Models, Inference & Algorithms (MIA)

Please email mia-team@broadinstitute.org with a line of introduction to receive our weekly emails, including all relevant details for upcoming talks.

Schedule changes will be noted on the website and in MIAcast. MIA is now in person with a virtual option available:

9:00am Primer

10:00am Meeting

10:50am Discussion

The Models, Inference & Algorithms (MIA) Initiative at the Broad Institute supports learning and collaboration across the interface of biology and medicine with mathematics, statistics, machine learning, and computer science. Our weekly meeting features a primer, breakfast, seminar, and discussion; these are open and pedagogical, emphasizing lucid exposition of computational ideas over rapid-fire communication of results. Other MIA functions include hosting workshops, developing educational resources, advising leadership, and supporting the computational community.

Current co-chairs: Aleksandrina Goeva Salil Bhate (since Jan 2023) & Thouis Jones (since Jan 2022)

MIA's efforts are driven by the Steering Committee: Aleksandrina Goeva (Jan 2021 - Dec 2022) Alex Bloemendal (co-chair, Fall 2015 - Jan 2022), Elizabeth Wood, Emma Stickgold, Juan Caicedo, Lateisha Copeland-Guadarrama, Marzieh Haghighi, Mehrtash Babadi, Mor Nitzan, Ray Jones, and Sam Friedman, Wengong Jin, Salil Bhate, Orr Ashenberg, Eli Bingham, Matthew Amodio, David Fischer, Ashley Conard.

Jon Bloom and Alex Bloemendal founded MIA in the Fall of 2015. Jon Bloom served as a co-chair through July 2019. Past Steering Committee members: Allen Goodman, Debora Marks, David Benjamin, Dylan Kotliar, Gopal Sarma (co-chair, Jul 2019 - Jan 2021), James McFarland, Jon Bloom, Hilary Finucane, Sam Riesenfeld, Yakir Reshef, Aviad Tsherniak, Max Shen, Brian Cleary, Mollie Morg, and Anika Gupta, Martin Jankowiak, Arnav Mehta.

MIA Overview: Watch this introduction to the past, present, and future of MIA, and how you can help drive the fusion of machine learning and biomedicine. Check out the Kendall Square Codebreakers in the Harvard Crimson.

MIA Playlist: Watch and share our growing library of MIA videos.

Talking Machines: Listen to interviews with Eric Lander, Aviv Regev, and Nick Patterson.

Spring 2023 Schedule: 9 am Primer, 10 am Meeting, 10:50 am Discussion unless noted otherwise, in-person in Monadnock. Please refer to our MIAcast (weekly email announcement) for Zoom meeting information. Email lcopelan@broadinstitute.org with questions and mia-team@broadinstitute.org to be added to our mailing list.

MIA Talks Search

Date	Speaker	Title
Feb 1	Brian Hie Stanford University School of Medicine	Learning to read and write protein evolution [Video]
Feb 8	Ruochi Zhang Eric and Wendy Schmidt Center	Primer: Charting the Landscape of 3D Genome Organization with Graph Representation Learning [Video]
Feb 8	Bo Xia Gene Regulation Observatory, Broad Institute; Society of Fellows, Harvard University	High-Throughput In Silico Genetic Screen for Discovering Novel 3D Genome Organization Regulation [Video]
Feb 15	Bruno Correia Laboratory of Protein Design & Immunoengineering (LPDI), EPFL	Computational protein design [Video]
Feb 15	Casper Goverde Laboratory of Protein Design & Immunoengineering (LPDI), EPFL	De novo design of proteins [Video]
Mar 1	Haoran Zhang MIT	Primer: Group Fairness in Chest X-ray Diagnosis: Helpful or Harmful? [Video]
Mar 1	Judy Wawira Gichoya Emory University School of Medicine	Hiding in plain sight – What does AI’s ability to detect patterns not visible to radiologists mean? [Video]
Mar 8	Simon Rasmussen NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark	Variational autoencoders for analysis and integration of multi-omics and multi-modal data [Video]
Mar 8	Ricardo Hernandez Medina NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark	Deep dive into multi-omics variational autoencoding [Video]
Mar 22	Jian Shu, PhD Massachusetts General Hospital, Harvard Medical School Associate Member Broad Institute of MIT and Harvard	Image2Omics: Generating Omics Data from Images [Video]
Mar 22	Charles Comiter Massachusetts Institute of Technology Massachusetts General Hospital, Harvard Medical School Broad Institute of MIT and Harvard	Inference of single cell profiles from histology stains with the Single-Cell omics from Histology Analysis Framework (SCHAF) [Video]
Apr 5	Benjamin Sanchez-Lengeling Google Research, Brain Team	Intro to machine learning for molecules, small and large
Apr 12	Sarah Nyquist Gladstone Institutes	Current techniques for case-control comparisons in high-throughput transcriptomics and the need for contrastive methods
Apr 12	Didong Li University of North Carolina at Chapel Hill	Contrastive latent variable models to expose changes in case-control sequencing experiments
Apr 19	James Zou	Generative AI for biomedicine [Video]
Apr 19	James Zou	How to evaluate medical AI [Video]
Apr 26	Ben Deverman Broad Institute	ML-compatible experimental approaches to accelerate AAV engineering
Apr 26	Fatma Elzahraa Eid Broad Institute	Multi-trait protein engineering - a synergistic ML-wet lab approach to AAV engineering
May 10	Amirali Aghazadeh ECE, Georgia Tech	A Fourier Tour of Protein Function Prediction [Video]
May 10	David Brookes Dyno Therapeutics	Leveraging the Sparsity of Epistatic Interactions to Understand and Improve Models of Fitness Functions [Video]