# Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development

arXiv: https://arxiv.org/abs/2102.09548 · HTML: https://mlsanity.com/paper/2102.09548/

## Key facts

- Cited by 264 papers in the map (data through 14 Oct 2026).
- Builds on 43 of its 182 references that are in the map.
- First posted on arXiv 18 Feb 2021.

## Builds on (most cited first, 30 of 43)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [SuperGLUE: A Stickier Benchmark for General-Purpose Language Understanding Systems](https://mlsanity.com/paper/1905.00537/) (2019)
- [WILDS: A Benchmark of in-the-Wild Distribution Shifts](https://mlsanity.com/paper/2012.07421/) (2020)
- [Distributionally Robust Neural Networks for Group Shifts: On the Importance of Regularization for Worst-Case Generalization](https://mlsanity.com/paper/1911.08731/) (2019)
- [Deep CORAL: Correlation Alignment for Deep Domain Adaptation](https://mlsanity.com/paper/1607.01719/) (2016)
- [In Search of Lost Domain Generalization](https://mlsanity.com/paper/2007.01434/) (2020)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [Analyzing Learned Molecular Representations for Property Prediction](https://mlsanity.com/paper/1904.01561/) (2019)
- [Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation](https://mlsanity.com/paper/1806.02473/) (2018)
- [GuacaMol: Benchmarking Models for De Novo Molecular Design](https://mlsanity.com/paper/1811.09621/) (2018)
- [Grammar Variational Autoencoder](https://mlsanity.com/paper/1703.01925/) (2017)
- [Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models](https://mlsanity.com/paper/1811.12823/) (2018)
- [Molecular De Novo Design through Deep Reinforcement Learning](https://mlsanity.com/paper/1704.07555/) (2017)
- [Modeling polypharmacy side effects with graph convolutional networks](https://mlsanity.com/paper/1802.00543/) (2018)
- [Evaluating Protein Transfer Learning with TAPE](https://mlsanity.com/paper/1906.08230/) (2019)
- [Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction](https://mlsanity.com/paper/1811.02633/) (2018)
- [Optimization of Molecules via Deep Reinforcement Learning](https://mlsanity.com/paper/1810.08678/) (2018)
- [Fr'echet ChemNet Distance: A metric for generative models for molecules in drug discovery](https://mlsanity.com/paper/1803.09518/) (2018)
- [Invariant Risk Minimization Games](https://mlsanity.com/paper/2002.04692/) (2020)
- [Domain Generalization by Marginal Transfer Learning](https://mlsanity.com/paper/1711.07910/) (2017)
- [DeepDTA: Deep Drug-Target Binding Affinity Prediction](https://mlsanity.com/paper/1801.10193/) (2018)
- [Learning explanations that are hard to vary](https://mlsanity.com/paper/2009.00329/) (2020)
- [Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network](https://mlsanity.com/paper/1709.04555/) (2017)
- [Learning Multimodal Graph-to-Graph Translation for Molecular Optimization](https://mlsanity.com/paper/1812.01070/) (2018)
- [Molecule Edit Graph Attention Network: Modeling Chemical Reactions as Sequences of Graph Edits](https://mlsanity.com/paper/2006.15426/) (2020)

## Built on by (most cited first, 30 of 264)

- [ADBench: Anomaly Detection Benchmark](https://mlsanity.com/paper/2206.09426/) (2022)
- [ECOD: Unsupervised Outlier Detection Using Empirical Cumulative Distribution Functions](https://mlsanity.com/paper/2201.00382/) (2022)
- [Learning Causally Invariant Representations for Out-of-Distribution Generalization on Graphs](https://mlsanity.com/paper/2202.05441/) (2022)
- [Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders](https://mlsanity.com/paper/2203.12742/) (2022)
- [A Review of Large Language Models and Autonomous Agents in Chemistry](https://mlsanity.com/paper/2407.01603/) (2024)
- [Feynman-Kac Correctors in Diffusion: Annealing, Guidance, and Product of Experts](https://mlsanity.com/paper/2503.02819/) (2025)
- [Wild-Time: A Benchmark of in-the-Wild Distribution Shift over Time](https://mlsanity.com/paper/2211.14238/) (2022)
- [BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology](https://mlsanity.com/paper/2503.00096/) (2025)
- [Evaluating Explainability for Graph Neural Networks](https://mlsanity.com/paper/2208.09339/) (2022)
- [BOND: Benchmarking Unsupervised Outlier Node Detection on Static Attributed Graphs](https://mlsanity.com/paper/2206.10071/) (2022)
- [Local Latent Space Bayesian Optimization over Structured Inputs](https://mlsanity.com/paper/2201.11872/) (2022)
- [PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding](https://mlsanity.com/paper/2206.02096/) (2022)
- [Efficient Evolutionary Search Over Chemical Space with Large Language Models](https://mlsanity.com/paper/2406.16976/) (2024)
- [Learning Hierarchical Protein Representations via Complete 3D Graph Networks](https://mlsanity.com/paper/2207.12600/) (2022)
- [Differentiable Scaffolding Tree for Molecular Optimization](https://mlsanity.com/paper/2109.10469/) (2021)
- [GenMol: A Drug Discovery Generalist with Discrete Diffusion](https://mlsanity.com/paper/2501.06158/) (2025)
- [Gotta be SAFE: A New Framework for Molecular Design](https://mlsanity.com/paper/2310.10773/) (2023)
- [Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Language](https://mlsanity.com/paper/2303.03363/) (2023)
- [DrugAgent: Automating AI-aided Drug Discovery Programming through LLM Multi-Agent Collaboration](https://mlsanity.com/paper/2411.15692/) (2024)
- [GNNDelete: A General Strategy for Unlearning in Graph Neural Networks](https://mlsanity.com/paper/2302.13406/) (2023)
- [Does Invariant Graph Learning via Environment Augmentation Learn Invariance?](https://mlsanity.com/paper/2310.19035/) (2023)
- [RGFN: Synthesizable Molecular Generation Using GFlowNets](https://mlsanity.com/paper/2406.08506/) (2024)
- [TxGemma: Efficient and Agentic LLMs for Therapeutics](https://mlsanity.com/paper/2504.06196/) (2025)
- [Towards Foundational Models for Molecular Learning on Large-Scale Multi-Task Datasets](https://mlsanity.com/paper/2310.04292/) (2023)
- [Genetic-guided GFlowNets for Sample Efficient Molecular Optimization](https://mlsanity.com/paper/2402.05961/) (2024)
- [On the Scalability of GNNs for Molecular Graphs](https://mlsanity.com/paper/2404.11568/) (2024)
- [Diffusion Models as Constrained Samplers for Optimization with Unknown Constraints](https://mlsanity.com/paper/2402.18012/) (2024)
- [A Systematic Survey of Chemical Pre-trained Models](https://mlsanity.com/paper/2210.16484/) (2022)
- [Are large language models superhuman chemists?](https://mlsanity.com/paper/2404.01475/) (2024)
- [PyGOD: A Python Library for Graph Outlier Detection](https://mlsanity.com/paper/2204.12095/) (2022)

## Abstract (arXiv)

Therapeutics machine learning is an emerging field with incredible opportunities for innovatiaon and impact. However, advancement in this field requires formulation of meaningful learning tasks and careful curation of datasets. Here, we introduce Therapeutics Data Commons (TDC), the first unifying platform to systematically access and evaluate machine learning across the entire range of therapeutics. To date, TDC includes 66 AI-ready datasets spread across 22 learning tasks and spanning the discovery and development of safe and effective medicines. TDC also provides an ecosystem of tools and community resources, including 33 data functions and types of meaningful data splits, 23 strategies for systematic model evaluation, 17 molecule generation oracles, and 29 public leaderboards. All resources are integrated and accessible via an open Python library. We carry out extensive experiments on selected datasets, demonstrating that even the strongest algorithms fall short of solving key therapeutics challenges, including real dataset distributional shifts, multi-scale modeling of heterogeneous data, and robust generalization to novel data points. We envision that TDC can facilitate algorithmic and scientific advances and considerably accelerate machine-learning model development, validation and transition into biomedical and clinical implementation. TDC is an open-science initiative available at https://tdcommons.ai.