Upload app.py with huggingface_hub
Browse files
app.py
CHANGED
@@ -1,168 +1,137 @@
|
|
1 |
import spaces
|
2 |
-
import gradio as gr
|
3 |
-
import torch
|
4 |
|
5 |
-
|
6 |
-
import pandas as pd
|
7 |
-
import random
|
8 |
-
import io
|
9 |
-
import imageio
|
10 |
import os
|
|
|
|
|
|
|
|
|
|
|
11 |
import tempfile
|
12 |
import atexit
|
13 |
-
import glob
|
14 |
-
import csv
|
15 |
from datetime import datetime
|
16 |
-
import json
|
17 |
|
|
|
|
|
|
|
|
|
|
|
18 |
from rdkit import Chem
|
19 |
from rdkit.Chem import Draw
|
|
|
20 |
|
|
|
21 |
from evaluator import Evaluator
|
22 |
from loader import load_graph_decoder
|
23 |
|
24 |
-
#
|
25 |
-
|
26 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
27 |
|
28 |
-
|
29 |
|
30 |
-
#
|
31 |
-
evaluators = {prop: Evaluator(f'evaluators/{prop}.joblib', prop) for prop in all_properties}
|
32 |
|
33 |
-
|
34 |
-
|
|
|
35 |
|
36 |
-
|
37 |
-
|
|
|
|
|
|
|
38 |
|
39 |
def cleanup_temp_files():
|
40 |
"""Clean up temporary GIF files on exit."""
|
41 |
-
for file in glob.glob(os.path.join(temp_dir, "*.gif")):
|
42 |
-
try:
|
43 |
-
os.remove(file)
|
44 |
-
except Exception as e:
|
45 |
-
print(f"Error deleting {file}: {e}")
|
46 |
try:
|
|
|
|
|
47 |
os.rmdir(temp_dir)
|
48 |
except Exception as e:
|
49 |
-
print(f"Error
|
50 |
|
51 |
-
# Register the cleanup function to be called on exit
|
52 |
atexit.register(cleanup_temp_files)
|
53 |
|
|
|
|
|
54 |
def random_properties():
|
55 |
-
|
|
|
56 |
|
57 |
def load_model(model_choice):
|
|
|
58 |
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
|
59 |
model = load_graph_decoder(path=model_choice)
|
60 |
-
|
61 |
-
|
62 |
-
# Create a flagged folder if it doesn't exist
|
63 |
-
flagged_folder = "flagged"
|
64 |
-
os.makedirs(flagged_folder, exist_ok=True)
|
65 |
|
66 |
def save_interesting_log(smiles, properties, suggested_properties):
|
67 |
-
"""Save interesting polymer data to a CSV file."""
|
68 |
-
log_file = os.path.join(
|
|
|
69 |
file_exists = os.path.isfile(log_file)
|
70 |
-
|
71 |
-
with open(log_file, 'a', newline='') as csvfile:
|
72 |
-
fieldnames = ['timestamp', 'smiles'] + all_properties + [f'suggested_{prop}' for prop in all_properties]
|
73 |
-
writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
|
74 |
-
|
75 |
-
if not file_exists:
|
76 |
-
writer.writeheader()
|
77 |
-
|
78 |
-
log_data = {
|
79 |
-
'timestamp': datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
|
80 |
-
'smiles': smiles,
|
81 |
-
**{prop: value for prop, value in zip(all_properties, properties)},
|
82 |
-
**{f'suggested_{prop}': value for prop, value in suggested_properties.items()}
|
83 |
-
}
|
84 |
-
writer.writerow(log_data)
|
85 |
-
|
86 |
-
@spaces.GPU
|
87 |
-
def generate_graph(CH4, CO2, H2, N2, O2, guidance_scale, num_nodes, repeating_time, model_state, num_chain_steps, fps):
|
88 |
-
print('in generate_graph')
|
89 |
-
model, device = model_state
|
90 |
-
|
91 |
-
properties = [CH4, CO2, H2, N2, O2]
|
92 |
-
|
93 |
-
def is_nan_like(x):
|
94 |
-
return x == 0 or x == '' or (isinstance(x, float) and np.isnan(x))
|
95 |
-
|
96 |
-
properties = [None if is_nan_like(prop) else prop for prop in properties]
|
97 |
-
|
98 |
-
nan_message = "The following gas properties were treated as NaN: "
|
99 |
-
nan_gases = [gas for gas, prop in zip(all_properties, properties) if prop is None]
|
100 |
-
nan_message += ", ".join(nan_gases) if nan_gases else "None"
|
101 |
|
102 |
-
|
103 |
-
|
104 |
-
for _ in range(repeating_time):
|
105 |
-
# try:
|
106 |
-
model.to(device)
|
107 |
-
generated_molecule, img_list = model.generate(properties, device=device, guide_scale=guidance_scale, num_nodes=num_nodes, number_chain_steps=num_chain_steps)
|
108 |
-
|
109 |
-
# Create GIF if img_list is available
|
110 |
-
gif_path = None
|
111 |
-
if img_list and len(img_list) > 0:
|
112 |
-
imgs = [np.array(pil_img) for pil_img in img_list]
|
113 |
-
imgs.extend([imgs[-1]] * 10)
|
114 |
-
gif_path = os.path.join(temp_dir, f"polymer_gen_{random.randint(0, 999999)}.gif")
|
115 |
-
imageio.mimsave(gif_path, imgs, format='GIF', fps=fps, loop=0)
|
116 |
-
|
117 |
-
if generated_molecule is not None:
|
118 |
-
mol = Chem.MolFromSmiles(generated_molecule)
|
119 |
-
if mol is not None:
|
120 |
-
standardized_smiles = Chem.MolToSmiles(mol, isomericSmiles=True)
|
121 |
-
is_novel = standardized_smiles not in knwon_smiles['SMILES'].values
|
122 |
-
novelty_status = "Novel (Not in Labeled Set)" if is_novel else "Not Novel (Exists in Labeled Set)"
|
123 |
-
img = Draw.MolToImage(mol)
|
124 |
-
|
125 |
-
# Evaluate the generated molecule
|
126 |
-
suggested_properties = {}
|
127 |
-
for prop, evaluator in evaluators.items():
|
128 |
-
suggested_properties[prop] = evaluator([standardized_smiles])[0]
|
129 |
-
|
130 |
-
suggested_properties_text = "\n".join([f"**Suggested {prop}:** {value:.2f}" for prop, value in suggested_properties.items()])
|
131 |
-
|
132 |
-
return (
|
133 |
-
f"**Generated polymer SMILES:** `{standardized_smiles}`\n\n"
|
134 |
-
f"**{nan_message}**\n\n"
|
135 |
-
f"**{novelty_status}**\n\n"
|
136 |
-
f"**Suggested Properties:**\n{suggested_properties_text}",
|
137 |
-
img,
|
138 |
-
gif_path,
|
139 |
-
properties, # Add this
|
140 |
-
suggested_properties # Add this
|
141 |
-
)
|
142 |
-
else:
|
143 |
-
return (
|
144 |
-
f"**Generation failed:** Could not generate a valid molecule.\n\n**{nan_message}**",
|
145 |
-
None,
|
146 |
-
gif_path,
|
147 |
-
properties,
|
148 |
-
None,
|
149 |
-
)
|
150 |
-
# except Exception as e:
|
151 |
-
# print(f"Error in generation: {e}")
|
152 |
-
# continue
|
153 |
-
|
154 |
-
return f"**Generation failed:** Could not generate a valid molecule after {repeating_time} attempts.\n\n**{nan_message}**", None, None
|
155 |
|
156 |
-
|
157 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
158 |
|
159 |
-
|
160 |
-
|
161 |
-
|
162 |
-
"model_labeled": "Graph DiT (trained on labeled)"
|
163 |
-
}
|
164 |
|
165 |
def numpy_to_python(obj):
|
|
|
166 |
if isinstance(obj, np.integer):
|
167 |
return int(obj)
|
168 |
elif isinstance(obj, np.floating):
|
@@ -175,175 +144,326 @@ def numpy_to_python(obj):
|
|
175 |
return {k: numpy_to_python(v) for k, v in obj.items()}
|
176 |
else:
|
177 |
return obj
|
178 |
-
|
179 |
-
def on_generate(CH4, CO2, H2, N2, O2, guidance_scale, num_nodes, repeating_time, model_state, num_chain_steps, fps):
|
180 |
-
print('in on_generate', on_generate)
|
181 |
-
result = generate_graph(CH4, CO2, H2, N2, O2, guidance_scale, num_nodes, repeating_time, model_state, num_chain_steps, fps)
|
182 |
-
# Check if the generation was successful
|
183 |
-
if result[0].startswith("**Generated polymer SMILES:**"):
|
184 |
-
smiles = result[0].split("**Generated polymer SMILES:** `")[1].split("`")[0]
|
185 |
-
properties = json.dumps(numpy_to_python(result[3]))
|
186 |
-
suggested_properties = json.dumps(numpy_to_python(result[4]))
|
187 |
-
# Return the result with an enabled feedback button
|
188 |
-
return [*result[:3], smiles, properties, suggested_properties, gr.Button(interactive=True)]
|
189 |
-
else:
|
190 |
-
# Return the result with a disabled feedback button
|
191 |
-
return [*result[:3], "", "[]", "[]", gr.Button(interactive=False)]
|
192 |
|
193 |
-
|
194 |
-
|
195 |
-
|
196 |
-
|
197 |
-
|
198 |
-
|
199 |
-
|
200 |
-
|
201 |
-
|
202 |
-
|
203 |
-
|
204 |
-
return gr.Textbox(value="Thank you for your feedback!", visible=True)
|
205 |
|
206 |
-
#
|
207 |
-
|
208 |
-
return gr.Button(interactive=False)
|
209 |
|
210 |
-
|
211 |
-
|
212 |
-
# Navigation Bar
|
213 |
-
with gr.Row(elem_id="navbar"):
|
214 |
-
gr.Markdown("""
|
215 |
-
<div style="text-align: center;">
|
216 |
-
<h1>ππ¬ Polymer Design with GraphDiT</h1>
|
217 |
-
<div style="display: flex; gap: 20px; justify-content: center; align-items: center; margin-top: 10px;">
|
218 |
-
<a href="https://github.com/liugangcode/Graph-DiT" target="_blank" style="display: flex; align-items: center; gap: 5px; text-decoration: none; color: inherit;">
|
219 |
-
<img src="https://img.icons8.com/ios-glyphs/30/000000/github.png" alt="GitHub" />
|
220 |
-
<span>View Code</span>
|
221 |
-
</a>
|
222 |
-
<a href="https://arxiv.org/abs/2401.13858" target="_blank" style="text-decoration: none; color: inherit;">
|
223 |
-
π View Paper
|
224 |
-
</a>
|
225 |
-
</div>
|
226 |
-
</div>
|
227 |
-
""")
|
228 |
|
229 |
-
|
230 |
-
gr.Markdown("""
|
231 |
-
## Introduction
|
232 |
|
233 |
-
|
234 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
235 |
|
236 |
-
|
237 |
-
|
238 |
-
|
239 |
-
|
240 |
-
|
241 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
242 |
)
|
243 |
|
244 |
-
|
245 |
-
with gr.Accordion("π Model Description", open=False):
|
246 |
-
gr.Markdown("""
|
247 |
-
### GraphDiT: Graph Diffusion Transformer
|
248 |
|
249 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
250 |
|
251 |
-
|
|
|
|
|
252 |
|
253 |
-
|
|
|
254 |
|
255 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
256 |
|
257 |
-
|
258 |
-
|
259 |
-
|
260 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
261 |
|
262 |
-
|
263 |
-
|
264 |
-
|
265 |
-
|
266 |
-
|
267 |
-
|
268 |
-
|
269 |
-
|
270 |
-
|
271 |
-
|
272 |
-
|
273 |
-
|
274 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
275 |
|
276 |
-
|
277 |
-
|
278 |
-
with gr.Row():
|
279 |
-
CH4_input = gr.Slider(0, property_ranges['CH4'][1], value=2.5, label=f"CHβ (Barrier) [0-{property_ranges['CH4'][1]:.1f}]")
|
280 |
-
CO2_input = gr.Slider(0, property_ranges['CO2'][1], value=15.4, label=f"COβ (Barrier) [0-{property_ranges['CO2'][1]:.1f}]")
|
281 |
-
H2_input = gr.Slider(0, property_ranges['H2'][1], value=21.0, label=f"Hβ (Barrier) [0-{property_ranges['H2'][1]:.1f}]")
|
282 |
-
N2_input = gr.Slider(0, property_ranges['N2'][1], value=1.5, label=f"Nβ (Barrier) [0-{property_ranges['N2'][1]:.1f}]")
|
283 |
-
O2_input = gr.Slider(0, property_ranges['O2'][1], value=2.8, label=f"Oβ (Barrier) [0-{property_ranges['O2'][1]:.1f}]")
|
284 |
-
|
285 |
-
with gr.Row():
|
286 |
-
guidance_scale = gr.Slider(1, 3, value=2, label="Guidance Scale from Properties")
|
287 |
-
num_nodes = gr.Slider(0, 50, step=1, value=0, label="Number of Nodes (0 for Random, Larger Graphs Take More Time)")
|
288 |
-
repeating_time = gr.Slider(1, 10, step=1, value=3, label="Repetition Until Success")
|
289 |
-
num_chain_steps = gr.Slider(0, 499, step=1, value=50, label="Number of Diffusion Steps to Visualize (Larger Numbers Take More Time)")
|
290 |
-
fps = gr.Slider(0.25, 10, step=0.25, value=5, label="Frames Per Second")
|
291 |
-
|
292 |
-
with gr.Row():
|
293 |
-
random_btn = gr.Button("π Randomize Properties (from Labeled Data)")
|
294 |
-
generate_btn = gr.Button("π Generate Polymer")
|
295 |
-
|
296 |
-
with gr.Row():
|
297 |
-
result_text = gr.Textbox(label="π Generation Result")
|
298 |
-
result_image = gr.Image(label="Final Molecule Visualization", type="pil")
|
299 |
-
result_gif = gr.Image(label="Generation Process Visualization", type="filepath", format="gif")
|
300 |
-
|
301 |
-
with gr.Row() as feedback_row:
|
302 |
-
feedback_btn = gr.Button("π I think this polymer is interesting!", visible=True, interactive=False)
|
303 |
-
feedback_result = gr.Textbox(label="Feedback Result", visible=False)
|
304 |
-
|
305 |
-
# Add model switching functionality
|
306 |
-
def switch_model(choice):
|
307 |
-
# Convert display name back to internal name
|
308 |
-
internal_name = next(key for key, value in model_name_mapping.items() if value == choice)
|
309 |
-
return load_model(internal_name)
|
310 |
-
|
311 |
-
model_choice.change(switch_model, inputs=[model_choice], outputs=[model_state])
|
312 |
-
|
313 |
-
# Hidden components to store generation data
|
314 |
-
hidden_smiles = gr.Textbox(visible=False)
|
315 |
-
hidden_properties = gr.JSON(visible=False)
|
316 |
-
hidden_suggested_properties = gr.JSON(visible=False)
|
317 |
-
|
318 |
-
# Set up event handlers
|
319 |
-
random_btn.click(
|
320 |
-
set_random_properties,
|
321 |
-
outputs=[CH4_input, CO2_input, H2_input, N2_input, O2_input]
|
322 |
-
)
|
323 |
|
324 |
-
|
325 |
-
on_generate,
|
326 |
-
inputs=[CH4_input, CO2_input, H2_input, N2_input, O2_input, guidance_scale, num_nodes, repeating_time, model_state, num_chain_steps, fps],
|
327 |
-
outputs=[result_text, result_image, result_gif, hidden_smiles, hidden_properties, hidden_suggested_properties, feedback_btn]
|
328 |
-
)
|
329 |
|
330 |
-
feedback_btn.click(
|
331 |
-
process_feedback,
|
332 |
-
inputs=[gr.Checkbox(value=True, visible=False), hidden_smiles, hidden_properties, hidden_suggested_properties],
|
333 |
-
outputs=[feedback_result]
|
334 |
-
).then(
|
335 |
-
lambda: gr.Button(interactive=False),
|
336 |
-
outputs=[feedback_btn]
|
337 |
-
)
|
338 |
-
|
339 |
-
CH4_input.change(reset_feedback_button, outputs=[feedback_btn])
|
340 |
-
CO2_input.change(reset_feedback_button, outputs=[feedback_btn])
|
341 |
-
H2_input.change(reset_feedback_button, outputs=[feedback_btn])
|
342 |
-
N2_input.change(reset_feedback_button, outputs=[feedback_btn])
|
343 |
-
O2_input.change(reset_feedback_button, outputs=[feedback_btn])
|
344 |
-
random_btn.click(reset_feedback_button, outputs=[feedback_btn])
|
345 |
-
|
346 |
-
# Launch the interface
|
347 |
if __name__ == "__main__":
|
348 |
-
|
349 |
-
|
|
|
1 |
import spaces
|
|
|
|
|
2 |
|
3 |
+
# Standard Libraries
|
|
|
|
|
|
|
|
|
4 |
import os
|
5 |
+
import io
|
6 |
+
import csv
|
7 |
+
import json
|
8 |
+
import glob
|
9 |
+
import random
|
10 |
import tempfile
|
11 |
import atexit
|
|
|
|
|
12 |
from datetime import datetime
|
|
|
13 |
|
14 |
+
# Third-Party Libraries
|
15 |
+
import numpy as np
|
16 |
+
import pandas as pd
|
17 |
+
import torch
|
18 |
+
import imageio
|
19 |
from rdkit import Chem
|
20 |
from rdkit.Chem import Draw
|
21 |
+
import gradio as gr
|
22 |
|
23 |
+
# Local Modules
|
24 |
from evaluator import Evaluator
|
25 |
from loader import load_graph_decoder
|
26 |
|
27 |
+
# --------------------------- Configuration Constants --------------------------- #
|
28 |
+
|
29 |
+
DATA_DIR = 'data'
|
30 |
+
EVALUATORS_DIR = 'evaluators'
|
31 |
+
FLAGGED_FOLDER = "flagged"
|
32 |
+
KNOWN_LABELS_FILE = os.path.join(DATA_DIR, 'known_labels.csv')
|
33 |
+
KNOWN_SMILES_FILE = os.path.join(DATA_DIR, 'known_polymers.csv')
|
34 |
+
|
35 |
+
ALL_PROPERTIES = ['CH4', 'CO2', 'H2', 'N2', 'O2']
|
36 |
+
MODEL_NAME_MAPPING = {
|
37 |
+
"model_all": "Graph DiT (trained on labeled + unlabeled)",
|
38 |
+
"model_labeled": "Graph DiT (trained on labeled)"
|
39 |
+
}
|
40 |
+
|
41 |
+
GIF_TEMP_PREFIX = "polymer_gifs_"
|
42 |
+
|
43 |
+
# --------------------------- Data Loading --------------------------- #
|
44 |
+
|
45 |
+
def load_known_data():
|
46 |
+
"""Load known labels and SMILES data from CSV files."""
|
47 |
+
try:
|
48 |
+
known_labels = pd.read_csv(KNOWN_LABELS_FILE)
|
49 |
+
known_smiles = pd.read_csv(KNOWN_SMILES_FILE)
|
50 |
+
return known_labels, known_smiles
|
51 |
+
except Exception as e:
|
52 |
+
raise FileNotFoundError(f"Error loading data files: {e}")
|
53 |
+
|
54 |
+
# Load data
|
55 |
+
known_labels, known_smiles = load_known_data()
|
56 |
+
|
57 |
+
# --------------------------- Evaluator Setup --------------------------- #
|
58 |
+
|
59 |
+
def initialize_evaluators(properties, evaluators_dir):
|
60 |
+
"""Initialize evaluators for each property."""
|
61 |
+
evaluators = {}
|
62 |
+
for prop in properties:
|
63 |
+
evaluator_path = os.path.join(evaluators_dir, f'{prop}.joblib')
|
64 |
+
evaluators[prop] = Evaluator(evaluator_path, prop)
|
65 |
+
return evaluators
|
66 |
|
67 |
+
evaluators = initialize_evaluators(ALL_PROPERTIES, EVALUATORS_DIR)
|
68 |
|
69 |
+
# --------------------------- Property Ranges --------------------------- #
|
|
|
70 |
|
71 |
+
def get_property_ranges(labels, properties):
|
72 |
+
"""Get min and max values for each property."""
|
73 |
+
return {prop: (labels[prop].min(), labels[prop].max()) for prop in properties}
|
74 |
|
75 |
+
property_ranges = get_property_ranges(known_labels, ALL_PROPERTIES)
|
76 |
+
|
77 |
+
# --------------------------- Temporary Directory Setup --------------------------- #
|
78 |
+
|
79 |
+
temp_dir = tempfile.mkdtemp(prefix=GIF_TEMP_PREFIX)
|
80 |
|
81 |
def cleanup_temp_files():
|
82 |
"""Clean up temporary GIF files on exit."""
|
|
|
|
|
|
|
|
|
|
|
83 |
try:
|
84 |
+
for file in glob.glob(os.path.join(temp_dir, "*.gif")):
|
85 |
+
os.remove(file)
|
86 |
os.rmdir(temp_dir)
|
87 |
except Exception as e:
|
88 |
+
print(f"Error during cleanup: {e}")
|
89 |
|
|
|
90 |
atexit.register(cleanup_temp_files)
|
91 |
|
92 |
+
# --------------------------- Utility Functions --------------------------- #
|
93 |
+
|
94 |
def random_properties():
|
95 |
+
"""Select a random set of properties from known labels."""
|
96 |
+
return known_labels[ALL_PROPERTIES].sample(1).values.tolist()[0]
|
97 |
|
98 |
def load_model(model_choice):
|
99 |
+
"""Load the graph decoder model based on the choice."""
|
100 |
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
|
101 |
model = load_graph_decoder(path=model_choice)
|
102 |
+
model.to(device)
|
103 |
+
return model, device
|
|
|
|
|
|
|
104 |
|
105 |
def save_interesting_log(smiles, properties, suggested_properties):
|
106 |
+
"""Save interesting polymer data to a CSV log file."""
|
107 |
+
log_file = os.path.join(FLAGGED_FOLDER, "log.csv")
|
108 |
+
os.makedirs(FLAGGED_FOLDER, exist_ok=True)
|
109 |
file_exists = os.path.isfile(log_file)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
110 |
|
111 |
+
fieldnames = ['timestamp', 'smiles'] + ALL_PROPERTIES + [f'suggested_{prop}' for prop in ALL_PROPERTIES]
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
112 |
|
113 |
+
try:
|
114 |
+
with open(log_file, 'a', newline='') as csvfile:
|
115 |
+
writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
|
116 |
+
if not file_exists:
|
117 |
+
writer.writeheader()
|
118 |
+
|
119 |
+
log_data = {
|
120 |
+
'timestamp': datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
|
121 |
+
'smiles': smiles,
|
122 |
+
**{prop: value for prop, value in zip(ALL_PROPERTIES, properties)},
|
123 |
+
**{f'suggested_{prop}': value for prop, value in suggested_properties.items()}
|
124 |
+
}
|
125 |
+
writer.writerow(log_data)
|
126 |
+
except Exception as e:
|
127 |
+
print(f"Error saving log: {e}")
|
128 |
|
129 |
+
def is_nan_like(x):
|
130 |
+
"""Check if a value should be treated as NaN."""
|
131 |
+
return x == 0 or x == '' or (isinstance(x, float) and np.isnan(x))
|
|
|
|
|
132 |
|
133 |
def numpy_to_python(obj):
|
134 |
+
"""Convert NumPy objects to native Python types."""
|
135 |
if isinstance(obj, np.integer):
|
136 |
return int(obj)
|
137 |
elif isinstance(obj, np.floating):
|
|
|
144 |
return {k: numpy_to_python(v) for k, v in obj.items()}
|
145 |
else:
|
146 |
return obj
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
147 |
|
148 |
+
# --------------------------- Graph Generation Function --------------------------- #
|
149 |
+
|
150 |
+
@spaces.GPU
|
151 |
+
def generate_graph(CH4, CO2, H2, N2, O2, guidance_scale, num_nodes, repeating_time, model_state, num_chain_steps, fps):
|
152 |
+
"""
|
153 |
+
Generate a polymer graph based on the input properties and model.
|
154 |
+
Returns generation results including SMILES, images, and properties.
|
155 |
+
"""
|
156 |
+
print('Generating graph...')
|
157 |
+
model, device = model_state
|
158 |
+
properties = [CH4, CO2, H2, N2, O2]
|
|
|
159 |
|
160 |
+
# Handle NaN-like values
|
161 |
+
properties = [None if is_nan_like(prop) else prop for prop in properties]
|
|
|
162 |
|
163 |
+
nan_gases = [gas for gas, prop in zip(ALL_PROPERTIES, properties) if prop is None]
|
164 |
+
nan_message = "The following gas properties were treated as NaN: " + (", ".join(nan_gases) if nan_gases else "None")
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
165 |
|
166 |
+
num_nodes = None if num_nodes == 0 else num_nodes
|
|
|
|
|
167 |
|
168 |
+
for attempt in range(repeating_time):
|
169 |
+
try:
|
170 |
+
generated_molecule, img_list = model.generate(
|
171 |
+
properties,
|
172 |
+
device=device,
|
173 |
+
guide_scale=guidance_scale,
|
174 |
+
num_nodes=num_nodes,
|
175 |
+
number_chain_steps=num_chain_steps
|
176 |
+
)
|
177 |
|
178 |
+
gif_path = None
|
179 |
+
if img_list:
|
180 |
+
imgs = [np.array(pil_img) for pil_img in img_list]
|
181 |
+
imgs.extend([imgs[-1]] * 10) # Extend the last image for GIF
|
182 |
+
gif_path = os.path.join(temp_dir, f"polymer_gen_{random.randint(0, 999999)}.gif")
|
183 |
+
imageio.mimsave(gif_path, imgs, format='GIF', fps=fps, loop=0)
|
184 |
+
|
185 |
+
if generated_molecule:
|
186 |
+
mol = Chem.MolFromSmiles(generated_molecule)
|
187 |
+
if mol:
|
188 |
+
standardized_smiles = Chem.MolToSmiles(mol, isomericSmiles=True)
|
189 |
+
is_novel = standardized_smiles not in known_smiles['SMILES'].values
|
190 |
+
novelty_status = "Novel (Not in Labeled Set)" if is_novel else "Not Novel (Exists in Labeled Set)"
|
191 |
+
img = Draw.MolToImage(mol)
|
192 |
+
|
193 |
+
# Evaluate the generated molecule
|
194 |
+
suggested_properties = {prop: evaluator([standardized_smiles])[0] for prop, evaluator in evaluators.items()}
|
195 |
+
|
196 |
+
suggested_properties_text = "\n".join([f"**Suggested {prop}:** {value:.2f}" for prop, value in suggested_properties.items()])
|
197 |
+
|
198 |
+
return (
|
199 |
+
f"**Generated polymer SMILES:** `{standardized_smiles}`\n\n"
|
200 |
+
f"**{nan_message}**\n\n"
|
201 |
+
f"**{novelty_status}**\n\n"
|
202 |
+
f"**Suggested Properties:**\n{suggested_properties_text}",
|
203 |
+
img,
|
204 |
+
gif_path,
|
205 |
+
standardized_smiles,
|
206 |
+
properties,
|
207 |
+
suggested_properties
|
208 |
+
)
|
209 |
+
except Exception as e:
|
210 |
+
print(f"Attempt {attempt + 1} failed: {e}")
|
211 |
+
continue
|
212 |
+
|
213 |
+
# If all attempts fail
|
214 |
+
return (
|
215 |
+
f"**Generation failed:** Could not generate a valid molecule after {repeating_time} attempts.\n\n**{nan_message}**",
|
216 |
+
None,
|
217 |
+
None,
|
218 |
+
"",
|
219 |
+
[],
|
220 |
+
{}
|
221 |
)
|
222 |
|
223 |
+
# --------------------------- Feedback Processing --------------------------- #
|
|
|
|
|
|
|
224 |
|
225 |
+
def process_feedback(checkbox_value, smiles, properties, suggested_properties):
|
226 |
+
"""
|
227 |
+
Process user feedback. If the user finds the polymer interesting,
|
228 |
+
log it accordingly.
|
229 |
+
"""
|
230 |
+
if checkbox_value and smiles:
|
231 |
+
save_interesting_log(smiles, properties, suggested_properties)
|
232 |
+
return "Thank you for your feedback! This polymer has been saved to our interesting polymers log."
|
233 |
+
return "Thank you for your feedback!"
|
234 |
+
|
235 |
+
# --------------------------- Model Switching --------------------------- #
|
236 |
+
|
237 |
+
def switch_model(choice):
|
238 |
+
"""Switch the model based on user selection."""
|
239 |
+
internal_name = next(key for key, value in MODEL_NAME_MAPPING.items() if value == choice)
|
240 |
+
return load_model(internal_name)
|
241 |
+
|
242 |
+
# --------------------------- Gradio Interface Setup --------------------------- #
|
243 |
+
|
244 |
+
def create_gradio_interface():
|
245 |
+
"""Create and return the Gradio Blocks interface."""
|
246 |
+
with gr.Blocks(title="Polymer Design with GraphDiT") as iface:
|
247 |
+
# Navigation Bar
|
248 |
+
with gr.Row(elem_id="navbar"):
|
249 |
+
gr.Markdown("""
|
250 |
+
<div style="text-align: center;">
|
251 |
+
<h1>ππ¬ Polymer Design with GraphDiT</h1>
|
252 |
+
<div style="display: flex; gap: 20px; justify-content: center; align-items: center; margin-top: 10px;">
|
253 |
+
<a href="https://github.com/liugangcode/Graph-DiT" target="_blank" style="display: flex; align-items: center; gap: 5px; text-decoration: none; color: inherit;">
|
254 |
+
<img src="https://img.icons8.com/ios-glyphs/30/000000/github.png" alt="GitHub" />
|
255 |
+
<span>View Code</span>
|
256 |
+
</a>
|
257 |
+
<a href="https://arxiv.org/abs/2401.13858" target="_blank" style="text-decoration: none; color: inherit;">
|
258 |
+
π View Paper
|
259 |
+
</a>
|
260 |
+
</div>
|
261 |
+
</div>
|
262 |
+
""")
|
263 |
|
264 |
+
# Main Description
|
265 |
+
gr.Markdown("""
|
266 |
+
## Introduction
|
267 |
|
268 |
+
Input the desired gas barrier properties for CHβ, COβ, Hβ, Nβ, and Oβ to generate novel polymer structures. The results are visualized as molecular graphs and represented by SMILES strings if they are successfully generated. **Note:** Gas barrier values set to 0 will be treated as `NaN` (unconditionally). If the generation fails, please retry or increase the number of repetition attempts.
|
269 |
+
""")
|
270 |
|
271 |
+
# Model Selection
|
272 |
+
model_choice = gr.Radio(
|
273 |
+
choices=list(MODEL_NAME_MAPPING.values()),
|
274 |
+
label="Model Zoo",
|
275 |
+
value=MODEL_NAME_MAPPING["model_labeled"]
|
276 |
+
)
|
277 |
+
|
278 |
+
# Model Description Accordion
|
279 |
+
with gr.Accordion("π Model Description", open=False):
|
280 |
+
gr.Markdown("""
|
281 |
+
### GraphDiT: Graph Diffusion Transformer
|
282 |
+
|
283 |
+
GraphDiT is a graph diffusion model designed for targeted molecular generation. It employs a conditional diffusion process to iteratively refine molecular structures based on user-specified properties.
|
284 |
+
|
285 |
+
We have collected a labeled polymer database for gas permeability from [Membrane Database](https://research.csiro.au/virtualscreening/membrane-database-polymer-gas-separation-membranes/). Additionally, we utilize unlabeled polymer structures from [PolyInfo](https://polymer.nims.go.jp/).
|
286 |
+
|
287 |
+
The gas permeability ranges from 0 to over ten thousand, with only hundreds of labeled data points, making this task particularly challenging.
|
288 |
+
|
289 |
+
We are actively working on improving the model. We welcome any feedback regarding model usage or suggestions for improvement.
|
290 |
+
|
291 |
+
#### Currently, we have two variants of Graph DiT:
|
292 |
+
- **Graph DiT (trained on labeled + unlabeled)**: This model uses both labeled and unlabeled data for training, potentially leading to more diverse/novel polymer generation.
|
293 |
+
- **Graph DiT (trained on labeled)**: This model is trained exclusively on labeled data, which may result in higher validity but potentially less diverse/novel outputs.
|
294 |
+
""")
|
295 |
+
|
296 |
+
# Citation Accordion
|
297 |
+
with gr.Accordion("π Citation", open=False):
|
298 |
+
gr.Markdown("""
|
299 |
+
If you use this model or interface useful, please cite the following paper:
|
300 |
+
```bibtex
|
301 |
+
@article{graphdit2024,
|
302 |
+
title={Graph Diffusion Transformers for Multi-Conditional Molecular Generation},
|
303 |
+
author={Liu, Gang and Xu, Jiaxin and Luo, Tengfei and Jiang, Meng},
|
304 |
+
journal={NeurIPS},
|
305 |
+
year={2024},
|
306 |
+
}
|
307 |
+
```
|
308 |
+
""")
|
309 |
+
|
310 |
+
# Initialize Model State
|
311 |
+
model_state = gr.State(load_model("model_labeled"))
|
312 |
+
|
313 |
+
# Property Inputs
|
314 |
+
with gr.Row():
|
315 |
+
CH4_input = gr.Slider(
|
316 |
+
minimum=0,
|
317 |
+
maximum=property_ranges['CH4'][1],
|
318 |
+
value=2.5,
|
319 |
+
label=f"CHβ (Barrier) [0-{property_ranges['CH4'][1]:.1f}]"
|
320 |
+
)
|
321 |
+
CO2_input = gr.Slider(
|
322 |
+
minimum=0,
|
323 |
+
maximum=property_ranges['CO2'][1],
|
324 |
+
value=15.4,
|
325 |
+
label=f"COβ (Barrier) [0-{property_ranges['CO2'][1]:.1f}]"
|
326 |
+
)
|
327 |
+
H2_input = gr.Slider(
|
328 |
+
minimum=0,
|
329 |
+
maximum=property_ranges['H2'][1],
|
330 |
+
value=21.0,
|
331 |
+
label=f"Hβ (Barrier) [0-{property_ranges['H2'][1]:.1f}]"
|
332 |
+
)
|
333 |
+
N2_input = gr.Slider(
|
334 |
+
minimum=0,
|
335 |
+
maximum=property_ranges['N2'][1],
|
336 |
+
value=1.5,
|
337 |
+
label=f"Nβ (Barrier) [0-{property_ranges['N2'][1]:.1f}]"
|
338 |
+
)
|
339 |
+
O2_input = gr.Slider(
|
340 |
+
minimum=0,
|
341 |
+
maximum=property_ranges['O2'][1],
|
342 |
+
value=2.8,
|
343 |
+
label=f"Oβ (Barrier) [0-{property_ranges['O2'][1]:.1f}]"
|
344 |
+
)
|
345 |
|
346 |
+
# Generation Parameters
|
347 |
+
with gr.Row():
|
348 |
+
guidance_scale = gr.Slider(
|
349 |
+
minimum=1,
|
350 |
+
maximum=3,
|
351 |
+
value=2,
|
352 |
+
label="Guidance Scale from Properties"
|
353 |
+
)
|
354 |
+
num_nodes = gr.Slider(
|
355 |
+
minimum=0,
|
356 |
+
maximum=50,
|
357 |
+
step=1,
|
358 |
+
value=0,
|
359 |
+
label="Number of Nodes (0 for Random, Larger Graphs Take More Time)"
|
360 |
+
)
|
361 |
+
repeating_time = gr.Slider(
|
362 |
+
minimum=1,
|
363 |
+
maximum=10,
|
364 |
+
step=1,
|
365 |
+
value=3,
|
366 |
+
label="Repetition Until Success"
|
367 |
+
)
|
368 |
+
num_chain_steps = gr.Slider(
|
369 |
+
minimum=0,
|
370 |
+
maximum=499,
|
371 |
+
step=1,
|
372 |
+
value=50,
|
373 |
+
label="Number of Diffusion Steps to Visualize (Larger Numbers Take More Time)"
|
374 |
+
)
|
375 |
+
fps = gr.Slider(
|
376 |
+
minimum=0.25,
|
377 |
+
maximum=10,
|
378 |
+
step=0.25,
|
379 |
+
value=5,
|
380 |
+
label="Frames Per Second"
|
381 |
+
)
|
382 |
|
383 |
+
# Action Buttons
|
384 |
+
with gr.Row():
|
385 |
+
random_btn = gr.Button("π Randomize Properties (from Labeled Data)")
|
386 |
+
generate_btn = gr.Button("π Generate Polymer")
|
387 |
+
|
388 |
+
# Results Display
|
389 |
+
with gr.Row():
|
390 |
+
result_text = gr.Textbox(label="π Generation Result", lines=10)
|
391 |
+
result_image = gr.Image(label="Final Molecule Visualization", type="pil")
|
392 |
+
result_gif = gr.Image(label="Generation Process Visualization", type="filepath", format="gif")
|
393 |
+
|
394 |
+
# Feedback Section
|
395 |
+
with gr.Row():
|
396 |
+
feedback_btn = gr.Button("π I think this polymer is interesting!", interactive=False)
|
397 |
+
feedback_result = gr.Textbox(label="Feedback Result", visible=False)
|
398 |
+
|
399 |
+
# Hidden Components to Store Generation Data
|
400 |
+
hidden_smiles = gr.Textbox(visible=False)
|
401 |
+
hidden_properties = gr.JSON(visible=False)
|
402 |
+
hidden_suggested_properties = gr.JSON(visible=False)
|
403 |
+
|
404 |
+
# Event Handlers
|
405 |
+
|
406 |
+
# Model Selection Change
|
407 |
+
model_choice.change(
|
408 |
+
switch_model,
|
409 |
+
inputs=[model_choice],
|
410 |
+
outputs=[model_state]
|
411 |
+
)
|
412 |
+
|
413 |
+
# Randomize Properties Button
|
414 |
+
random_btn.click(
|
415 |
+
random_properties,
|
416 |
+
outputs=[CH4_input, CO2_input, H2_input, N2_input, O2_input]
|
417 |
+
)
|
418 |
+
|
419 |
+
# Generate Polymer Button
|
420 |
+
generate_btn.click(
|
421 |
+
generate_graph,
|
422 |
+
inputs=[
|
423 |
+
CH4_input, CO2_input, H2_input, N2_input, O2_input,
|
424 |
+
guidance_scale, num_nodes, repeating_time,
|
425 |
+
model_state, num_chain_steps, fps
|
426 |
+
],
|
427 |
+
outputs=[
|
428 |
+
result_text, result_image, result_gif,
|
429 |
+
hidden_smiles, hidden_properties, hidden_suggested_properties
|
430 |
+
]
|
431 |
+
).then(
|
432 |
+
lambda text, img, gif, smiles, props, sugg_props: (
|
433 |
+
smiles if text.startswith("**Generated polymer SMILES:**") else "",
|
434 |
+
json.dumps(numpy_to_python(props)),
|
435 |
+
json.dumps(numpy_to_python(sugg_props)),
|
436 |
+
gr.Button(interactive=text.startswith("**Generated polymer SMILES:**"))
|
437 |
+
),
|
438 |
+
inputs=[
|
439 |
+
result_text, result_image, result_gif,
|
440 |
+
hidden_smiles, hidden_properties, hidden_suggested_properties
|
441 |
+
],
|
442 |
+
outputs=[hidden_smiles, hidden_properties, hidden_suggested_properties, feedback_btn]
|
443 |
+
)
|
444 |
+
|
445 |
+
# Feedback Button Click
|
446 |
+
feedback_btn.click(
|
447 |
+
process_feedback,
|
448 |
+
inputs=[gr.Checkbox(label="Interested?", value=True, visible=False), hidden_smiles, hidden_properties, hidden_suggested_properties],
|
449 |
+
outputs=[feedback_result]
|
450 |
+
).then(
|
451 |
+
lambda: gr.Button(interactive=False),
|
452 |
+
outputs=[feedback_btn]
|
453 |
+
)
|
454 |
+
|
455 |
+
# Reset Feedback Button on Input Changes
|
456 |
+
for input_component in [CH4_input, CO2_input, H2_input, N2_input, O2_input, random_btn]:
|
457 |
+
input_component.change(
|
458 |
+
lambda: None,
|
459 |
+
outputs=[feedback_btn],
|
460 |
+
_js="() => feedback_btn.interactive = false"
|
461 |
+
)
|
462 |
|
463 |
+
return iface
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
464 |
|
465 |
+
# --------------------------- Main Execution --------------------------- #
|
|
|
|
|
|
|
|
|
466 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
467 |
if __name__ == "__main__":
|
468 |
+
interface = create_gradio_interface()
|
469 |
+
interface.launch(share=False)
|