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Predicting Molecular Toxicity (Lethal Dose) — PharmaHacks 2026

Challenge #1: Winner

Team

Joyanne Ma, Akhila Raj, Dorra Tray

Approach

We predict rat oral LD50 from molecular SMILES strings using:

  • Morgan fingerprints + physicochemical descriptors (RDKit)
  • XGBoost + Random Forest ensemble
  • SHAP analysis for interpretability

Results

  • Test R² = 0.6368
  • Test MAE = 0.4241
  • Test RMSE = 0.5697

How to run

  1. Open in Google Colab
  2. Run all cells top to bottom
  3. Final test evaluation is in the last section

Requirements

pyTDC, rdkit, xgboost, scikit-learn, shap, pandas, numpy, matplotlib, seaborn, pillow

About

End-to-end ML pipeline for toxicity prediction from SMILES using Morgan fingerprints, molecular descriptors, and ensemble models (RF, XGBoost).

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