Benchmarking Datasets & Metrics — Hands-on

Build trustworthy model benchmarks for QSAR/ADMET and related tasks using MoleculeNet and the Therapeutics Data Commons (TDC) . This hands-on module covers dataset curation, split strategies (random/scaffold/time/geography) , metric selection for imbalanced data, calibration & uncertainty, and leaderboard-quality reporting with complete reproducibility.

Benchmarking Datasets & Metrics (MoleculeNet/TDC)

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Session Index

Session 1 — Datasets, Curation & Splits Session 2 — Metrics, Imbalance & Calibration Session 3 — Baselines, Reproducibility & UQ Session 4 — Mini Capstone: Leaderboard

Session 1

Fee: Rs 18800

Datasets, Curation & Splits

MoleculeNet & TDC overview

tasks: cls/reg/multi-task data cards & provenance licensing & ethics

Curation & hygiene

standardization & dedupe unit/assay harmonization scaffold/time-aware splits

Leakage prevention

series & near-duplicate checks vendor/batch effects split diagnostics

Session 2

Fee: Rs 21800

Metrics, Imbalance & Calibration

Choosing the right metrics

ROC-AUC vs PR-AUC AUROC pitfalls on imbalance RMSE/MAE/R² for regression

Thresholds & calibration

Youden/F1/expected cost reliability/Brier/ECE cost-sensitive curves

Imbalance handling

stratified CV class weights & resampling confidence bands

Session 3

Fee: Rs 24800

Baselines, Reproducibility & Uncertainty

Model baselines & controls

linear/RF/XGB graph & transformer (lite) ablation & sanity checks

Reproducibility & seeds

config-managed runs fixed seeds & CI checks data/version hashes

Uncertainty & AD

ensembles & bootstraps conformal intervals applicability domain flags

Session 4

Fee: Rs 28800

Mini Capstone: Reproducible Leaderboard

Create a benchmark suite on 2–3 datasets (cls + reg)

Theory + Practical

Report with proper metrics & calibration

ROC/PR & RMSE/MAE reliability/ECE plots uncertainty/AD overlays

Deliverables

leaderboard (CSV/HTML) configs/notebooks & seeds dataset/data-card bundle

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Benchmarking Datasets & Metrics (MoleculeNet/TDC) | Robust Splits, Metrics & Reproducibility

Benchmarking Datasets & Metrics — Hands-on