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 fully virtual for the time being:

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 (since Jan 2021) & Thouis Jones (since Jan 2022)

MIA's efforts are driven by the Steering Committee: Alex Bloemendal (co-chair, Fall 2015 - Jan 2022)Anika Gupta, Arnav Mehta, Brian Cleary, Elizabeth Wood, Emma Stickgold, Juan Caicedo, Lois Doolittle, Martin Jankowiak, Marzieh Haghighi, Mehrtash Babadi, Mollie Morg, Mor Nitzan, Ray Jones, and Sam Friedman.

Jon Bloom and Alex Bloemendal founded MIA in Fall 2015. Jon Bloom served as a co-chair through July 2019. Past Steering Committe 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 and Max Shen.

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 2022 Schedule: 9am Primer, 10am Meeting, 10:50am Discussion unless noted otherwise, via Zoom. Please refer to our MIAcast (weekly email announcement) for Zoom meeting information. Email lrosinsk@broadinstitute.org with questions and mia-team@broadinstitute.org to be added to our mailing list.

Date	Speaker	Title
Jan 19	Samuel Church Dunn Lab, Yale University	Primer: Comparing gene expression data across species using evolutionary methods (note: 10am start) [Video]
Jan 19	Cassandra Extavour Depts. of Organismic and Evolutionary Biology, Molecular and Cellular Biology, Harvard University; Howard Hughes Medical Institute	Developing a systems approach to understanding adaptive evolutionary change using Hawaiian Drosophila as a model clade (note: 11am start)
Jan 26		NO MEETING THIS WEEK
Feb 2	Danilo Bzdok Dept. of Biomedical Engineering, McGill University; Mila Quebec AI Institute Galen Ballentine SUNY Downstate Medical Center	Primer: Canonical correlation analysis and the structure of psychedelic experience; Towards a neurophenomenological cartography of the cortex
Feb 2	Danilo Bzdok Dept. of Biomedical Engineering, McGill University; Mila Quebec AI Institute Galen Ballentine SUNY Downstate Medical Center Sam Freesun Friedman Data Sciences Platform, Broad Institute	Trips and neurotransmitters; Discovering principled patterns across 6850 hallucinogenic experiences
Feb 9	Chris Rohlicek Popic Lab, Broad Institute Victoria Popic Broad Institute	Primer: A deep learning approach to structural variant discovery [Video]
Feb 9	Chris Rohlicek Popic Lab, Broad Institute Victoria Popic Broad Institute	Cue: A framework for cross-platform structural variant calling and genotyping with deep learning [Video]
Feb 16	Abhishek Sarkar Computational Biology and Data Science group, Vesalius Therapeutics	Primer: Clarifying confusion in scRNA-seq analysis [Video]
Feb 16	Peter Carbonetto Dept. of Human Genetics, and the Research Computing Center, University of Chicago	Learning the "parts" of cells using topic models [Video]
Feb 23		NO MEETING THIS WEEK
Mar 2	Marco Cuturi Apple; Center for Research in Economics and Statistics, Institut Polytechnique de Paris	Primer: From matchings to optimal transport, use cases and algorithms [Video]
Mar 2	Marius Lange Dept. of Computational Health, Helmholtz Munich; Dept. of Mathematics, Technical University of Munich	Moscot: A scalable toolbox for optimal transport problems in single cell genomics [Video]
Mar 9	Dylan Kotliar Harvard Medical School	Primer: Capturing structure in high-dimensional data using K nearest neighbor graphs [Video]
Mar 9	Laurie Rumker Raychaudhuri Lab, Bioinformatics and Integrative Genomics Program, Harvard Medical School Yakir Reshef Raychaudhuri Lab, Harvard Medical School; Brigham and Women’s Hospital	Quantifying axes of inter-sample variability among transcriptional neighborhoods in single-cell datasets [Video]
Mar 16		NO MEETING THIS WEEK
Mar 23		NO MEETING THIS WEEK
Mar 30		No Primer
Mar 30	Salil Bhate Eric and Wendy Schmit Center Postdoctoral Fellow, Caicedo and Uhler labs, Broad Institute	Towards semantic representations of tissue organization from high-parameter imaging data [Video]
Apr 6		No Primer
Apr 6	Greg Yang Deep Learning Group, Microsoft Research	Tuning Large Neural Networks via Zero-Shot Hyperparameter Transfer [Video]
Apr 13	Erin Mordecai Dept. of Biology, Stanford University Jamie Caldwell High Meadows Environmental Institute, Princeton University	The impact of climate, social setting, and susceptibility on dengue dynamics: a case study using compartmental models, empirical dynamic modeling, and meta-analysis; Part I [Video]
Apr 13	Nicole Nova Dept. of Biology, Stanford University; Center for Computational, Evolutionary and Human Genomics Devin Kirk Dept. of Biology, Stanford University; University of British Columbia	The impact of climate, social setting, and susceptibility on dengue dynamics: a case study using compartmental models, empirical dynamic modeling, and meta-analysis; Part II [Video]
Apr 20		NO MEETING THIS WEEK
Apr 27		Primer: TBD
Apr 27	Uri Alon Dept. of Molecular Cell Biology, Weizmann Institute of Science	Design principles of hormone circuits
May 4		NO MEETING THIS WEEK
May 11	Younhun Kim PhD student, Mathematics Department, MIT	Primer: Scaling microbial dynamics with Bayesian nonparametrics
May 11	Travis Gibson Division of Computational Pathology, Brigham and Women’s Hospital, Harvard Medical School; Massachusetts Institute of Technology	Intrinsic instability of the dysbiotic microbiome revealed through dynamical systems inference at ecosystem-scale
May 18		NO MEETING THIS WEEK
May 25		No Primer
May 25	Wolfgang Pernice Columbia University Irving Medical Center	Deep learning based morphological profiling for rare diseases genomic medicine