb=arg.emb,
hidden=arg.hidden,
decomp=arg.decomp,
numbases=arg.num_bases,
numblocks=arg.num_blocks,
depth=arg.depth,
do=arg.do,
biases=arg.biases,
prune=arg.prune,
edge_dropout=arg.edge_dropout)
elif arg.model == 'sampling':
model = kgmodels.SimpleLP(triples=train,
n=len(i2n),
r=len(i2r),
emb=arg.emb,
h=arg.hidden,
ksample=arg.k,
csample=arg.c,
multi=arg.multi,
decoder=arg.decoder)
else:
raise Exception(f'model not recognized: {arg.model}')
if torch.cuda.is_available():
prt('Using CUDA.')
model.cuda()
if arg.opt == 'adam':
opt = torch.optim.Adam(model.parameters(), lr=arg.lr[0])
elif arg.opt == 'adamw':
opt = torch.optim.AdamW(model.parameters(), lr=arg.lr[0])
elif arg.opt == 'adagrad':
opt = torch.optim.Adagrad(model.parameters(), lr=arg.lr[0])
elif arg.opt == 'sgd':
opt = torch.optim.SGD(model.parameters(),
lr=arg.lr[0],
nesterov=True,
momentum=arg.momentum)
else:
raise Exception()
# nr of negatives sampled
ng = arg.negative_rate
seen = 0
for e in range(sum(arg.epochs)):
depth = 0
set_lr(opt, arg.lr[0])
if e >= arg.epochs[0]:
depth = 1
set_lr(opt, arg.lr[1])
if e >= sum(arg.epochs[:2]):
depth = 2
set_lr(opt, arg.lr[2])
seeni, sumloss = 0, 0.0
if arg.c is not None:
tic()
model.precompute_globals()
print(f'precomp took {toc():.2}s')
tsample, tforward, tbackward, ttotal, tloss, tstep = 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
for fr in EP(0, train.size(0), arg.batch):
tic()
model.train(True)
if arg.limit is not None and seeni > arg.limit:
break
#
# if torch.cuda.is_available() and random.random() < 0.01:
# print(f'\nPeak gpu memory use is {torch.cuda.max_memory_cached() / 1e9:.2} Gb')
to = min(train.size(0), fr + arg.batch)
with torch.no_grad():
positives = train[fr:to]
b, _ = positives.size()
tic()
# sample negatives
if arg.corrupt_global: # global corruption (sample random true triples to corrupt)
indices = torch.randint(size=(b * ng, ),
low=0,
high=train.size(0))
negatives = train[indices, :].view(
b, ng, 3) # -- triples to be corrupted
else: # local corruption (directly corrupt the current batch)
negatives = positives.clone()[:, None, :].expand(
b, ng, 3).contiguous()
corrupt(negatives, len(i2n))
triples = torch.cat([positives[:, None, :], negatives],
dim=1)
if torch.cuda.is_available():
triples = triples.cuda()
if arg.loss == 'bce':
labels = torch.cat(
[torch.ones(b, 1),
torch.zeros(b, ng)], dim=1)
elif arg.loss == 'ce':
labels = torch.zeros(b, dtype=torch.long)
# -- CE loss treats the problem as a multiclass classification problem: for a positive triple,
# together with its k corruptions, identify which is the true triple. This is always triple 0,
# but the score function is order equivariant, so i can't see the index of the triple it's
# classifying.
if torch.cuda.is_available():
labels = labels.cuda()
tsample += toc()
opt.zero_grad()
tic()
out = model(triples, depth=depth)
assert out.size() == (b, ng + 1)
tic()
if arg.loss == 'bce':
loss = F.binary_cross_entropy_with_logits(out, labels)
elif arg.loss == 'ce':
loss = F.cross_entropy(out, labels)
if arg.l2weight is not None:
l2 = sum([p.pow(2).sum() for p in model.parameters()])
loss = loss + arg.l2weight * l2
tloss += toc()
tforward += toc()
tic()
loss.backward()
tbackward += toc()
sumloss += float(loss.item())
tic()
opt.step()
tstep += toc()
seen += b
seeni += b
ttotal += toc()
prt(f'epoch {e} (d{depth}); training loss {sumloss/seeni:.4} s {tsample:.3}s, f {tforward:.3}s (loss {tloss:.3}s), b {tbackward:.3}, st {tstep:.3}, t {ttotal:.3}s'
)
# Evaluate
if (e % arg.eval_int == 0 and e != 0) or e == sum(arg.epochs) - 1:
with torch.no_grad():
model.train(False)
ranks = []
mrr = hitsat1 = hitsat3 = hitsat10 = 0.0
if arg.eval_size is None:
testsub = test
else:
testsub = test[random.sample(range(test.size(0)),
k=arg.eval_size)]
tseen = 0
for tail in [True, False]: # head or tail prediction
for s, p, o in (testsub if repeats > 1 else
tqdm.tqdm(testsub)):
s, p, o = s.item(), p.item(), o.item()
if tail:
ot = o
del o
raw_candidates = [(s, p, o)
for o in range(len(i2n))]
candidates = filter(raw_candidates, alltriples,
(s, p, ot))
else:
st = s
del s
raw_candidates = [(s, p, o)
for s in range(len(i2n))]
candidates = filter(raw_candidates, alltriples,
(st, p, o))
candidates = torch.tensor(candidates)
scores = util.batch(model,
candidates,
batch_size=arg.batch * 2,
depth=depth)
# -- the batch size needs to be a little conservative here, due to the high variance in nr of
# triples sampled.
sorted_candidates = [
tuple(p[0])
for p in sorted(zip(candidates.tolist(),
scores.tolist()),
key=lambda p: -p[1])
]
rank = (sorted_candidates.index((s, p, ot)) +
1) if tail else (sorted_candidates.index(
(st, p, o)) + 1)
ranks.append(rank)
hitsat1 += (rank == 1)
hitsat3 += (rank <= 3)
hitsat10 += (rank <= 10)
mrr += 1.0 / rank
tseen += 1
mrr = mrr / tseen
hitsat1 = hitsat1 / tseen
hitsat3 = hitsat3 / tseen
hitsat10 = hitsat10 / tseen
prt(f'epoch {e}: MRR {mrr:.4}\t hits@1 {hitsat1:.4}\t hits@3 {hitsat3:.4}\t hits@10 {hitsat10:.4}'
)
prt(f' ranks : {ranks[:10]}')
test_mrrs.append(mrr)
print('training finished.')
temrrs = torch.tensor(test_mrrs)
print(
f'mean test MRR {temrrs.mean():.3} ({temrrs.std():.3}) \t{test_mrrs}'
)
#out = util.get_linecount(fname, timeit=True)
util.tic('Loading tweets w/ %s' % hashtag)
tweet_text = []
tweet_addr = []
i = 0
filestream = open(fname, 'r')
for line in filestream:
tweet = json.loads(line)
tweet_content = tweet['title']
user_location = tweet['tweet']['user']['location']
if from_washington(user_location):
tweet_text.append(tweet_content)
tweet_addr.append(1)
elif from_massachusetts(user_location):
tweet_text.append(tweet_content)
tweet_addr.append(-1)
#print tweet_content
i += 1
if i % 10000 == 0:
print "Loading tweet #{}".format(i)
filestream.close()
util.toc()
def cluster_n_analyze(dim=2):
print "Dimension = %d" % dim
# reducing dimensions
print "Reducing dimensions..."
util.tic()
normalizer = Normalizer(copy=False)
svd_cls = TruncatedSVD(n_components=dim,
n_iter=10,
random_state=random_state)
nmf_cls = NMF(n_components=dim, init='random', random_state=random_state)
X_dim_red = {}
#svd = make_pipeline(svd_cls, normalizer) if normalize else svd_cls
svd = make_pipeline(normalizer, svd_cls) if normalize else svd_cls
X_dim_red['SVD'] = svd.fit_transform(X_tfidf)
print svd_cls.explained_variance_ratio_
#nmf = make_pipeline(nmf_cls, normalizer) if normalize else nmf_cls
nmf = make_pipeline(normalizer, nmf_cls) if normalize else nmf_cls
X_dim_red['NMF'] = nmf.fit_transform(X_tfidf)
#print X_dim_red['SVD'][0]
util.toc()
# apply non-linear transformation here
if transform_method == 'exp':
X_dim_red['SVD'] = np.exp(X_dim_red['SVD'])
X_dim_red['NMF'] = np.exp(X_dim_red['NMF'])
elif transform_method == 'sqrt':
X_dim_red['NMF'] = np.sqrt(X_dim_red['NMF'])
elif transform_method == 'log':
X_dim_red['NMF'] = util.clamp(-10, np.log(X_dim_red['NMF']), 10)
elif transform_method == 'customized':
# different transformation to SVD and NMF
X_dim_red['SVD'] += np.max(X_dim_red['SVD'])
X_dim_red['SVD'] = X_dim_red['SVD']**2
X_dim_red['NMF'] = util.clamp(-10, np.log(X_dim_red['NMF']), 10)
# clustering
#print X_dim_red['SVD'][0]
print "Clustering..."
util.tic()
kmeans = {}
kmeans['SVD'] = KMeans(n_clusters=2,
random_state=random_state).fit(X_dim_red['SVD'])
kmeans['NMF'] = KMeans(n_clusters=2,
random_state=random_state).fit(X_dim_red['NMF'])
util.toc()
# Purity statistics
print "Purity stats report:"
print "Dimension = %d" % dim
for method in ['SVD', 'NMF']:
scores = []
scores.append(homogeneity_score(y_true, kmeans[method].labels_))
scores.append(completeness_score(y_true, kmeans[method].labels_))
scores.append(adjusted_rand_score(y_true, kmeans[method].labels_))
scores.append(
adjusted_mutual_info_score(y_true, kmeans[method].labels_))
# document statistics
if method not in perf_stats:
perf_stats[method] = [[], [], [], []]
for idx, arr in enumerate(perf_stats[method]):
arr.append(scores[idx])
perf_stats[method][idx] = arr
# print...
print "======== Method: %s ========" % method
print "Confusion Matrix:"
print metrics.confusion_matrix(y_true, kmeans[method].labels_)
print "Homogeneity_score = {:4f}".format(scores[0])
print "Completeness_score = {:4f}".format(scores[1])
print "Adjusted_rand_score = {:4f}".format(scores[2])
print "Adjusted_mutual_info_score = {:4f}".format(scores[3])
# stop if no visualization is needed
if not visualize:
return
# Visualization
for method in ['SVD', 'NMF']:
print method
xs, ys = [[], []], [[], []]
xt, yt = [[], []], [[], []]
xe0, ye0 = [], []
xe1, ye1 = [], []
labels = kmeans[method].labels_
# switch group if confusion matrix proved it to be a better match
conf_mat = metrics.confusion_matrix(y_true, kmeans[method].labels_)
if conf_mat[0][0] + conf_mat[1][1] < conf_mat[0][1] + conf_mat[1][0]:
# since it only contains 0 and 1...
labels = [1 - x for x in labels]
for idx, val in enumerate(X_dim_red[method]):
# projection: may find some other method
xval = val[0]
yval = val[1]
label = labels[idx]
truth = y_true[idx]
if label == 0 and truth == 1:
# errorneously put into category 0
xe0.append(xval)
ye0.append(yval)
elif label == 1 and truth == 0:
# errorneously put into category 1
xe1.append(xval)
ye1.append(yval)
xs[label].append(xval)
ys[label].append(yval)
xt[truth].append(xval)
yt[truth].append(yval)
#if method == 'NMF':
# plt.xscale('log')
# plt.yscale('log')
plt.figure()
plt.scatter(xs[0],
ys[0],
c='r' if colorcode else 'k',
marker=',',
lw=0,
s=1)
plt.scatter(xs[1],
ys[1],
c='b' if colorcode else 'k',
marker=',',
lw=0,
s=1)
if not showtrue and colorcode:
plt.scatter(xe0, ye0, c='g', marker=',', lw=0, s=1)
plt.scatter(xe1, ye1, c='y', marker=',', lw=0, s=1)
optional_str = ": kmeans\n" if showtrue else ""
plt.title("%s%s" % (method, optional_str))
transf_opt = 'pre_transf' if transform_method == 'none' else 'post_transf'
plt.savefig('scatter_%s_dim%d_%s.png' % (method, dim, transf_opt))
plt.show()
if showtrue:
plt.figure()
plt.scatter(xt[0], yt[0], c='r', marker=',', lw=0, s=1)
plt.scatter(xt[1], yt[1], c='b', marker=',', lw=0, s=1)
plt.title("%s: true\ndim = %d" % (method, dim))
plt.show()
def go(arg):
if arg.seed < 0:
seed = random.randint(0, 1000000)
print('random seed: ', seed)
else:
torch.manual_seed(arg.seed)
tbw = SummaryWriter(log_dir=arg.tb_dir) # Tensorboard logging
# load the data (validation unless arg.final is true, then test)
arg.data = here('data/enwik8.gz') if arg.data is None else arg.data
data_train, data_val, data_test = enwik8(arg.data)
data_train, data_test = (torch.cat([data_train, data_val], dim=0), data_test) \
if arg.final else (data_train, data_val)
# create the model
model = GTransformer(emb=arg.embedding_size,
heads=arg.num_heads,
depth=arg.depth,
seq_length=arg.context,
num_tokens=NUM_TOKENS,
attention_type=arg.attention_type)
if torch.cuda.is_available():
model.cuda()
opt = torch.optim.Adam(lr=arg.lr, params=model.parameters())
# Linear learning rate warmup
sch = torch.optim.lr_scheduler.LambdaLR(
opt, lambda i: min(i / (arg.lr_warmup / arg.batch_size), 1.0))
# Training loop
# -- We don't loop over the data, instead we sample a batch of random subsequences each time. This is not strictly
# better or worse as a training method, it's just a little simpler.
#
instances_seen = 0
for i in tqdm.trange(arg.num_batches):
opt.zero_grad()
source, target = sample_batch(data_train,
length=arg.context,
batch_size=arg.batch_size)
instances_seen += source.size(0)
if torch.cuda.is_available():
source, target = source.cuda(), target.cuda()
tic()
output = model(source) # forward pass
t = toc()
# Compute the loss
loss = F.nll_loss(output.transpose(2, 1), target, reduction='mean')
tbw.add_scalar('transformer/train-loss',
float(loss.item()) * LOG2E, i * arg.batch_size,
instances_seen)
tbw.add_scalar('transformer/time-forward', t, instances_seen)
loss.backward() # backward pass
# clip gradients
# -- If the total gradient vector has a length > x, we clip it back down to x.
if arg.gradient_clipping > 0.0:
nn.utils.clip_grad_norm_(model.parameters(), arg.gradient_clipping)
opt.step() # stochastic gradient descent step
sch.step() # update the learning rate
# Validate every `arg.test_every` steps. First we compute the
# compression on the validation data (or a subset),
# then we generate some random text to monitor progress.
if i != 0 and (i % arg.test_every == 0 or i == arg.num_batches - 1):
with torch.no_grad():
## Sample and print a random sequence
# Slice a random seed from the test data, and sample a continuation from the model.
seedfr = random.randint(0, data_test.size(0) - arg.context)
seed = data_test[seedfr:seedfr + arg.context].to(torch.long)
if torch.cuda.is_available():
seed = seed.cuda()
sample_sequence(model,
seed=seed,
max_context=arg.context,
verbose=True,
length=arg.sample_length)
## Compute validation bits per byte
upto = data_test.size(
0) if i == arg.num_batches - 1 else arg.test_subset
data_sub = data_test[:upto]
bits_per_byte = compute_compression(
model,
data_sub,
context=arg.context,
batch_size=arg.test_batchsize)
# -- Since we're not computing gradients, we can increase the batch size a little from what we used in
# training.
print(f'epoch{i}: {bits_per_byte:.4} bits per byte')
tbw.add_scalar(f'transformer/eval-loss', bits_per_byte,
i * arg.batch_size, instances_seen)
def go(arg):
global repeats
repeats = arg.repeats
tbdir = arg.tb_dir if arg.tb_dir is not None else os.path.join('./runs', get_slug(arg))[:250]
tbw = SummaryWriter(log_dir=tbdir)
dev = 'cuda' if torch.cuda.is_available() else 'cpu'
test_mrrs = []
train, val, test, (n2i, i2n), (r2i, i2r) = \
embed.load(arg.name)
# set of all triples (for filtering)
alltriples = set()
for s, p, o in torch.cat([train, val, test], dim=0):
s, p, o = s.item(), p.item(), o.item()
alltriples.add((s, p, o))
truedicts = util.truedicts(alltriples)
if arg.final:
train, test = torch.cat([train, val], dim=0), test
else:
train, test = train, val
subjects = torch.tensor(list({s for s, _, _ in train}), dtype=torch.long, device=d())
predicates = torch.tensor(list({p for _, p, _ in train}), dtype=torch.long, device=d())
objects = torch.tensor(list({o for _, _, o in train}), dtype=torch.long, device=d())
ccandidates = (subjects, predicates, objects)
print(len(i2n), 'nodes')
print(len(i2r), 'relations')
print(train.size(0), 'training triples')
print(test.size(0), 'test triples')
print(train.size(0) + test.size(0), 'total triples')
for r in tqdm.trange(repeats) if repeats > 1 else range(repeats):
"""
Define model
"""
model = embed.LinkPredictor(
triples=train, n=len(i2n), r=len(i2r), embedding=arg.emb, biases=arg.biases,
edropout = arg.edo, rdropout=arg.rdo, decoder=arg.decoder, reciprocal=arg.reciprocal,
init_method=arg.init_method, init_parms=arg.init_parms)
if torch.cuda.is_available():
prt('Using CUDA.')
model.cuda()
if arg.opt == 'adam':
opt = torch.optim.Adam(model.parameters(), lr=arg.lr)
elif arg.opt == 'adamw':
opt = torch.optim.AdamW(model.parameters(), lr=arg.lr)
elif arg.opt == 'adagrad':
opt = torch.optim.Adagrad(model.parameters(), lr=arg.lr)
elif arg.opt == 'sgd':
opt = torch.optim.SGD(model.parameters(), lr=arg.lr, nesterov=True, momentum=arg.momentum)
else:
raise Exception()
sched = torch.optim.lr_scheduler.ReduceLROnPlateau(patience=arg.patience, optimizer=opt, mode='max', factor=0.95, threshold=0.0001) \
if arg.sched else None
#-- defaults taken from libkge
# nr of negatives sampled
weight = torch.tensor([arg.nweight, 1.0], device=d()) if arg.nweight else None
seen = 0
for e in range(arg.epochs):
seeni, sumloss = 0, 0.0
tforward = tbackward = 0
rforward = rbackward = 0
tprep = tloss = 0
tic()
for fr in trange(0, train.size(0), arg.batch):
to = min(train.size(0), fr + arg.batch)
model.train(True)
opt.zero_grad()
positives = train[fr:to].to(d())
for ctarget in [0, 1, 2]: # which part of the triple to corrupt
ng = arg.negative_rate[ctarget]
if ng > 0:
with torch.no_grad():
bs, _ = positives.size()
tic()
if arg.limit_negatives:
cand = ccandidates[ctarget]
mx = cand.size(0)
idx = torch.empty(bs, ng, dtype=torch.long, device=d()).random_(0, mx)
corruptions = cand[idx]
else:
mx = len(i2r) if ctarget == 1 else len(i2n)
corruptions = torch.empty(bs, ng, dtype=torch.long, device=d()).random_(0, mx)
tprep += toc()
s, p, o = positives[:, 0:1], positives[:, 1:2], positives[:, 2:3]
if ctarget == 0:
s = torch.cat([s, corruptions], dim=1)
if ctarget == 1:
p = torch.cat([p, corruptions], dim=1)
if ctarget == 2:
o = torch.cat([o, corruptions], dim=1)
# -- NB: two of the index vectors s, p o are now size (bs, 1) and the other is (bs, ng+1)
# We will let the model broadcast these to give us a score tensor of (bs, ng+1)
# In most cases we can optimize the decoder to broadcast late for better speed.
if arg.loss == 'bce':
labels = torch.cat([torch.ones(bs, 1, device=d()), torch.zeros(bs, ng, device=d())], dim=1)
elif arg.loss == 'ce':
labels = torch.zeros(bs, dtype=torch.long, device=d())
# -- CE loss treats the problem as a multiclass classification problem: for a positive triple,
# together with its k corruptions, identify which is the true triple. This is always triple 0.
# (It may seem like the model could easily cheat by always choosing triple 0, but the score
# function is order equivariant, so it can't choose by ordering.)
recip = None if not arg.reciprocal else ('head' if ctarget == 0 else 'tail')
# -- We use the tail relations if the target is the relation (usually p-corruption is not used)
tic()
out = model(s, p, o, recip=recip)
tforward += toc()
assert out.size() == (bs, ng + 1), f'{out.size()=} {(bs, ng + 1)=}'
tic()
if arg.loss == 'bce':
loss = F.binary_cross_entropy_with_logits(out, labels, weight=weight, reduction=arg.lred)
elif arg.loss == 'ce':
loss = F.cross_entropy(out, labels, reduction=arg.lred)
assert not torch.isnan(loss), 'Loss has become NaN'
sumloss += float(loss.item())
seen += bs; seeni += bs
tloss += toc()
tic()
loss.backward()
tbackward += toc()
# No step yet, we accumulate the gradients over all corruptions.
# -- this causes problems with modules like batchnorm, so be careful when porting.
tic()
regloss = None
if arg.reg_eweight is not None:
regloss = model.penalty(which='entities', p=arg.reg_exp, rweight=arg.reg_eweight)
if arg.reg_rweight is not None:
regloss = model.penalty(which='relations', p=arg.reg_exp, rweight=arg.reg_rweight)
rforward += toc()
tic()
if regloss is not None:
sumloss += float(regloss.item())
regloss.backward()
rbackward += toc()
opt.step()
tbw.add_scalar('biases/train_loss', float(loss.item()), seen)
if e == 0:
print(f'\n pred: forward {tforward:.4}, backward {tbackward:.4}')
print (f' reg: forward {rforward:.4}, backward {rbackward:.4}')
print (f' prep {tprep:.4}, loss {tloss:.4}')
print (f' total: {toc():.4}')
# -- NB: these numbers will not be accurate for GPU runs unless CUDA_LAUNCH_BLOCKING is set to 1
# Evaluate
if ((e+1) % arg.eval_int == 0) or e == arg.epochs - 1:
with torch.no_grad():
model.train(False)
if arg.eval_size is None:
testsub = test
else:
testsub = test[random.sample(range(test.size(0)), k=arg.eval_size)]
mrr, hits, ranks = util.eval(
model=model, valset=testsub, truedicts=truedicts, n=len(i2n),
batch_size=arg.test_batch, verbose=True)
if arg.check_simple: # double-check using a separate, slower implementation
mrrs, hitss, rankss = util.eval_simple(
model=model, valset=testsub, alltriples=alltriples, n=len(i2n), verbose=True)
assert ranks == rankss
assert mrr == mrrs
print(f'epoch {e}: MRR {mrr:.4}\t hits@1 {hits[0]:.4}\t hits@3 {hits[1]:.4}\t hits@10 {hits[2]:.4}')
tbw.add_scalar('biases/mrr', mrr, e)
tbw.add_scalar('biases/h@1', hits[0], e)
tbw.add_scalar('biases/h@3', hits[1], e)
tbw.add_scalar('biases/h@10', hits[2], e)
if sched is not None:
sched.step(mrr) # reduce lr if mrr stalls
test_mrrs.append(mrr)
print('training finished.')
temrrs = torch.tensor(test_mrrs)
print(f'mean test MRR {temrrs.mean():.3} ({temrrs.std():.3}) \t{test_mrrs}')
def solve(
inputs='inputs', outputs='outputs',
rps=True, renewables=True,
demand_response=False,
ev=None,
pumped_hydro=False, ph_year=None, ph_mw=None,
tag=None,
thread=None, nthreads=3
):
# load and solve the model, using specified configuration
# NOTE: this version solves repeatedly with different DR targets
global switch_model, switch_instance, results, output_dir
modules = ['switch_mod', 'fuel_cost', 'project.no_commit', 'switch_patch', 'batteries']
if rps:
modules.append('rps')
if not renewables:
modules.append('no_renewables')
if demand_response:
modules.append('simple_dr')
# repeat with a range of DR shares
all_dr_shares = [0.00, 0.20, 0.40, 0.05, 0.15, 0.25, 0.35, 0.30, 0.10]
if thread is None:
dr_shares = all_dr_shares
else:
# take every nth element from all_dr_shares, starting with element i, where i=thread (1-based) and n=nthreads
dr_shares = [all_dr_shares[x] for x in range(thread-1, len(all_dr_shares), nthreads)]
else: # no_demand_response
dr_shares = [0.00]
if ev is None:
# not specified, leave out ev's
pass
elif ev:
# user asked for ev
modules.append('ev')
else:
# user asked for no_ev (count transport emissions but don't allow EVs)
modules.append('no_ev')
if pumped_hydro:
modules.append('pumped_hydro')
log('using modules: {m}\n'.format(m=modules))
log("defining model... "); tic()
switch_model = define_AbstractModel(*modules)
switch_model.iis = Suffix(direction=Suffix.IMPORT)
switch_model.dual = Suffix(direction=Suffix.IMPORT)
# force construction of a fixed amount of pumped hydro
if ph_mw is not None:
print "Forcing construction of {m} MW of pumped hydro.".format(m=ph_mw)
switch_model.Build_Pumped_Hydro_MW = Constraint(switch_model.LOAD_ZONES, rule=lambda m, z:
m.Pumped_Hydro_Capacity_MW[z, m.PERIODS.last()] == ph_mw
)
# force construction of pumped hydro only in a certain period
if ph_year is not None:
print "Allowing construction of pumped hydro only in {p}.".format(p=ph_year)
switch_model.Build_Pumped_Hydro_Year = Constraint(
switch_model.LOAD_ZONES, switch_model.PERIODS,
rule=lambda m, z, p:
m.BuildPumpedHydroMW[z, p] == 0 if p != ph_year else Constraint.Skip
)
toc() # done defining model
log("loading model data from {} dir... ".format(inputs)); tic()
switch_instance = switch_model.load_inputs(inputs_dir=inputs)
toc()
output_dir = outputs
setup_results_dir()
create_batch_results_file(switch_instance, tag=tag)
log("dr_shares = " + str(dr_shares) + "\n")
for dr_share in dr_shares:
if demand_response:
switch_instance.demand_response_max_share = dr_share
switch_instance.preprocess()
tic()
log("solving model with max DR={dr}...\n".format(dr=dr_share))
results = opt.solve(switch_instance, keepfiles=False, tee=True, # options='dualopt', # not sure how to put this in opt.options
symbolic_solver_labels=True, suffixes=['dual', 'iis'])
log("Solver finished; "); toc()
# results.write()
log("loading solution... "); tic()
# Pyomo changed their interface for loading results somewhere
# between 4.0.x and 4.1.x in a way that was not backwards compatible.
# Make the code accept either version
if hasattr(switch_instance, 'solutions'):
# Works in Pyomo version 4.1.x
switch_instance.solutions.load_from(results)
else:
# Works in Pyomo version 4.0.9682
switch_instance.load(results)
toc()
if results.solver.termination_condition == TerminationCondition.infeasible:
print "Model was infeasible; Irreducible Infeasible Set (IIS) returned by solver:"
print "\n".join(c.cname() for c in switch_instance.iis)
if util.interactive_session:
print "Unsolved model is available as switch_instance."
raise RuntimeError("Infeasible model")
if util.interactive_session:
print "Model solved successfully."
print "Solved model is available as switch_instance."
print "\n\n======================================================="
print "Solved model"
print "======================================================="
print "Total cost: ${v:,.0f}".format(v=value(switch_instance.Minimize_System_Cost))
if pumped_hydro:
switch_instance.BuildPumpedHydroMW.pprint()
append_batch_results(switch_instance, tag=tag)
t = "" if tag is None else str(tag) + "_"
write_results(switch_instance, tag=t+'dr_share_'+str(dr_share))
def solve(
inputs_dir='inputs', inputs_subdir='', outputs_dir='outputs',
rps=True, renewables=True, wind=None, central_pv=None,
batteries=True,
demand_response_simple=True, dr_shares=[0.3],
ev=True,
pumped_hydro=True, ph_year=None, ph_mw=None,
hydrogen=True,
fed_subsidies=False,
biofuel_limit=0.05,
ev_flat=False,
scenario_name=None, tag=None
):
# load and solve the model, using specified configuration
# NOTE: this version solves repeatedly with different DR targets
global switch_model, switch_instance, results, output_dir
# quick fix to use scenario name and (optional) tag
tag = None if scenario_name is None else append_tag(scenario_name, tag)
# quick fix for inputs_dir / inputs_subdir
inputs_dir = os.path.join(inputs_dir, inputs_subdir)
modules = ['switch_mod', 'fuel_markets', 'fuel_markets_expansion', 'project.no_commit',
'switch_patch', 'rps']
modules.append('emission_rules') # no burning LSFO after 2017 except in cogen plants
for m in ['ev', 'pumped_hydro', 'fed_subsidies', 'demand_response_simple', 'hydrogen', 'batteries']:
if locals()[m] is True:
modules.append(m)
if demand_response_simple is not True:
dr_shares = [0.00]
# TODO: treat the 'no_*' modules as standard scenario names
# (i.e., include no_renewables, etc. instead of excluding renewables, etc.)
if renewables is False:
modules.append('no_renewables')
if wind is False:
modules.append('no_wind')
if central_pv is False:
modules.append('no_central_pv')
if ev is False:
# user asked for no_ev (count transport emissions but don't allow EVs)
modules.append('no_ev')
log('using modules: {m}\n'.format(m=modules))
log("defining model... "); tic()
switch_model = define_AbstractModel(*modules)
switch_model.iis = Suffix(direction=Suffix.IMPORT)
switch_model.dual = Suffix(direction=Suffix.IMPORT)
# TODO: put scenario flags into a switch_model.config dictionary and then
# do the following model modifications within the respective modules.
# force construction of a fixed amount of pumped hydro
if ph_mw is not None:
print "Forcing construction of {m} MW of pumped hydro.".format(m=ph_mw)
switch_model.Build_Pumped_Hydro_MW = Constraint(switch_model.LOAD_ZONES, rule=lambda m, z:
m.Pumped_Hydro_Capacity_MW[z, m.PERIODS.last()] == ph_mw
)
# force construction of pumped hydro only in a certain period
if ph_year is not None:
print "Allowing construction of pumped hydro only in {p}.".format(p=ph_year)
switch_model.Build_Pumped_Hydro_Year = Constraint(
switch_model.PH_PROJECTS, switch_model.PERIODS,
rule=lambda m, pr, pe:
m.BuildPumpedHydroMW[pr, pe] == 0 if pe != ph_year else Constraint.Skip
)
if biofuel_limit is not None:
print "Limiting (bio)fuels to {l}% of electricity production.".format(l=biofuel_limit*100.0)
switch_model.rps_fuel_limit = biofuel_limit
if ev_flat and ev:
print "Charging EVs as baseload."
switch_model.ChargeEVs_flat = Constraint(
switch_model.LOAD_ZONES, switch_model.TIMEPOINTS,
rule=lambda m, z, tp:
m.ChargeEVs[z, tp] * m.ts_duration_hrs[m.tp_ts[tp]] == m.ev_mwh_ts[z, m.tp_ts[tp]]
)
# add an alternative objective function that smoothes out various non-cost variables
def Smooth_Free_Variables_obj_rule(m):
# minimize production (i.e., maximize curtailment / minimize losses)
obj = sum(
getattr(m, component)[lz, t]
for lz in m.LOAD_ZONES
for t in m.TIMEPOINTS
for component in m.LZ_Energy_Components_Produce)
# also minimize the magnitude of demand adjustments
if hasattr(m, "DemandResponse"):
print "Will smooth DemandResponse."
obj = obj + sum(m.DemandResponse[z, t]*m.DemandResponse[z, t] for z in m.LOAD_ZONES for t in m.TIMEPOINTS)
# also minimize the magnitude of EV charging
if hasattr(m, "ChargeEVs"):
print "Will smooth EV charging."
obj = obj + sum(m.ChargeEVs[z, t]*m.ChargeEVs[z, t] for z in m.LOAD_ZONES for t in m.TIMEPOINTS)
return obj
switch_model.Smooth_Free_Variables = Objective(rule=Smooth_Free_Variables_obj_rule, sense=minimize)
toc() # done defining model
log("loading model data from {} dir... ".format(inputs_dir)); tic()
switch_instance = switch_model.load_inputs(inputs_dir=inputs_dir)
toc()
if rps is False:
# deactivate the main RPS constraint
# (we do this instead of omitting the whole RPS module,
# so we can report RPS-qualified power even if the RPS is not in effect)
# NOTE: for now, there's no easy way to pass solver flags into individual modules
# which would probably be a cleaner solution
switch_instance.RPS_Enforce.deactivate()
switch_instance.preprocess()
# investigate the cost_components_annual elements
# import pdb; pdb.set_trace()
output_dir = outputs_dir # assign to global variable with slightly different name (ugh)
setup_results_dir()
create_batch_results_file(switch_instance, scenario=tag)
log("dr_shares = " + str(dr_shares) + "\n")
for dr_share in dr_shares:
if demand_response_simple:
switch_instance.demand_response_max_share = dr_share
switch_instance.preprocess()
log("solving model with max DR={dr}...\n".format(dr=dr_share))
# make sure the minimum-cost objective is in effect
switch_instance.Smooth_Free_Variables.deactivate()
switch_instance.Minimize_System_Cost.activate()
results = _solve(switch_instance)
if results.solver.termination_condition == TerminationCondition.infeasible:
print "Model was infeasible; Irreducible Infeasible Set (IIS) returned by solver:"
print "\n".join(c.cname() for c in switch_instance.iis)
if util.interactive_session:
print "Unsolved model is available as switch_instance."
raise RuntimeError("Infeasible model")
append_batch_results(switch_instance, scenario=tag+'_unsmooth')
if len(dr_shares) > 1:
t = ("" if tag is None else str(tag) + '_') + 'dr_share_' + str(dr_share)
else:
t = tag
if solver == "cplex":
# Freeze all direct-cost variables, and then solve the model against
# a smoothing objective instead of a cost objective.
# (only applied for quadratic solvers, i.e., cplex)
write_results(switch_instance, tag=t+'_unsmooth') # keep pre-smoothing results, in case smoothing crashes
old_duals = [
(z, t, switch_instance.dual[switch_instance.Energy_Balance[z, t]])
for z in switch_instance.LOAD_ZONES
for t in switch_instance.TIMEPOINTS]
fix_obj_expression(switch_instance.Minimize_System_Cost)
switch_instance.Minimize_System_Cost.deactivate()
switch_instance.Smooth_Free_Variables.activate()
switch_instance.preprocess()
log("smoothing free variables...\n")
results = _solve(switch_instance)
# restore hourly duals from the original solution
for (z, t, d) in old_duals:
switch_instance.dual[switch_instance.Energy_Balance[z, t]] = d
# unfix the variables
fix_obj_expression(switch_instance.Minimize_System_Cost, False)
log("finished smoothing free variables; "); toc()
if util.interactive_session:
print "Model solved successfully."
print "Solved model is available as switch_instance."
print "\n\n======================================================="
print "Solved model"
print "======================================================="
print "Total cost: ${v:,.0f}".format(v=value(switch_instance.Minimize_System_Cost))
# if pumped_hydro:
# switch_instance.BuildPumpedHydroMW.pprint()
if hasattr(switch_instance, "ChargeBattery"):
double_charge = [
(
z, t,
switch_instance.ChargeBattery[z, t].value,
switch_instance.DischargeBattery[z, t].value
)
for z in switch_instance.LOAD_ZONES
for t in switch_instance.TIMEPOINTS
if switch_instance.ChargeBattery[z, t].value > 0
and switch_instance.DischargeBattery[z, t].value > 0
]
if len(double_charge) > 0:
print ""
print "WARNING: batteries are simultaneously charged and discharged in some hours."
print "This is usually done to relax the biofuel limit."
for (z, t, c, d) in double_charge:
print 'ChargeBattery[{z}, {t}]={c}, DischargeBattery[{z}, {t}]={d}'.format(
z=z, t=switch_instance.tp_timestamp[t],
c=c, d=d
)
append_batch_results(switch_instance, scenario=tag)
if len(dr_shares) > 1:
t = ("" if tag is None else str(tag) + '_') + 'dr_share_' + str(dr_share)
else:
t = tag
write_results(switch_instance, tag=t)
def solve(
inputs='inputs',
rps=True, demand_response=True, renewables=True, ev=None, pumped_hydro=True,
ph_year=None, ph_mw=None,
tag=None
):
global switch_model, switch_instance, results
modules = ['switch_mod', 'fuel_cost', 'project.no_commit', 'switch_patch', 'batteries']
if rps:
modules.append('rps')
if not renewables:
modules.append('no_renewables')
if demand_response:
modules.append('simple_dr')
if ev is None:
# not specified, leave out ev's
pass
elif ev:
# user asked for ev
modules.append('ev')
else:
# user asked for no_ev
modules.append('no_ev')
if pumped_hydro:
modules.append('pumped_hydro')
log('using modules: {m}\n'.format(m=modules))
log("defining model... "); tic()
switch_model = define_AbstractModel(*modules)
switch_model.iis = Suffix(direction=Suffix.IMPORT)
switch_model.dual = Suffix(direction=Suffix.IMPORT)
# force construction of a fixed amount of pumped hydro
if pumped_hydro and ph_mw is not None:
print "Forcing construction of {m} MW of pumped hydro.".format(m=ph_mw)
switch_model.Build_Pumped_Hydro_MW = Constraint(switch_model.LOAD_ZONES, rule=lambda m, z:
m.Pumped_Hydro_Capacity_MW[z, m.PERIODS.last()] == ph_mw
)
# force construction of pumped hydro only in a certain period
if pumped_hydro and ph_year is not None:
print "Allowing construction of pumped hydro only in {p}.".format(p=ph_year)
switch_model.Build_Pumped_Hydro_Year = Constraint(
switch_model.LOAD_ZONES, switch_model.PERIODS,
rule=lambda m, z, p:
m.BuildPumpedHydroMW[z, p] == 0 if p != ph_year else Constraint.Skip
)
toc() # done defining model
log("loading model data from {} dir... ".format(inputs)); tic()
switch_instance = switch_model.load_inputs(inputs_dir=inputs)
toc()
log("solving model...\n"); tic()
results = opt.solve(switch_instance, keepfiles=False, tee=True,
symbolic_solver_labels=True, suffixes=['dual', 'iis'])
log("Solver finished; "); toc()
# results.write()
log("loading solution... "); tic()
# Pyomo changed their interface for loading results somewhere
# between 4.0.x and 4.1.x in a way that was not backwards compatible.
# Make the code accept either version
if hasattr(switch_instance, 'solutions'):
# Works in Pyomo version 4.1.x
switch_instance.solutions.load_from(results)
else:
# Works in Pyomo version 4.0.9682
switch_instance.load(results)
toc()
if results.solver.termination_condition == TerminationCondition.infeasible:
print "Model was infeasible; Irreducible Infeasible Set (IIS) returned by solver:"
print "\n".join(c.cname() for c in switch_instance.iis)
if util.interactive_session:
print "Unsolved model is available as switch_instance."
raise RuntimeError("Infeasible model")
if util.interactive_session:
print "Model solved successfully."
print "Solved model is available as switch_instance."
print "\n\n======================================================="
print "Solved model"
print "======================================================="
print "Total cost: ${v:,.0f}".format(v=value(switch_instance.Minimize_System_Cost))
if pumped_hydro:
switch_instance.BuildPumpedHydroMW.pprint()
write_results(switch_instance, tag=tag)
