import spaces import gradio as gr import torch import numpy as np import pandas as pd import random import io import imageio import os import tempfile import atexit import glob import csv from datetime import datetime import json from rdkit import Chem from rdkit.Chem import Draw from evaluator import Evaluator from loader import load_graph_decoder # Load the CSV data known_labels = pd.read_csv('data/known_labels.csv') knwon_smiles = pd.read_csv('data/known_polymers.csv') all_properties = ['CH4', 'CO2', 'H2', 'N2', 'O2'] # Initialize evaluators evaluators = {prop: Evaluator(f'evaluators/{prop}.joblib', prop) for prop in all_properties} # Get min and max values for each property property_ranges = {prop: (known_labels[prop].min(), known_labels[prop].max()) for prop in all_properties} # Create a temporary directory for GIFs temp_dir = tempfile.mkdtemp(prefix="polymer_gifs_") def cleanup_temp_files(): """Clean up temporary GIF files on exit.""" for file in glob.glob(os.path.join(temp_dir, "*.gif")): try: os.remove(file) except Exception as e: print(f"Error deleting {file}: {e}") try: os.rmdir(temp_dir) except Exception as e: print(f"Error deleting temporary directory {temp_dir}: {e}") # Register the cleanup function to be called on exit atexit.register(cleanup_temp_files) def random_properties(): return known_labels[all_properties].sample(1).values.tolist()[0] def load_model(model_choice): device = torch.device("cuda" if torch.cuda.is_available() else "cpu") model = load_graph_decoder(path=model_choice) return (model, device) # Create a flagged folder if it doesn't exist flagged_folder = "flagged" os.makedirs(flagged_folder, exist_ok=True) def save_interesting_log(smiles, properties, suggested_properties): """Save interesting polymer data to a CSV file.""" log_file = os.path.join(flagged_folder, "log.csv") file_exists = os.path.isfile(log_file) with open(log_file, 'a', newline='') as csvfile: fieldnames = ['timestamp', 'smiles'] + all_properties + [f'suggested_{prop}' for prop in all_properties] writer = csv.DictWriter(csvfile, fieldnames=fieldnames) if not file_exists: writer.writeheader() log_data = { 'timestamp': datetime.now().strftime("%Y-%m-%d %H:%M:%S"), 'smiles': smiles, **{prop: value for prop, value in zip(all_properties, properties)}, **{f'suggested_{prop}': value for prop, value in suggested_properties.items()} } writer.writerow(log_data) @spaces.GPU def generate_graph(CH4, CO2, H2, N2, O2, guidance_scale, num_nodes, repeating_time, model_state, num_chain_steps, fps): model, device = model_state properties = [CH4, CO2, H2, N2, O2] def is_nan_like(x): return x == 0 or x == '' or (isinstance(x, float) and np.isnan(x)) properties = [None if is_nan_like(prop) else prop for prop in properties] nan_message = "The following gas properties were treated as NaN: " nan_gases = [gas for gas, prop in zip(all_properties, properties) if prop is None] nan_message += ", ".join(nan_gases) if nan_gases else "None" num_nodes = None if num_nodes == 0 else num_nodes for _ in range(repeating_time): # try: model.to(device) generated_molecule, img_list = model.generate(properties, guide_scale=guidance_scale, num_nodes=num_nodes, number_chain_steps=num_chain_steps) # Create GIF if img_list is available gif_path = None if img_list and len(img_list) > 0: imgs = [np.array(pil_img) for pil_img in img_list] imgs.extend([imgs[-1]] * 10) gif_path = os.path.join(temp_dir, f"polymer_gen_{random.randint(0, 999999)}.gif") imageio.mimsave(gif_path, imgs, format='GIF', fps=fps, loop=0) if generated_molecule is not None: mol = Chem.MolFromSmiles(generated_molecule) if mol is not None: standardized_smiles = Chem.MolToSmiles(mol, isomericSmiles=True) is_novel = standardized_smiles not in knwon_smiles['SMILES'].values novelty_status = "Novel (Not in Labeled Set)" if is_novel else "Not Novel (Exists in Labeled Set)" img = Draw.MolToImage(mol) # Evaluate the generated molecule suggested_properties = {} for prop, evaluator in evaluators.items(): suggested_properties[prop] = evaluator([standardized_smiles])[0] suggested_properties_text = "\n".join([f"**Suggested {prop}:** {value:.2f}" for prop, value in suggested_properties.items()]) return ( f"**Generated polymer SMILES:** `{standardized_smiles}`\n\n" f"**{nan_message}**\n\n" f"**{novelty_status}**\n\n" f"**Suggested Properties:**\n{suggested_properties_text}", img, gif_path, properties, # Add this suggested_properties # Add this ) else: return ( f"**Generation failed:** Could not generate a valid molecule.\n\n**{nan_message}**", None, gif_path, properties, None, ) # except Exception as e: # print(f"Error in generation: {e}") # continue return f"**Generation failed:** Could not generate a valid molecule after {repeating_time} attempts.\n\n**{nan_message}**", None, None def set_random_properties(): return random_properties() # Create a mapping of internal names to display names model_name_mapping = { "model_all": "Graph DiT (trained on labeled + unlabeled)", "model_labeled": "Graph DiT (trained on labeled)" } def numpy_to_python(obj): if isinstance(obj, np.integer): return int(obj) elif isinstance(obj, np.floating): return float(obj) elif isinstance(obj, np.ndarray): return obj.tolist() elif isinstance(obj, list): return [numpy_to_python(item) for item in obj] elif isinstance(obj, dict): return {k: numpy_to_python(v) for k, v in obj.items()} else: return obj def on_generate(CH4, CO2, H2, N2, O2, guidance_scale, num_nodes, repeating_time, model_state, num_chain_steps, fps): result = generate_graph(CH4, CO2, H2, N2, O2, guidance_scale, num_nodes, repeating_time, model_state, num_chain_steps, fps) # Check if the generation was successful if result[0].startswith("**Generated polymer SMILES:**"): smiles = result[0].split("**Generated polymer SMILES:** `")[1].split("`")[0] properties = json.dumps(numpy_to_python(result[3])) suggested_properties = json.dumps(numpy_to_python(result[4])) # Return the result with an enabled feedback button return [*result[:3], smiles, properties, suggested_properties, gr.Button(interactive=True)] else: # Return the result with a disabled feedback button return [*result[:3], "", "[]", "[]", gr.Button(interactive=False)] def process_feedback(checkbox_value, smiles, properties, suggested_properties): if checkbox_value: # Check if properties and suggested_properties are already Python objects if isinstance(properties, str): properties = json.loads(properties) if isinstance(suggested_properties, str): suggested_properties = json.loads(suggested_properties) save_interesting_log(smiles, properties, suggested_properties) return gr.Textbox(value="Thank you for your feedback! This polymer has been saved to our interesting polymers log.", visible=True) else: return gr.Textbox(value="Thank you for your feedback!", visible=True) # ADD THIS FUNCTION def reset_feedback_button(): return gr.Button(interactive=False) # Create the Gradio interface using Blocks with gr.Blocks(title="Polymer Design with GraphDiT") as iface: # Navigation Bar with gr.Row(elem_id="navbar"): gr.Markdown("""

πŸ”—πŸ”¬ Polymer Design with GraphDiT

GitHub View Code πŸ“„ View Paper
""") # Main Description gr.Markdown(""" ## Introduction 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. """) # Model Selection model_choice = gr.Radio( choices=list(model_name_mapping.values()), label="Model Zoo", # value="Graph DiT (trained on labeled + unlabeled)" value="Graph DiT (trained on labeled)" ) # Model Description Accordion with gr.Accordion("πŸ” Model Description", open=False): gr.Markdown(""" ### GraphDiT: Graph Diffusion Transformer 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. 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/). The gas permeability ranges from 0 to over ten thousand, with only hundreds of labeled data points, making this task particularly challenging. We are actively working on improving the model. We welcome any feedback regarding model usage or suggestions for improvement. #### Currently, we have two variants of Graph DiT: - **Graph DiT (trained on labeled + unlabeled)**: This model uses both labeled and unlabeled data for training, potentially leading to more diverse/novel polymer generation. - **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. """) # Citation Accordion with gr.Accordion("πŸ“„ Citation", open=False): gr.Markdown(""" If you use this model or interface useful, please cite the following paper: ```bibtex @article{graphdit2024, title={Graph Diffusion Transformers for Multi-Conditional Molecular Generation}, author={Liu, Gang and Xu, Jiaxin and Luo, Tengfei and Jiang, Meng}, journal={NeurIPS}, year={2024}, } ``` """) model_state = gr.State(lambda: load_model("model_labeled")) with gr.Row(): CH4_input = gr.Slider(0, property_ranges['CH4'][1], value=2.5, label=f"CHβ‚„ (Barrier) [0-{property_ranges['CH4'][1]:.1f}]") CO2_input = gr.Slider(0, property_ranges['CO2'][1], value=15.4, label=f"COβ‚‚ (Barrier) [0-{property_ranges['CO2'][1]:.1f}]") H2_input = gr.Slider(0, property_ranges['H2'][1], value=21.0, label=f"Hβ‚‚ (Barrier) [0-{property_ranges['H2'][1]:.1f}]") N2_input = gr.Slider(0, property_ranges['N2'][1], value=1.5, label=f"Nβ‚‚ (Barrier) [0-{property_ranges['N2'][1]:.1f}]") O2_input = gr.Slider(0, property_ranges['O2'][1], value=2.8, label=f"Oβ‚‚ (Barrier) [0-{property_ranges['O2'][1]:.1f}]") with gr.Row(): guidance_scale = gr.Slider(1, 3, value=2, label="Guidance Scale from Properties") num_nodes = gr.Slider(0, 50, step=1, value=0, label="Number of Nodes (0 for Random, Larger Graphs Take More Time)") repeating_time = gr.Slider(1, 10, step=1, value=3, label="Repetition Until Success") num_chain_steps = gr.Slider(0, 499, step=1, value=50, label="Number of Diffusion Steps to Visualize (Larger Numbers Take More Time)") fps = gr.Slider(0.25, 10, step=0.25, value=5, label="Frames Per Second") with gr.Row(): random_btn = gr.Button("πŸ”€ Randomize Properties (from Labeled Data)") generate_btn = gr.Button("πŸš€ Generate Polymer") with gr.Row(): result_text = gr.Textbox(label="πŸ“ Generation Result") result_image = gr.Image(label="Final Molecule Visualization", type="pil") result_gif = gr.Image(label="Generation Process Visualization", type="filepath", format="gif") with gr.Row() as feedback_row: feedback_btn = gr.Button("🌟 I think this polymer is interesting!", visible=True, interactive=False) feedback_result = gr.Textbox(label="Feedback Result", visible=False) # Add model switching functionality def switch_model(choice): # Convert display name back to internal name internal_name = next(key for key, value in model_name_mapping.items() if value == choice) return load_model(internal_name) model_choice.change(switch_model, inputs=[model_choice], outputs=[model_state]) # Hidden components to store generation data hidden_smiles = gr.Textbox(visible=False) hidden_properties = gr.JSON(visible=False) hidden_suggested_properties = gr.JSON(visible=False) # Set up event handlers random_btn.click( set_random_properties, outputs=[CH4_input, CO2_input, H2_input, N2_input, O2_input] ) generate_btn.click( on_generate, inputs=[CH4_input, CO2_input, H2_input, N2_input, O2_input, guidance_scale, num_nodes, repeating_time, model_state, num_chain_steps, fps], outputs=[result_text, result_image, result_gif, hidden_smiles, hidden_properties, hidden_suggested_properties, feedback_btn] ) feedback_btn.click( process_feedback, inputs=[gr.Checkbox(value=True, visible=False), hidden_smiles, hidden_properties, hidden_suggested_properties], outputs=[feedback_result] ).then( lambda: gr.Button(interactive=False), outputs=[feedback_btn] ) CH4_input.change(reset_feedback_button, outputs=[feedback_btn]) CO2_input.change(reset_feedback_button, outputs=[feedback_btn]) H2_input.change(reset_feedback_button, outputs=[feedback_btn]) N2_input.change(reset_feedback_button, outputs=[feedback_btn]) O2_input.change(reset_feedback_button, outputs=[feedback_btn]) random_btn.click(reset_feedback_button, outputs=[feedback_btn]) # Launch the interface if __name__ == "__main__": # iface.launch(share=True) iface.launch(share=False)