Our short paper on Interactive Visual Explanations for Deep Drug Repurposing received the Best Paper Award at ICML 2021 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.
We are excited to share the preprint on Therapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics. TDC is available at http://tdcommons.ai.
The new algorithmic approach investigates population-scale patient safety data and reveals inequalities in adverse events before and during COVID-19 pandemic.
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.
We are excited to see published our paper on DeepPurpose, a deep learning library for drug-target interaction prediction, and our paper on skipGNN, a graph neural network for predicting molecular interactions.
Our research won the Bayer Early Excellence in Science Award. We are honored to have received this recognition!
We are thrilled to announce Therapeutics Data Commons (TDC)! We invite you to join TDC. TDC is an open-source and community-driven effort.
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.
Hot off the press! MARS, an approach for discovering novel cell types across heterogeneous single-cell experiments is just published in Nature Methods.
The MITxHarvard Women in AI initiative talked with Marinka about AI, machine learning, and the role of new technologies in biomedical research.
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.
We have a new opening for a postdoctoral research fellow in novel machine learning methods to combat COVID-19! Submit your application by September 1, 2020.
DeepPurpose is a deep learning library for drug-target interaction prediction and applications to drug repurposing and virtual screening.
Subgraph neural networks learn powerful subgraph representations that create fundamentally new opportunities for predictions beyond nodes, edges, and entire graphs.
GNNGuard can defend graph neural networks against a variety of training-time attacks. Remarkably, GNNGuard can restore state-of-the-art performance of any GNN in the face of adversarial attacks.
G-Meta is a meta-learning approach for graphs that quickly adapts to new prediction tasks using only a handful of data points. G-Meta works in most challenging, few-shot learning settings and scales to massive interactomics data as we show on our new Networks of Life dataset comprising of 1,840 networks.
A new paper introducing the Open Graph Benchmark, a diverse set of challenging and realistic benchmark datasets for graph machine learning.
Marinka is co-editing a special issue of IEEE Big Data on AI for COVID-19. In light of the urgent need for data-driven solutions to mitigate the COVID-19 pandemic, the special issue will aim for a fast-track peer review.
A new preprint describing a graph neural network approach for the prediction of molecular interactions, including drug-drug, drug-target, protein-protein, and gene-disease interactions.
The call for ECML-PKDD 2020 PhD Forum Track is now online. If you are a PhD student, submit your work on machine learning and knowledge discovery.
We are excited to share our latest results on how networks and graph machine-learning help us search for a cure for COVID-19.
We are joining AI Cures initiative at MIT! We will develop machine learning methods for finding promising antiviral molecules for COVID-19 and other emerging pathogens.
Haoxin, Michelle, and Xiang joined the lab. Welcome! We look forward to seeing you all in the lab!
A new preprint on meta learning for identifying and naming cell types, even cell types that have never been seen before and do not exist in the training data. Check it out!
Marinka is co-editing a special issue of ACM/IEEE TCBB on Deep learning and graph embeddings for network biology. Submit your finest work!
Kathleen, Jingyi, Kexin, Yujie, and Stone joined the lab. Welcome!