Open Source Data

Therapeutics Data Commons

Machine Learning Datasets and Tasks for Therapeutics

TDC is the first unifying framework to systematically access and evaluate machine learning across the entire range of therapeutics.

At its core, TDC is a collection of curated datasets and learning tasks to serve as a meeting point for domain and ML scientists. TDC also provides an ecosystem of tools, libraries, leaderboards, and community resources, including data functions, strategies for systematic model evaluation, meaningful data splits, data processors, and molecule generation oracles. All datasets and learning tasks are integrated and accessible via an open-source library.

View the TDC Website

BioSNAP

Stanford Biomedical Network Dataset Collection

BioSNAP is a collection diverse biomedical networks, inclusing protein-protein interaction networks, single-cell similarity networks, drug-drug interaction networks.

BioSNAP datasets contain metadata on graphs and node features, and can be easily linked to external repositories of biological knowledge.

View the BioSNAP Website

OGB

The Open Graph Benchmark

OGB is a collection of benchmark datasets, data loaders, and evaluators for graph machine learning. Datasets cover a variety of graph machine learning tasks and real-world applications.

The OGB data loaders are fully compatible with popular graph deep learning frameworks, including Pytorch Geometric and DGL. They provide automatic dataset downloading, standardized dataset splits, and unified performance evaluation.

View the OGB Website

Disease pathways

Disease pathways overlaid on the human interactome

View Disease Pathway Dataset

Multimodal cancer network

Multimodal network centered on genes frequently mutated in cancer patients

The multimodal cancer network integrates information on chemicals, diseases, molecular functions, genes, and protein.

The dataset has 21 types of biologically meaningful associations (edge types): chemical-chemical, chemical-protein, disease-chemical, disease-disease, disease-function, disease-gene, function-function, gene-gene (split into 6 edge types by interaction type), gene-protein, protein-function, and protein-protein interactions.

The network has 20 K nodes and 3.4 M edges.

View the Multimodal Cancer Network

Giga-scale biological network

The giga-scale biological network is one of the largest networks ever constructed in biology. The network integrates protein and genetic interaction data from more than two thousand species.

The network has 10 M nodes and 2.3 B edges.

View the Giga-Scale Biological Network

Tree of life

Protein interactomes across the tree of life

The dataset contains protein interactomes from 1,840 species across the tree of life. The dataset contains rich metadata about prrteins, including their homology relationships

The dataset also contains metadata about species, including taxonomy of species, phylogenetic reltionships, and ecological information on environments and habitats in which species live.

View the Tree of Life dataset

Polypharmacy network

Network of drugs, proteins, and side effects

The polypharmacy network is a highly multi-relational network, consisting of protein-protein interactions, drug-protein targets, and drug-drug interactions encoded by polypharmacy side effects.

The network has 20 K nodes and 5 M edges, which are split into 1 K distinct edge types.

View the Polypharmacy Network

Tissue-specific protein dataset

The dataset contains protein-protein interaction networks specific to 107 human tissues, a tissue hierarchy of anatomical relationships between tissues, and tissue-specific gene-function annotations.

View the Tissue-Specific Protein Dataset

Human knowledge network

The human knowledge network contains interactions between proteins, diseases, biological processes, side effects, and drugs.

The network has 98 K nodes and 8 M edges, which are split into 42 distinct types of biologically relevant molecular interactions.

View the Human Knowledge Network

Latest News

Apr 2021:   Representation Learning for Biomedical Nets

In our survey on representation learning for biomedical networks we discuss how long-standing principles of network biology and medicine provide the conceptual grounding for representation learning, explain its successes, and inform future advances.

Mar 2021:   Receiving Amazon Research Award

We are excited about receiving Amazon Faculty Research Award on Actionable Graph Learning for Finding Cures for Emerging Diseases. Thank you to Amazon Science for supporting our research.

Mar 2021:   Michelle's Graduate Research Fellowship

Michelle M. Li won the NSF Graduate Research Fellowship Award. Congratulations!

Mar 2021:   Hot Off the Press: Multiscale Interactome

Hot off the press! We develop a multiscale interactome approach to explain disease treatments. The approach can predict drug-disease treatments, identify proteins and biological functions related to treatment, and identify genes that alter treatment’s efficacy and adverse reactions.

Mar 2021:   Graph Networks in Computational Biology

We are excited to share slides from our recent lecture on Graph Neural Networks in Computational Biology, which we gave at Stanford ML for Graphs course.

Mar 2021:   Fair and Stable Graph Representation Learning

We are thrilled to share the latest preprint on fair and stable graph representation learning.

Feb 2021:   New Preprint on Therapeutics Data Commons

Jan 2021:   An Algorithmic Approach to Patient Safety

The new algorithmic approach investigates population-scale patient safety data and reveals inequalities in adverse events before and during COVID-19 pandemic.

Jan 2021:   Workshop on AI in Health at the Web Conference

We are excited to co-organize Workshop on AI in Health: Transferring and Integrating Knowledge for Better Health at the Web (WWW) conference. The call for papers is open! We also announce the AI in Health Data Challenge.

Jan 2021:   Tutorial on ML for Drug Development

We will present a tutorial on ML/AI for drug discovery and development at IJCAI conference. See the tutorial website.

Dec 2020:   Two New Papers Published

Dec 2020:   Bayer Early Excellence in Science Award

Our research won the Bayer Early Excellence in Science Award. We are honored to have received this recognition!

Nov 2020:   Therapeutics Data Commons (TDC)

We are thrilled to announce Therapeutics Data Commons (TDC)! We invite you to join TDC. TDC is an open-source and community-driven effort.

Nov 2020:   National Symposium on the Future of Drugs

On behalf of the NSF, we are organizing the National Symposium on Drug Repurposing for Future Pandemics. We have a stellar lineup of invited speakers! Register at www.drugsymposium.org.

Oct 2020:   MARS: Novel Cell Types in Single-cell Datasets

Sep 2020:   Four Papers Accepted at NeurIPS

Thrilled that our lab has 4 papers accepted at NeurIPS 2020! Congratulations to fantastic students and collaborators, Michelle, Xiang, Kexin, Sam, and Emily.

Sep 2020:   MITxHarvard Women in AI Interview

The MITxHarvard Women in AI initiative talked with Marinka about AI, machine learning, and the role of new technologies in biomedical research.

Aug 2020:   Trustworthy AI for Healthcare

We are excited to be co-organizing a workshop at AAAI 2021 on Trustworthy AI for Healthcare! We have a stellar lineup of speakers. Details to follow soon!

Aug 2020:   Network Drugs for COVID-19

What are network drugs? Drugs for COVID-19 predicted by network medicine, our graph neural networks (GNNs), and our rank aggregation algorithms, followed by experimental confirmations. The full paper is finally out!

Jul 2020:   Podcast on ML for Drug Development

Tune in to the podcast with Marinka about machine learning to drug development. The discussion focuses on open research questions in the field, including how to limit the search space of high-throughput screens, design drugs entirely from scratch, and identify likely side-effects of combining drugs in novel ways.

Zitnik Lab  ·  Harvard  ·  Department of Biomedical Informatics