Spaces:
Sleeping
Sleeping
Vaishnav14220 commited on
Commit ·
1a40f18
1
Parent(s): 7303cbc
Add ORD forward reaction prediction demo app
Browse files- .gitignore +26 -0
- README.md +51 -6
- app.py +143 -0
- requirements.txt +6 -0
.gitignore
ADDED
|
@@ -0,0 +1,26 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
__pycache__/
|
| 2 |
+
*.py[cod]
|
| 3 |
+
*$py.class
|
| 4 |
+
*.so
|
| 5 |
+
.Python
|
| 6 |
+
build/
|
| 7 |
+
develop-eggs/
|
| 8 |
+
dist/
|
| 9 |
+
downloads/
|
| 10 |
+
eggs/
|
| 11 |
+
.eggs/
|
| 12 |
+
lib/
|
| 13 |
+
lib64/
|
| 14 |
+
parts/
|
| 15 |
+
sdist/
|
| 16 |
+
var/
|
| 17 |
+
wheels/
|
| 18 |
+
*.egg-info/
|
| 19 |
+
.installed.cfg
|
| 20 |
+
*.egg
|
| 21 |
+
.env
|
| 22 |
+
.venv
|
| 23 |
+
env/
|
| 24 |
+
venv/
|
| 25 |
+
ENV/
|
| 26 |
+
.DS_Store
|
README.md
CHANGED
|
@@ -1,13 +1,58 @@
|
|
| 1 |
---
|
| 2 |
-
title:
|
| 3 |
-
emoji:
|
| 4 |
-
colorFrom:
|
| 5 |
-
colorTo:
|
| 6 |
sdk: gradio
|
| 7 |
sdk_version: 5.49.1
|
| 8 |
app_file: app.py
|
| 9 |
pinned: false
|
| 10 |
-
license:
|
|
|
|
|
|
|
|
|
|
|
|
|
| 11 |
---
|
| 12 |
|
| 13 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
---
|
| 2 |
+
title: ORD Forward Reaction Prediction
|
| 3 |
+
emoji: 🧪
|
| 4 |
+
colorFrom: blue
|
| 5 |
+
colorTo: green
|
| 6 |
sdk: gradio
|
| 7 |
sdk_version: 5.49.1
|
| 8 |
app_file: app.py
|
| 9 |
pinned: false
|
| 10 |
+
license: apache-2.0
|
| 11 |
+
models:
|
| 12 |
+
- smitathkr1/ord-forward-t5
|
| 13 |
+
datasets:
|
| 14 |
+
- smitathkr1/ord-reactions
|
| 15 |
---
|
| 16 |
|
| 17 |
+
# ORD Forward Reaction Prediction - T5 Model
|
| 18 |
+
|
| 19 |
+
This is a demo space for testing the `smitathkr1/ord-forward-t5` model, which predicts chemical reaction products from reactants.
|
| 20 |
+
|
| 21 |
+
## Model Details
|
| 22 |
+
|
| 23 |
+
- **Model**: T5-based forward reaction prediction model
|
| 24 |
+
- **Training Data**: 2.3M reactions from the Open Reaction Database (ORD)
|
| 25 |
+
- **Training Status**: 5 epochs completed
|
| 26 |
+
- **Dataset**: [smitathkr1/ord-reactions](https://huggingface.co/datasets/smitathkr1/ord-reactions)
|
| 27 |
+
|
| 28 |
+
## Usage
|
| 29 |
+
|
| 30 |
+
Enter reactants in SMILES format (e.g., `CC(C)N1CCN(C)CC1.Brc1ccccc1`) and the model will predict the product.
|
| 31 |
+
|
| 32 |
+
### Input Format
|
| 33 |
+
- Reactants should be in SMILES notation
|
| 34 |
+
- Multiple reactants can be separated by '.'
|
| 35 |
+
- Example: `amine.aryl_halide` → `product`
|
| 36 |
+
|
| 37 |
+
### Parameters
|
| 38 |
+
- **Max Length**: Maximum length of the generated product SMILES
|
| 39 |
+
- **Num Beams**: Number of beams for beam search (higher = more thorough search)
|
| 40 |
+
- **Temperature**: Sampling temperature (higher = more diverse outputs)
|
| 41 |
+
|
| 42 |
+
## Examples
|
| 43 |
+
|
| 44 |
+
The model was trained on various reaction types from the ORD database, including:
|
| 45 |
+
- Buchwald-Hartwig amination reactions
|
| 46 |
+
- Cross-coupling reactions
|
| 47 |
+
- And many other organic reactions
|
| 48 |
+
|
| 49 |
+
## Citation
|
| 50 |
+
|
| 51 |
+
If you use this model, please cite:
|
| 52 |
+
- The Open Reaction Database: https://open-reaction-database.org/
|
| 53 |
+
- Model: https://huggingface.co/smitathkr1/ord-forward-t5
|
| 54 |
+
- Dataset: https://huggingface.co/datasets/smitathkr1/ord-reactions
|
| 55 |
+
|
| 56 |
+
## License
|
| 57 |
+
|
| 58 |
+
Apache 2.0
|
app.py
ADDED
|
@@ -0,0 +1,143 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
import gradio as gr
|
| 2 |
+
from transformers import T5ForConditionalGeneration, T5Tokenizer
|
| 3 |
+
import torch
|
| 4 |
+
|
| 5 |
+
# Load the model and tokenizer
|
| 6 |
+
model_name = "smitathkr1/ord-forward-t5"
|
| 7 |
+
print(f"Loading model: {model_name}")
|
| 8 |
+
tokenizer = T5Tokenizer.from_pretrained(model_name)
|
| 9 |
+
model = T5ForConditionalGeneration.from_pretrained(model_name)
|
| 10 |
+
|
| 11 |
+
# Set device
|
| 12 |
+
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
|
| 13 |
+
model.to(device)
|
| 14 |
+
model.eval()
|
| 15 |
+
|
| 16 |
+
def predict_reaction(reactants_smiles, max_length=150, num_beams=5, temperature=1.0):
|
| 17 |
+
"""
|
| 18 |
+
Predict the product of a chemical reaction given reactants in SMILES format.
|
| 19 |
+
|
| 20 |
+
Args:
|
| 21 |
+
reactants_smiles: SMILES string of reactants (can be separated by '.')
|
| 22 |
+
max_length: Maximum length of generated sequence
|
| 23 |
+
num_beams: Number of beams for beam search
|
| 24 |
+
temperature: Sampling temperature
|
| 25 |
+
|
| 26 |
+
Returns:
|
| 27 |
+
Predicted product SMILES
|
| 28 |
+
"""
|
| 29 |
+
try:
|
| 30 |
+
# Prepare input
|
| 31 |
+
input_text = reactants_smiles.strip()
|
| 32 |
+
|
| 33 |
+
# Tokenize input
|
| 34 |
+
inputs = tokenizer(
|
| 35 |
+
input_text,
|
| 36 |
+
return_tensors="pt",
|
| 37 |
+
max_length=512,
|
| 38 |
+
truncation=True,
|
| 39 |
+
padding=True
|
| 40 |
+
).to(device)
|
| 41 |
+
|
| 42 |
+
# Generate prediction
|
| 43 |
+
with torch.no_grad():
|
| 44 |
+
outputs = model.generate(
|
| 45 |
+
inputs["input_ids"],
|
| 46 |
+
max_length=max_length,
|
| 47 |
+
num_beams=num_beams,
|
| 48 |
+
temperature=temperature,
|
| 49 |
+
early_stopping=True,
|
| 50 |
+
do_sample=False
|
| 51 |
+
)
|
| 52 |
+
|
| 53 |
+
# Decode output
|
| 54 |
+
predicted_product = tokenizer.decode(outputs[0], skip_special_tokens=True)
|
| 55 |
+
|
| 56 |
+
return predicted_product
|
| 57 |
+
|
| 58 |
+
except Exception as e:
|
| 59 |
+
return f"Error: {str(e)}"
|
| 60 |
+
|
| 61 |
+
# Example inputs from ORD dataset
|
| 62 |
+
examples = [
|
| 63 |
+
["CC(C)N1CCN(C)CC1.Brc1ccccc1"], # Buchwald-Hartwig amination example
|
| 64 |
+
["CCN1CCNCC1.Ic1ccccc1"], # Another coupling reaction
|
| 65 |
+
["CC(=O)N1CCNCC1.Clc1ccccc1"], # Chloro coupling
|
| 66 |
+
]
|
| 67 |
+
|
| 68 |
+
# Create Gradio interface
|
| 69 |
+
iface = gr.Interface(
|
| 70 |
+
fn=predict_reaction,
|
| 71 |
+
inputs=[
|
| 72 |
+
gr.Textbox(
|
| 73 |
+
label="Reactants (SMILES)",
|
| 74 |
+
placeholder="Enter reactants in SMILES format (e.g., CC(C)N1CCN(C)CC1.Brc1ccccc1)",
|
| 75 |
+
lines=2
|
| 76 |
+
),
|
| 77 |
+
gr.Slider(
|
| 78 |
+
minimum=50,
|
| 79 |
+
maximum=300,
|
| 80 |
+
value=150,
|
| 81 |
+
step=10,
|
| 82 |
+
label="Max Length"
|
| 83 |
+
),
|
| 84 |
+
gr.Slider(
|
| 85 |
+
minimum=1,
|
| 86 |
+
maximum=10,
|
| 87 |
+
value=5,
|
| 88 |
+
step=1,
|
| 89 |
+
label="Num Beams"
|
| 90 |
+
),
|
| 91 |
+
gr.Slider(
|
| 92 |
+
minimum=0.1,
|
| 93 |
+
maximum=2.0,
|
| 94 |
+
value=1.0,
|
| 95 |
+
step=0.1,
|
| 96 |
+
label="Temperature"
|
| 97 |
+
)
|
| 98 |
+
],
|
| 99 |
+
outputs=gr.Textbox(
|
| 100 |
+
label="Predicted Product (SMILES)",
|
| 101 |
+
lines=2
|
| 102 |
+
),
|
| 103 |
+
examples=examples,
|
| 104 |
+
title="🧪 ORD Forward Reaction Prediction - T5 Model",
|
| 105 |
+
description="""
|
| 106 |
+
## Forward Reaction Prediction using T5
|
| 107 |
+
|
| 108 |
+
This model predicts chemical reaction products from reactants using a T5 model trained on 2.3M reactions from the Open Reaction Database (ORD).
|
| 109 |
+
|
| 110 |
+
**Model:** `smitathkr1/ord-forward-t5` (5 epochs completed)
|
| 111 |
+
|
| 112 |
+
**Dataset:** [smitathkr1/ord-reactions](https://huggingface.co/datasets/smitathkr1/ord-reactions)
|
| 113 |
+
|
| 114 |
+
### How to use:
|
| 115 |
+
1. Enter reactants in SMILES format (separate multiple reactants with '.')
|
| 116 |
+
2. Adjust generation parameters if needed
|
| 117 |
+
3. Click Submit to get the predicted product
|
| 118 |
+
|
| 119 |
+
### Example reactions:
|
| 120 |
+
- Buchwald-Hartwig amination reactions
|
| 121 |
+
- Various coupling reactions from the ORD database
|
| 122 |
+
""",
|
| 123 |
+
article="""
|
| 124 |
+
### About the Model
|
| 125 |
+
This T5 model was trained on 2.3 million reactions from the Open Reaction Database.
|
| 126 |
+
The training has completed 5 epochs so far.
|
| 127 |
+
|
| 128 |
+
### Citation
|
| 129 |
+
If you use this model, please cite the Open Reaction Database:
|
| 130 |
+
- [Open Reaction Database](https://open-reaction-database.org/)
|
| 131 |
+
|
| 132 |
+
### Notes
|
| 133 |
+
- Input should be valid SMILES strings
|
| 134 |
+
- The model predicts forward reactions (reactants → products)
|
| 135 |
+
- Adjust beam search parameters for different prediction strategies
|
| 136 |
+
""",
|
| 137 |
+
theme=gr.themes.Soft(),
|
| 138 |
+
allow_flagging="never"
|
| 139 |
+
)
|
| 140 |
+
|
| 141 |
+
# Launch the app
|
| 142 |
+
if __name__ == "__main__":
|
| 143 |
+
iface.launch()
|
requirements.txt
ADDED
|
@@ -0,0 +1,6 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
transformers>=4.30.0
|
| 2 |
+
torch>=2.0.0
|
| 3 |
+
gradio>=4.0.0
|
| 4 |
+
sentencepiece
|
| 5 |
+
protobuf
|
| 6 |
+
accelerate
|