Data, Machines, and AI (DMAI) Reading Group

Data, Machines, and AI (DMAI) is a reading group where we discuss advanced AI topics and most recent research in machine learning and data science, all in the context of biomedical data.

Schedule

Reading group meetings are held every two weeks. We have a speaker for every meeting. The speaker selects a paper and sends it to the group coordinator one week before the presentation. The coordinator shares the information with the group. Everyone is expected to read the paper carefully before the group meeting.

Each meeting lasts for 1 hour and consists of three parts:

  • Paper presentation (20 minutes): The speaker presents the paper, including background, motivation, key challenges, methods and modeling assumptions, datasets, and experiments. The focus is on models, algorithms, and learning methods.
  • Insights (5-10 minutes): The speaker shares their insights with the group. This includes insights related to the merits of the research, possible future directions, how can this research can be used in our ongoing projects, any drawbacks and ideas on how to fix them, any related-papers (other approaches to study the same problem), etc.
  • Discussion (25-30 minutes): Q&A and broader debate, brainstorming what questions in biomedical data these methods can help us answer, availability of data and source code implementation, any other topic attendees want to talk about.

These are interactive events; questions and comments are welcome throughout the meeting!

Speakers

Every meeting has a dedicated speaker whose responsibility is to select a paper and present it. We use a rotation system for speakers. Members of the reading group can expect to speak 1-3 times a year.

Paper selection

Generally, papers presented at the reading group are published in top-tier venues (conferences and journals) in the last two years:

  • Interdisciplinary journals:
    • Nature, Science, and Cell family, NEJM, PNAS, Lancet journals, JAMA journals
  • Machine learning and data science:
    • Conferences: ICML, NeurIPS, ICLR, ACL, EMNLP, KDD, ICDM, AAAI, IJCAI, UAI, FAT*, AISTATS, WSDM, SIGIR
    • Bioinformatics conferences: ISMB, RECOMB, PSB
    • Journals: TPAMI, JMLR, TKDD, TKDE, Bioinformatics, JAMIA, PLoS Computational Biology, BMC journals, ACS family

Please note this is only a sampling of relevant venues. We are generally interested in exciting, intriguing, and thought-provoking papers, no matter their publication venue, including preprints (e.g., arXiv, bioRxiv, and medRxiv).

Time

Every other Thursday at 4:30-5:30pm.

Location

Virtual meetings on Zoom. We will resume in-person meetings as soon as we return to campus.

Coordinator

If you have any questions, email the reading group coordinator (Xiang Zhang, <xiang_zhang@hms.harvard.edu>). Suggestions are very much welcome!

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