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.

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

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.

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.

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.

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

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.

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

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.

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.

We are excited to be at ICML 2021 where we will present 1 paper at Workshop on Socially Responsible Machine Learning, 1 paper at Workshop on Theoretic Foundation, Criticism, and Application Trend of Explainable AI, 2 papers at Workshop on Interpretable Machine Learning in Healthcare, and 1 paper at Workshop on Computational Biology. Congratulations to fantastic students!

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.

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

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.

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.

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.

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.

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

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.

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.