1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169 | """
This experiment runs the hyperbolic tsne code on the MINNST data set changing several parameters:
- theta: [0.0, 0.1, 0.2, ..., 1.0]
For each configuration combination, it saves the embedding coordinates, a plot of the embedding, and
timing data for the iterations.
If a run does not finish, the results are not saved.
The code only computes the runs that do not have a folder.
"""
###########
# IMPORTS #
###########
import json
import traceback
from pathlib import Path
import numpy as np
from scipy.sparse import issparse, save_npz
from hyperbolicTSNE.quality_evaluation_ import hyperbolic_nearest_neighbor_preservation
from matplotlib import pyplot as plt
from hyperbolicTSNE import load_data, Datasets, SequentialOptimizer, initialization, HyperbolicTSNE
from hyperbolicTSNE.util import find_last_embedding
from hyperbolicTSNE.visualization import plot_poincare
#################################
# GENERAL EXPERIMENT PARAMETERS #
#################################
BASE_DIR = "../results/nnp_per_theta_MNIST"
DATASETS_DIR = "../datasets" # directory to read the data from
# Constants
SEED = 42 # seed to initialize random processes
PERP = 30 # perplexity value to be used throughout the experiments
VANILLA = False # whether to use momentum or not
EXAG = 12 # the factor by which the attractive forces are amplified during early exaggeration
hd_params = {"perplexity": PERP}
dataset = Datasets.MNIST # The dataset to run the experiment on
###################
# EXPERIMENT LOOP #
###################
dataX, dataLabels, D, V = load_data( # Load the data
dataset,
data_home=DATASETS_DIR,
random_state=SEED,
to_return="X_labels_D_V",
hd_params=hd_params
)
X_embedded = initialization( # create an initial embedding of the data into 2-dimensional space via PCA
n_samples=dataX.shape[0],
n_components=2,
X=dataX,
random_state=SEED,
method="pca"
)
# Save final embedding
_, ax = plt.subplots()
ax.set_title("Hyperbolic NNP")
ax.set_xlabel('Precision')
ax.set_ylabel('Recall')
LR = (dataX.shape[0] * 1) / (EXAG * 1000) # Compute the learning rate
for theta in [x / 10 for x in range(0, 11, 1)]: # Iterate over the different values for theta
print(f"[nnp_per_theta] Processing {dataset}, Theta: {theta}")
opt_params = SequentialOptimizer.sequence_poincare(
learning_rate_ex=LR, # specify learning rate for the early exaggeration
learning_rate_main=LR, # specify learning rate for the non-exaggerated gradient descent
exaggeration=EXAG,
vanilla=VANILLA,
momentum_ex=0.5, # momentum to be used during early exaggeration
momentum=0.8, # momentum to be used during non-exaggerated gradient descent
exact=False,
n_iter_check=10, # Needed for early stopping criterion
size_tol=0.999, # Size of the embedding to be used as early stopping criterion
angle=theta
)
run_dir = Path(f"{BASE_DIR}/theta_{theta}/")
if run_dir.exists():
# Skip already computed embeddings
print(f"[nnp_per_theta] - Exists so not computing it: {run_dir}")
else:
run_dir.mkdir(parents=True, exist_ok=True)
params = {
"lr": LR,
"perplexity": PERP,
"seed": SEED,
"theta": theta
}
print(f"[nnp_per_theta] - Starting with Theta: {theta}")
opt_params["logging_dict"] = {
"log_path": str(run_dir.joinpath("embeddings"))
}
# Save the high-dimensional neighborhood matrices for later use
json.dump(params, open(run_dir.joinpath("params.json"), "w"))
if issparse(D):
save_npz(run_dir.joinpath("D.npz"), D)
else:
np.save(run_dir.joinpath("D.npy"), D)
if issparse(V):
save_npz(run_dir.joinpath("P.npz"), V)
else:
np.save(run_dir.joinpath("P.npy"), V)
hdeo_hyper = HyperbolicTSNE( # Initialize an embedding object
init=X_embedded,
n_components=X_embedded.shape[1],
metric="precomputed",
verbose=2,
opt_method=SequentialOptimizer,
opt_params=opt_params
)
error_title = ""
try:
res_hdeo_hyper = hdeo_hyper.fit_transform((D, V)) # Compute the hyperbolic embedding
except ValueError:
error_title = "_error"
res_hdeo_hyper = find_last_embedding(opt_params["logging_dict"]["log_path"])
traceback.print_exc(file=open(str(run_dir) + "traceback.txt", "w"))
print("[nnp_per_theta] - Run failed ...")
else: # we save the data if there were no errors
print("[nnp_per_theta] - Finished running, saving run data directory ...")
# Save the final embedding coordinates
np.save(run_dir.joinpath("final_embedding.npy"), res_hdeo_hyper)
# Save a plot of the final embedding
fig = plot_poincare(res_hdeo_hyper, labels=dataLabels)
fig.savefig(run_dir.joinpath(f"final_embedding{error_title}.png"))
plt.close(fig)
np.save(run_dir.joinpath("logging_dict.npy"), opt_params["logging_dict"])
# Compute Precision and Recall values for the embedding
_, precisions, recalls, _ = hyperbolic_nearest_neighbor_preservation(
dataX,
res_hdeo_hyper,
k_start=1,
k_max=30,
D_X=None,
exact_nn=True,
consider_order=False,
strict=False,
to_return="full"
)
np.save(run_dir.joinpath(f"precisions_theta_{theta}.npy"), precisions)
np.save(run_dir.joinpath(f"recalls_theta_{theta}.npy"), recalls)
print()
|