Open Source Datasets

Population-Scale Patient Safety Dataset

Adverse Events of Medications across Patient Groups and the Entire Range of Human Diseases and Approved Drugs

We present a comprehensive catalog of 10,443,476 adverse event reports (involving 19,193 adverse events and 3,624 drugs) from the U.S. Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS), collected from January 2013 to September 2020. The new resource can help discover relationships between drugs and safety events, especially in cases of rare events and effects within population subgroups that differ in their risks of specific clinical outcomes and are disproportionately affected by preventable inequities.

View the Patient Safety Dataset

Subgraph Datasets

Datasets for Subgraph Representation Learing Research

We design novel synthetic datasets and real-world social and biological datasets, each consisting of an underlying base graph and subgraphs with associated labels.

View the SubGNN Website

Therapeutics Data Commons

Machine Learning Datasets and Tasks for Drug Discovery and Development

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 AI/ML-ready 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


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

Fair Graph Datasets

Graph datasets comprising of high-stakes decisions in criminal justice and financial lending domains

Graph datasets comprise of critical decisions in criminal justice (if a defendant should be released on bail) and financial lending (if an individual should be given loan) domains. These attributed graphs contain sensitive/protected attributes, which makes them suitable for studying algorithmic fairness.

View the NIFTY website


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

Oct 2021:   Adverse Drug Effects During the Pandemic

The COVID-19 pandemic has reshaped health and medicine in ways both dramatic and subtle. Some of the less obvious shifts can only emerge from analysis of millions of pieces of data—patient records, medical notes, clinical encounter reports. Check out the story in Harvard Medicine News highlighting our research.

Oct 2021:   Graph-Guided Networks for Time Series

New preprint! We introduce Raindrop, a graph-guided network for learning representations of irregularly sampled multivariate time series.

Oct 2021:   Massive Analysis of Differential Adverse Events

Hot off the press in Nature Computational Science! We develop an algorithmic approach for massive analysis of drug adverse events. Our analyses of 10,443,476 adverse event reports have implications for safe medication use and public health policy, and can enable comparison of COVID-19 pandemic to other health emergencies.

Sep 2021:   Leveraging Cell Ontology to Classify Cell Types

Hot off the press in Nature Communications! We developed OnClass, an algorithm and accompanying software for automatically classifying cells into cell types that are part of the controlled vocabulary that forms the Cell Ontology.

Sep 2021:   Major New Release of TDC

We are very excited to announce a major release of Therapeutics Data Commons! In the 0.3.0 release we restructured the codebase, simplified the backend and kept user interfaces the same. We also provide detailed documentation for our TDC package.

Aug 2021:   Trustworthy AI for Healthcare at AAAI

We will be organizing a meeting on Trustworthy AI for Healthcare at AAAI 2022. Stay tuned for details and call for papers.

Aug 2021:   New Paper on Therapeutics Data Commons

Our latest paper on Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development will appear at NeurIPS. We are excited to contribute novel datasets and benchmarks in the broad area of therapeutics.

Aug 2021:   AI for Science at NeurIPS

We are organizing the AI for Science workshop at NeurIPS 2021 and have a stellar lineup of invited speakers.

Aug 2021:   Best Poster Award at ICML Comp Biology

Congratulations to Michelle for winning the Best Poster Award for her work on deep contextual learners for protein networks at the ICML Workshop on Computational Biology.

Jul 2021:   Best Paper Award at ICML Interpretable ML

Our short paper on Interactive Visual Explanations for Deep Drug Repurposing received the Best Paper Award at the ICML Interpretable ML in Healthcare Workshop. Stay tuned for more news on this evolving project.

Jul 2021:   Five presentations at ICML 2021

Jun 2021:   Theory and Evaluation for Explanations

We introduce the first axiomatic framework for theoretically analyzing, evaluating, and comparing GNN explanation methods. We formalize key properties that all methods should satisfy to generate reliable explanations: faithfulness, stability, and fairness.

Jun 2021:   Deep Contextual Learners for Protein Networks

New preprint on contextualized protein embeddings aims to characterize genes with disease-specific interactions and elucidate disease manifestation in specific cell types.

May 2021:   New Paper Accepted at UAI

Our unified framework for fair and stable graph representation learning has just been accepted at UAI. We establish a theoretical connection between counterfactual fairness and stability and use it in a framework that can be used with any GNN to learn fair and stable embeddings.

Apr 2021:   Hot Off the Press: COVID-19 Repurposing in PNAS

Hot off the press! We deployed AI/ML and network medicine algorithms to rank 6,340 drugs for their expected efficacy against SARS-CoV-2. We screened in human cells the top-ranked drugs, identifying six drugs that reduced viral infection, four of which could be repurposed to treat COVID-19.

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.

Zitnik Lab  ·  Harvard  ·  Department of Biomedical Informatics