Postdoctoral Research Fellow in AI/ML

Overview

Prof. Marinka Zitnik invites applications for a Postdoctoral Research Fellowship position at Harvard University.

The selected candidate will be expected to lead research in novel methods in the broad area of deep learning for graphs, with a particular focus on knowledge graphs, transfer learning, few-shot learning, graph representation learning architectures, image-intensive graphs, and text/language-intensive graphs. In addition, the candidate will also devise novel actionable algorithms and use them for applications in biomedical discovery, drug discovery and development, and therapeutics, all in partnership with collaborators.

Qualifications

We seek highly-motivated applicants with background in one or more of the following areas: machine learning, explainable AI/ML, computational healthcare, and network science. Successful applicants will be strong technically as well as have an inclination towards real-world problems.

We are looking for applicants with demonstrably strong research skills, ideally, with multiple publications in top venues in machine learning, artificial intelligence, and data mining (e.g., ICML, NeurIPS, ICLR, KDD, AAAI, IJCAI, UAI), and/or top-tier interdisciplinary journals (e.g., Nature family of journals, PNAS).

Candidates must have a Ph.D. or equivalent degree in computer science, statistics, or a closely related field. Strong programming skills and experience with machine learning and/or its applications to biology and medicine are required.

Application process

The position is available immediately and can be renewed annually. Interested applicants should submit the following documents via email to Prof. Zitnik and use the subject line “Postdoctoral Fellowship Application in AI/ML”:

  • Curriculum Vitae (please include links to your academic webpage and any software you developed, e.g., GitHub repositories)
  • Two representative publications (preprints are acceptable)
  • Statement of Research (2 pages) describing prior research experience and future research plans
  • Three letters of recommendation (will be solicited after the initial review)

We are currently reviewing applications for this position. Interested candidates are encouraged to submit their applications as soon as possible.

Advisor

Marinka Zitnik is an Assistant Professor at Harvard University with appointments in the Department of Biomedical Informatics, Broad Institute of MIT and Harvard, and Harvard Data Science. Dr. Zitnik is a computer scientist studying machine learning, focusing on challenges brought forward by data in science, medicine, and health. Before Harvard, she was a postdoctoral fellow in Computer Science at Stanford and also a member of the Chan Zuckerberg Biohub.

Dr. Zitnik has published extensively in top ML venues (e.g., NeurIPS, ICLR, ICML) and leading interdisciplinary journals (e.g., Nature Methods, Nature Communications, PNAS). She has organized numerous workshops and tutorials in the nexus of AI, deep learning, drug discovery, and medical AI at leading conferences (NeurIPS, ICLR, ICML, ISMB, AAAI, WWW), where she is also in the organizing committees. She also organized the National Symposium on drugs for future pandemics on behalf of the NSF.

Dr. Zitnik’s algorithms have had a tangible impact, which has garnered the interests of government, academic, and industry researchers and has put new tools in the hands of practitioners. Her methods are used by major institutions, including Baylor College of Medicine, Karolinska Institute, Stanford Medical School, Massachusetts General Hospital, and the pharmaceutical industry.

Dr. Zitnik’s research recently won best paper and research awards from the International Society for Computational Biology, Bayer Early Excellence in Science Award, Amazon Faculty Research Award, a Rising Star Award in EECS, and a Next Generation Recognition in Biomedicine, being the only young scientist who received such recognition in both EECS and Biomedicine.


Harvard is an Equal Opportunity/Affirmative Action Employer. Women and minorities are especially encouraged to apply.

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