Conference paper · 2025
PyTDC: A multimodal machine learning training, evaluation, and inference platform for biomedical foundation models
Alejandro Velez-Arce, Marinka Zitnik
Forty-second International Conference on Machine Learning (ICML 2025)
Research index
Papers and talks
PyTDC publications are listed separately from foundational Therapeutics Data Commons papers. Workshop papers and preprints are labeled as such.
PyTDC
Workshop paper · 2024
Signals in the Cells: Multimodal and Contextualized Machine Learning Foundations for Therapeutics
Alejandro Velez-Arce, Xiang Lin, Kexin Huang, Michelle M. Li, Wenhao Gao, Bradley Pentelute, Tianfan Fu, Manolis Kellis, Marinka Zitnik
NeurIPS 2024 Workshop on AI for New Drug Modalities
Workshop paper, not a NeurIPS conference proceedings paper.
Talk · 2024
Signals in the Cells: Multimodal and Contextualized Machine Learning Foundations for Therapeutics
Alejandro Velez-Arce
Western Bioinformatics Seminar Series
Seminar presentation; not a peer-reviewed paper.
Related preprints
Preprint · 2024
TDC-2: Multimodal Foundation for Therapeutic Science
Alejandro Velez-Arce, Kexin Huang, Michelle Li, Xiang Lin, Wenhao Gao, Tianfan Fu, Manolis Kellis, Bradley L. Pentelute, Marinka Zitnik
bioRxiv preprint; presented at MoML 2024
Preprint. Authors taken from bioRxiv version 2 (doi:10.1101/2024.06.12.598655).
Foundational TDC
PyTDC is built on Therapeutics Data Commons (TDC), an earlier collection of ML-ready datasets and tasks for drug discovery. The paper below describes TDC; it is not a PyTDC publication.
Foundational TDC paper · 2021
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development
Kexin Huang, Tianfan Fu, Wenhao Gao, Yue Zhao, Yusuf Roohani, Jure Leskovec, Connor W. Coley, Cao Xiao, Jimeng Sun, Marinka Zitnik
NeurIPS Datasets and Benchmarks, 2021
Foundational TDC paper. Describes the Therapeutics Data Commons dataset collection that PyTDC builds on; it is not a PyTDC publication.
How to cite
If you use the PyTDC platform, cite the ICML 2025 paper. If you use a specific TDC dataset or function, also cite the original resource paper listed on that dataset’s page. Software is MIT-licensed; dataset and model artifacts follow their upstream licenses.