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README.md

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+---
+language: en
+license: mit
+tags:
+  - chemistry
+  - toxicology
+  - molecular-property-prediction
+  - tox21
+  - pytorch
+datasets:
+  - scikit-fingerprints/MoleculeNet_Tox21
+metrics:
+  - roc_auc
+---
+
+# Molecular Toxicity Predictor
+
+Multi-task neural network that screens small molecules across the **Tox21** panel of 12 in-vitro toxicity assays.
+
+## Model Description
+
+- **Architecture:** Multi-task MLP — 2048 → 1024 → 512 → 12
+- **Input:** Morgan fingerprints (ECFP4, radius=2, 2048 bits) via RDKit
+- **Output:** Probability of activity for each of 12 toxicity assays
+- **Loss:** Masked binary cross-entropy (NaN labels are excluded per task)
+- **Metric:** Mean AUC-ROC across tasks
+
+## Tox21 Assays
+
+| Task | Target |
+|------|--------|
+| NR-AR | Androgen receptor |
+| NR-AR-LBD | Androgen receptor ligand-binding domain |
+| NR-AhR | Aryl hydrocarbon receptor |
+| NR-Aromatase | Aromatase enzyme inhibition |
+| NR-ER | Estrogen receptor alpha |
+| NR-ER-LBD | Estrogen receptor LBD |
+| NR-PPAR-gamma | Peroxisome proliferator-activated receptor gamma |
+| SR-ARE | Antioxidant response element |
+| SR-ATAD5 | Genotoxicity / DNA damage (ATAD5 reporter) |
+| SR-HSE | Heat shock response element |
+| SR-MMP | Mitochondrial membrane potential |
+| SR-p53 | p53 tumour suppressor / DNA damage |
+
+## Training Data
+
+- **Dataset:** [Tox21 via MoleculeNet](https://huggingface.co/datasets/scikit-fingerprints/MoleculeNet_Tox21)
+- **Train:** 6,264 molecules | **Val:** 783 | **Test:** 784 (80/10/10 split from 7,831 total)
+- Labels are sparse — ~17% NaN on average; untested entries are treated as missing, not negative
+
+## Usage
+
+```python
+import json
+import numpy as np
+import torch
+import torch.nn as nn
+from rdkit import Chem
+from rdkit.Chem import rdFingerprintGenerator
+from huggingface_hub import hf_hub_download
+
+TASKS = [
+    "NR-AR", "NR-AR-LBD", "NR-AhR", "NR-Aromatase",
+    "NR-ER", "NR-ER-LBD", "NR-PPAR-gamma",
+    "SR-ARE", "SR-ATAD5", "SR-HSE", "SR-MMP", "SR-p53",
+]
+
+class ToxMLP(nn.Module):
+    def __init__(self, n_inputs=2048, n_outputs=12, dropout=0.3):
+        super().__init__()
+        self.net = nn.Sequential(
+            nn.Linear(n_inputs, 1024), nn.BatchNorm1d(1024), nn.ReLU(), nn.Dropout(dropout),
+            nn.Linear(1024, 512),      nn.BatchNorm1d(512),  nn.ReLU(), nn.Dropout(dropout),
+            nn.Linear(512, n_outputs),
+        )
+    def forward(self, x):
+        return self.net(x)
+
+model_path = hf_hub_download("Hari5115/molecular-toxicity-predictor", "best_model.pt")
+model = ToxMLP()
+model.load_state_dict(torch.load(model_path, map_location="cpu"))
+model.eval()
+
+fp_gen = rdFingerprintGenerator.GetMorganGenerator(radius=2, fpSize=2048)
+mol    = Chem.MolFromSmiles("CC(=O)Oc1ccccc1C(=O)O")  # aspirin
+fp     = torch.tensor([list(fp_gen.GetFingerprint(mol))], dtype=torch.float32)
+
+with torch.no_grad():
+    probs = torch.sigmoid(model(fp)).squeeze().numpy()
+
+for task, p in zip(TASKS, probs):
+    print(f"{task}: {p:.1%}")
+```
+
+## Results
+
+Test set performance (mean AUC-ROC: **0.8170**):
+
+| Task | AUC-ROC |
+|------|---------|
+| NR-AR | 0.752 |
+| NR-AR-LBD | 0.890 |
+| NR-AhR | 0.892 |
+| NR-Aromatase | 0.792 |
+| NR-ER | 0.751 |
+| NR-ER-LBD | 0.808 |
+| NR-PPAR-gamma | 0.742 |
+| SR-ARE | 0.803 |
+| SR-ATAD5 | 0.847 |
+| SR-HSE | 0.811 |
+| SR-MMP | 0.847 |
+| SR-p53 | 0.868 |
+
+Random Forest baseline (val): 0.8306 — MLP val: **0.8544**
+
+## Limitations
+
+- Morgan fingerprints capture local chemical structure but miss 3D conformation and long-range interactions.
+- The model is trained on a relatively small dataset (~6,000 molecules); extrapolation to novel chemical classes may be unreliable.
+- **For research and educational purposes only. Not a substitute for certified toxicological testing.**
+
+## Dataset Credit
+
+Tox21 data provided by the NIH National Center for Advancing Translational Sciences (NCATS).  
+Accessed via [scikit-fingerprints/MoleculeNet_Tox21](https://huggingface.co/datasets/scikit-fingerprints/MoleculeNet_Tox21) on HuggingFace.
+
+## License
+
+MIT