README.md

---
language: en
license: mit
library_name: pytorch
tags:
- chemistry
- toxicity-prediction
- graph-neural-network
- drug-discovery
- tox21
- multi-task-learning
- uncertainty-quantification
pipeline_tag: feature-extraction
datasets:
- tox21
metrics:
- name: CV AUC Mean
  type: roc_auc
  value: 0.7856
- name: CV AUC Std
  type: roc_auc_std
  value: 0.0394
- name: Number of Tasks
  type: count
  value: 10
model-index:
- name: ToxiPredict GNN
  results:
  - task:
      type: toxicity-prediction
      name: Multi-Task Toxicity Prediction
    dataset:
      type: tox21
      name: Tox21
      config: 12-bioassay
    metrics:
    - type: roc_auc
      value: 0.7856
      name: 5-Fold CV Mean AUC
    - type: roc_auc_std
      value: 0.0394
      name: 5-Fold CV AUC Standard Deviation
---

# ToxiPredict — Multi-Task GNN for Toxicophore Prediction

Uncertainty-aware multi-task graph neural network trained on the Tox21 dataset for predicting toxicity across 10 biological endpoints, with 5-fold cross-validated performance.

## Model Description

| Property | Value |
|----------|-------|
| **Architecture** | MultiTaskGNN_ResGATv2_JK_VN |
| **Input** | Molecular graphs (SMILES → 45-dim node, 11-dim edge features) |
| **Output** | 10 binary toxicity predictions + uncertainty weights |
| **Parameters** | 12 learnable homoscedastic uncertainty log-variance parameters |
| **Training Data** | Tox21 (6264 training compounds after scaffold split) |
| **Validation** | 5-fold Bemis-Murcko scaffold cross-validation |
| **Framework** | PyTorch 2.10 + PyTorch Geometric 2.6 |

## Performance

**5-Fold Cross-Validation: 0.7856 ± 0.0394 Mean AUC**

The model was evaluated using Bemis-Murcko scaffold split, ensuring that structurally similar molecules are grouped in the same fold. This provides a realistic estimate of generalization to novel chemical scaffolds.

| Task | Type |
|------|------|
| NR-AR | Nuclear Receptor |
| NR-AhR | Nuclear Receptor |
| NR-Aromatase | Nuclear Receptor |
| NR-ER | Nuclear Receptor |
| NR-PPAR-gamma | Nuclear Receptor |
| SR-ARE | Stress Response |
| SR-ATAD5 | Stress Response |
| SR-HSE | Stress Response |
| SR-MMP | Stress Response |
| SR-p53 | Stress Response |

## Architecture Details

The model extends standard GAT with three key innovations:

1. **Residual GATv2 Convolutions**: Two-layer GATv2 with residual connections and 4 attention heads per layer, providing dynamic attention mechanisms that adapt to molecular substructures.
2. **JumpingKnowledge (JK) Aggregation**: Concatenates intermediate layer representations before prediction, preserving both local and global structural information.
3. **Virtual Node**: A learned virtual node connected to all atoms enables global molecular context propagation across the graph.
4. **Homoscedastic Uncertainty Weighting**: Learnable per-task log-variance parameters dynamically balance gradient contributions during multi-task training.

## Usage

```python
import torch
from safetensors.torch import load_file
from huggingface_hub import hf_hub_download

# Download model
model_path = hf_hub_download(
    repo_id="Arko007/toxipredict-gnn-models",
    filename="model.safetensors"
)
state_dict = load_file(model_path)

# Load config
config_path = hf_hub_download(
    repo_id="Arko007/toxipredict-gnn-models",
    filename="model_config.json"
)
import json
with open(config_path) as f:
    config = json.load(f)

# Initialize model with same architecture
model = MultiTaskGNN_ResGATv2_JK_VN(
    node_dim=config["node_dim"],
    edge_dim=config["edge_dim"],
    hidden_dim=config["hidden_dim"],
    num_tasks=config["num_tasks"],
    dropout=config["dropout"]
)
model.load_state_dict(state_dict)
model.eval()
```

## Training Details

- **Optimizer**: Adam (lr=1e-3, weight_decay=1e-5)
- **Batch Size**: 64
- **Max Epochs**: 200 (early stopping patience=20)
- **Loss**: Homoscedastic uncertainty-weighted binary cross-entropy
- **Hardware**: NVIDIA T4 GPU (Kaggle)
- **Training Time**: ~12 minutes per run

## References

- Tox21 Challenge: [https://tripod.nih.gov/tox21/challenge/](https://tripod.nih.gov/tox21/challenge/)
- GATv2: Brody et al., ICLR 2022
- JumpingKnowledge: Xu et al., ICML 2018
- Homoscedastic Uncertainty: Kendall et al., NeurIPS 2017

## License

MIT