MIA Talks Search

Spring 2023
Date	Speaker	Title
May 10	Amirali Aghazadeh ECE, Georgia Tech	A Fourier Tour of Protein Function Prediction [Video]	Spring 2023
May 10	David Brookes Dyno Therapeutics	Leveraging the Sparsity of Epistatic Interactions to Understand and Improve Models of Fitness Functions [Video]	Spring 2023
Apr 26	Ben Deverman Broad Institute	ML-compatible experimental approaches to accelerate AAV engineering	Spring 2023
Apr 26	Fatma Elzahraa Eid Broad Institute	Multi-trait protein engineering - a synergistic ML-wet lab approach to AAV engineering	Spring 2023


Date	Speaker	Title
Apr 19	James Zou	Generative AI for biomedicine

Spring 2023
Date	Speaker	Title
Apr 19	James Zou	Generative AI for biomedicine [Video]	Spring 2023
Apr 19	James Zou	How to evaluate medical AI [Video]	Spring 2023
Apr 12	Sarah Nyquist Gladstone Institutes	Current techniques for case-control comparisons in high-throughput transcriptomics and the need for contrastive methods	Spring 2023
Apr 12	Didong Li University of North Carolina at Chapel Hill	Contrastive latent variable models to expose changes in case-control sequencing experiments	Spring 2023
Apr 5	Benjamin Sanchez-Lengeling Google Research, Brain Team	Intro to machine learning for molecules, small and large	Spring 2023
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]	Spring 2023
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]	Spring 2023
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]	Spring 2023
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]	Spring 2023
Mar 1	Haoran Zhang MIT	Primer: Group Fairness in Chest X-ray Diagnosis: Helpful or Harmful? [Video]	Spring 2023


Date	Speaker	Title
Mar 1		Hiding in plain sight – What does AI’s ability to detect patterns not visible to radiologists mean?

Spring 2023
Date	Speaker	Title
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]	Spring 2023
Feb 15	Bruno Correia Laboratory of Protein Design & Immunoengineering (LPDI), EPFL	Computational protein design [Video]	Spring 2023
Feb 15	Casper Goverde Laboratory of Protein Design & Immunoengineering (LPDI), EPFL	De novo design of proteins [Video]	Spring 2023
Feb 8	Ruochi Zhang Eric and Wendy Schmidt Center	Primer: Charting the Landscape of 3D Genome Organization with Graph Representation Learning [Video]	Spring 2023

Spring 2023
Date	Speaker	Title
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]	Spring 2023
Feb 1	Brian Hie Stanford University School of Medicine	Learning to read and write protein evolution [Video]	Spring 2023

Fall 2022
Date	Speaker	Title
Dec 7	Cheng Zhang Principal Researcher at Microsoft Nick Pawlowski Senior Researcher in Machine Intelligence at Microsoft Research	Primer: An Introduction to Causal Discovery and Inference	Fall 2022
Dec 7	Nick Pawlowski Senior Researcher in Machine Intelligence at Microsoft Research Cheng Zhang Principal Researcher at Microsoft	Deep End-to-end Causal Inference	Fall 2022
Nov 23		NO MEETING WEEK	Fall 2022
Nov 16	Oana Ursu Department of Cellular and Tissue Genomics - Oncology, Genentech	Primer: Analytical challenges and opportunities for studying cell state transitions at the single cell level [Video]	Fall 2022
Nov 16	Charlotte Bunne Computer Science, ETH Zurich	Neural Optimal Transport for Inferring Single-Cell Responses to Perturbations [Video]	Fall 2022
Nov 2		NO MEETING	Fall 2022
Oct 26		No Primer	Fall 2022
Oct 26	Wolfgang Pernice Columbia University Irving Medical Center	Deep learning based morphological profiling for rare disease genomic medicine	Fall 2022
Oct 19	Li Li Camargo Lab, Boston Children's Hospital	Primer: Lineage tracing for tissue development and cell differentiation	Fall 2022
Oct 19	Shou-Wen Wang Damon Runyon Computational Biology Fellow, Harvard Medical School	Learning cell differentiation dynamics from lineage tracing datasets [Video]	Fall 2022
Oct 12	Rayan Chikhi Institut Pasteur & CNRS	Primer: The envelope of sequence bioinformatics in 2022 [Video]	Fall 2022
Oct 12	Artem Babaian Department of Molecular Genetics; Donnelly Centre for Cellular and Biomolecular Research; University of Toronto	The limits of Virus Discovery, and how to overcome them [Video]	Fall 2022
Oct 5	Emily Alsentzer ML/NLP for healthcare, Postdoc at Brigham and Women's Hospital / Harvard Medical School	Primer: Promise and Challenges of Language Models in the Clinical Domain [Video]	Fall 2022
Oct 5	Pulkit Singh Broad Institute of MIT and Harvard Christopher Reeder Broad Institute of MIT and Harvard	Unlocking the Power of Electronic Health Record data using Deep Learning based Natural Language Processing [Video]	Fall 2022
Sep 28	Xiaojie Qiu Postdoctoral Fellow in the Weissman Lab of MIT and Whitehead Institute	Towards predictive spatiotemporal modeling of single cells	Fall 2022
Sep 28	Reuben Saunders University of California, San Francisco	Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq [Video]	Fall 2022
Sep 21	David Kelley Calico Labs	Primer: Gene expression prediction from DNA sequences [Video]	Fall 2022
Sep 21	Carl de Boer Assistant Professor, School of Biomedical Engineering UBC	Using deep learning regulatory models and random DNA for evolutionary inference [Video]	Fall 2022

Fall 2022
Date	Speaker	Title
Sep 14	Martin Jankowiak Broad Institute of MIT and Harvard	Primer: An Introduction to Bayesian Variable Selection [Video]	Fall 2022
Sep 14	Martin Jankowiak Broad Institute of MIT and Harvard	Applications of Bayesian Variable Selection to Bioinformatics [Video]	Fall 2022

Spring 2022
Date	Speaker	Title
May 25		No Primer	Spring 2022
May 25	Wolfgang Pernice Columbia University Irving Medical Center	Deep learning based morphological profiling for rare diseases genomic medicine	Spring 2022
May 18		NO MEETING THIS WEEK	Spring 2022
May 11	Younhun Kim PhD student, Mathematics Department, MIT	Primer: Scaling microbial dynamics with Bayesian nonparametrics	Spring 2022
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	Spring 2022
May 4		NO MEETING THIS WEEK	Spring 2022
Apr 27		Primer: TBD	Spring 2022
Apr 27	Uri Alon Dept. of Molecular Cell Biology, Weizmann Institute of Science	Design principles of hormone circuits	Spring 2022
Apr 20		NO MEETING THIS WEEK	Spring 2022
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]	Spring 2022
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]	Spring 2022
Apr 6		No Primer	Spring 2022
Apr 6	Greg Yang Deep Learning Group, Microsoft Research	Tuning Large Neural Networks via Zero-Shot Hyperparameter Transfer [Video]	Spring 2022
Mar 30		No Primer	Spring 2022
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]	Spring 2022
Mar 23		NO MEETING THIS WEEK	Spring 2022
Mar 16		NO MEETING THIS WEEK	Spring 2022
Mar 9	Dylan Kotliar Harvard Medical School	Primer: Capturing structure in high-dimensional data using K nearest neighbor graphs [Video]	Spring 2022

Spring 2022
Date	Speaker	Title
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]	Spring 2022
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]	Spring 2022
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]	Spring 2022
Feb 23		NO MEETING THIS WEEK	Spring 2022
Feb 16	Abhishek Sarkar Computational Biology and Data Science group, Vesalius Therapeutics	Primer: Clarifying confusion in scRNA-seq analysis [Video]	Spring 2022
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]	Spring 2022
Feb 9	Chris Rohlicek Popic Lab, Broad Institute Victoria Popic Broad Institute	Primer: A deep learning approach to structural variant discovery [Video]	Spring 2022
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]	Spring 2022
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	Spring 2022
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	Spring 2022
Jan 26		NO MEETING THIS WEEK	Spring 2022
Jan 19	Samuel Church Dunn Lab, Yale University	Primer: Comparing gene expression data across species using evolutionary methods (note: 10am start) [Video]	Spring 2022
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)	Spring 2022

Fall 2021
Date	Speaker	Title
Dec 1	Nathan Cheng Finucane Lab, Broad Institute Hilary Finucane Broad Institute; Massachusetts General Hospital	Polygenic priority score for GWAS gene prioritization [Video]	Fall 2021
Dec 1	Brian Trippe Broderick Group, Massachusetts Institute of Technology	A new approach for high-dimensional hierarchical modeling [Video]	Fall 2021
Nov 24		NO MEETING THIS WEEK	Fall 2021
Nov 17		NO MEETING THIS WEEK	Fall 2021
Nov 10	Felix Dietlein Van Allen Lab, Dana-Farber Cancer Institute; Broad Institute	Primer: Genomic tools for interpreting patterns of somatic driver and passenger mutations in cancer [Video]	Fall 2021
Nov 10	Haitham Elmarakeby Van Allen Lab, Dana-Farber Cancer Institute; Broad Institute	Biologically informed deep neural network for prostate cancer discovery [Video]	Fall 2021
Nov 3		NO MEETING THIS WEEK	Fall 2021

Fall 2021
Date	Speaker	Title
Oct 27	Hani Goodarzi Depts. of Biochemistry & Biophysics, Urology, University of California San Francisco	Primer: Capturing regulatory information encoded in RNA secondary structure [Video]	Fall 2021
Oct 27	Mehran Karimzadeh Goodarzi Lab, University of California San Francisco; Vector Institute Matvei Khoroshkin Goodarzi Lab, University of California San Francisco	Computational tools for deciphering the RNA structural code [Video]	Fall 2021
Oct 20	Bianca Dumitrascu Department of Computer Science and Technology, University of Cambridge Miri Adler Broad Institute Aleksandrina Goeva Broad Institute	Lightning talks (9am start, no primer) [Video]	Fall 2021
Oct 13	Alyssa Wilson Seung Lab, Princeton Neuroscience Institute, Princeton University	Scalable analysis of electron microscopy connectomics data: Revealing neural circuit properties using contrastive deep learning [Video]	Fall 2021
Oct 13	Nathaniel Diamant Broad Institute	No such thing as unlabeled: Self-supervised learning on medical data [Video]	Fall 2021
Oct 6	Pranav Rajpurkar Dept. of Biomedical Informatics, Harvard Medical School	Primer: Advancements and challenges for deep learning in medical imaging [Video]	Fall 2021
Oct 6	Bryan Gopal Stanford University Ryan Han Stanford University Gautham Raghupathi Stanford University	3KG: Contrastive learning of 12-lead electrocardiograms using physiologically-inspired augmentations [Video]	Fall 2021
Sep 29	Fabian Theis Institute of Computational Biology, Helmholtz Zentrum München Maren Buettner Institute of Computational Biology, Helmholtz Zentrum München	Primer: Latent space learning in single cell genomics: Current approaches and challenges [Video]	Fall 2021
Sep 29	Mohammad Lotfollahi¹ Technical University of Munich David Fischer² Institute of Computational Biology, Helmholtz Zentrum München	Deep interpretable perturbation modeling in single cell genomics¹; Learning cell communication from spatial graphs of cells² [Video]	Fall 2021
Sep 22	Georgia Gkioxari Facebook AI	Visual recognition from one or more images [Video]	Fall 2021
Sep 22	Juan Caicedo Broad Institute	Representation learning for single-cell, image-based phenotyping [Video]	Fall 2021
Sep 15		NO MEETING THIS WEEK	Fall 2021
Sep 8		No primer	Fall 2021
Sep 8	Jonathan Bloom Cellarity Alexandra-Chloé Villani Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital; Harvard Medical School; Broad Institute Angela Pisco Chan Zuckerberg Biohub Daniel Burkhardt Cellarity Malte Lücken Institute of Computational Biology, Helmholtz Zentrum Munich	Multimodal single-cell data, open benchmarks, and a NeurIPS 2021 competition (Note: 9am start) [Video]	Fall 2021

Spring 2021
Date	Speaker	Title
Jun 2	Marina Riabiz King's College London	Primer: Optimal thinning of mcmc output with application to cardiac electrophysiology [Video]	Spring 2021
Jun 2	Lester Mackey Depts. of Statistics and Computer Science, Stanford University; Microsoft Research New England	Probabilistic inference and learning with Stein’s method [Video]	Spring 2021
May 26		NO MEETING THIS WEEK	Spring 2021
May 19		NO MEETING THIS WEEK	Spring 2021
May 12	Michelle Li Bioinformatics and Integrative Genomics Program, Zitnik Lab, Harvard Medical School	Primer: Deep learning for biomedical networks: Methods, challenges, and frontiers [Video]	Spring 2021
May 12	Marinka Zitnik Dept. of Biomedical Informatics, Harvard University; Broad Institute	Actionable machine learning for drug discovery and development [Video]	Spring 2021

Spring 2021
Date	Speaker	Title
May 5	Alan Amin Marks Lab, Harvard Medical School	Primer: Estimation and testing with generative nonparametric Bayesian models [Video]	Spring 2021
May 5	Eli Weinstein Marks Lab, Harvard Medical School	Building and evaluating generative models of biological sequences, from proteins to whole genomes [Video]	Spring 2021
Apr 29		No primer	Spring 2021
Apr 29	Sara Mostafavi Paul G. Allen School of Computer Science and Engineering, University of Washington	Deep learning of immune differentiation (Note: 12pm start) [Video]	Spring 2021
Apr 28		NO MEETING THIS WEEK	Spring 2021
Apr 21		NO MEETING THIS WEEK	Spring 2021
Apr 14		NO MEETING THIS WEEK	Spring 2021
Apr 7		No primer	Spring 2021
Apr 7	Ronen Mukamel Loh Lab, Harvard Medical School; Division of Genetics, Brigham and Women's Hospital; Broad Institute	Imputed repeat polymorphisms point to protein-coding variants driving genetic associations [Video]	Spring 2021
Mar 31	Hoon Cho Broad Institute	Primer: Density-aware visualization and sketching of single-cell transcriptomic data [Video]	Spring 2021
Mar 31	Leland McInnes Tutte Institute for Mathematics and Computing	Low dimensional embeddings of words and documents (and how they might apply to single-cell data) [Video]	Spring 2021
Mar 24	Jung-Eun (June) Shin Marks Lab, Harvard Medical School	Primer: Generative models of antibodies for functionally optimized library design [Video]	Spring 2021
Mar 24	Mafalda Dias Marks Lab, Harvard Medical School Jonathan Frazer Marks Lab, Harvard Medical School	Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning [Video]	Spring 2021
Mar 17		NO MEETING THIS WEEK	Spring 2021
Mar 10	James Hay Center for Communicable Disease Dynamics, Harvard Chan School of Public Health	Primer: Using viral loads and within-host models to improve COVID-19 surveillance [Video]	Spring 2021
Mar 10	David Hong Dept. of Statistics, Wharton School, University of Pennsylvania	Simple, flexible and effective pooled testing via hypergraph factorization [Video]	Spring 2021
Mar 3	Emily Laubscher Van Valen Lab, California Institute of Technology	Primer: Integrating heterogeneous measurements in single cells [Video]	Spring 2021
Mar 3	David Van Valen Division of Biology and Biological Engineering, California Institute of Technology	Single-cell biology in a software 2.0 world [Video]	Spring 2021
Feb 24	Michael Mitzenmacher Dept. Computer Science, Harvard University	Primer: Locality sensitive hashing: A sort of history and introduction [Video]	Spring 2021
Feb 24	Hayden Metsky Sabeti Lab, Broad Institute	Viral diagnostic design with model-based optimization [Video]	Spring 2021

Spring 2021
Date	Speaker	Title
Feb 17		NO MEETING THIS WEEK	Spring 2021
Feb 10		No primer	Spring 2021
Feb 10	Martin Jankowiak Pyro Team, Broad Institute	Bayesian methods for adaptive experimental design [Video]	Spring 2021
Feb 3		No primer	Spring 2021
Feb 3	Christina Leslie Computational & Systems Biology Program, Memorial Sloan Kettering Cancer Center	The 3D genome and predictive models of gene regulation	Spring 2021
Jan 27	Michael Desai Depts. Organismic and Evolutionary Biology, Physics, Harvard University	Primer: Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments [Video]	Spring 2021
Jan 27		Predictable patterns in phenotypic evolution [Video]	Spring 2021

Fall 2020
Date	Speaker	Title
Dec 9	Niloy Biswas Dept. of Statistics, Harvard University	Large-scale Bayesian inference for GWAS with coupled Markov chain Monte Carlo [Video]	Fall 2020
Dec 9	Max Shen Liu Group, Regev Lab, Broad Institute; Dept. of Computational and Systems Biology, Massachusetts Institute of Technology	Determinants of base editing outcomes from target library analysis and machine learning [Video]	Fall 2020
Dec 2	Josh Goldford¹ ¹Physics of Living Systems, Massachusetts Institute of Technology Pankaj Mehta² ²Dept. of Physics, Boston University	Primer: Introduction to ecological models for microbiomes [Video]	Fall 2020
Dec 2	Pankaj Mehta Dept. of Physics, Boston University	Toward a statistical mechanics of microbiomes [Video]	Fall 2020
Nov 25		NO MEETING THIS WEEK	Fall 2020
Nov 18		No primer	Fall 2020
Nov 18	Asja Radja Mahadevan Group, Harvard University	Patterns on pollen: a polysaccharide phase transition process (Note: 11am start) [Video]	Fall 2020
Nov 11		NO MEETING THIS WEEK	Fall 2020
Nov 4		NO MEETING THIS WEEK	Fall 2020
Oct 28	Will Townes Engelhardt Group, Princeton University	Primer: Generalized linear models and latent factor models [Video]	Fall 2020
Oct 28	Jeff Miller Dept. of Biostatistics, Harvard University	Inference in generalized bilinear models [Video]	Fall 2020
Oct 21	Eli Bingham Pyro team, Broad Institute	Primer: Stochastic gradient-based variational inference [Video]	Fall 2020
Oct 21	Fritz Obermeyer Pyro team, Broad Institute	Deep probabilistic programming with Pyro [Video]	Fall 2020

Fall 2020
Date	Speaker	Title
Oct 14		No primer	Fall 2020
Oct 14	Jennifer Listgarten Dept. of Electrical Engineering and Computer Sciences, Center for Computational Biology, Berkeley AI Research Lab, UC Berkeley; Chan Zuckerberg Biohub	Machine learning-based design of proteins (and small molecules and beyond) (Note: 12pm start) [Video]	Fall 2020
Oct 7	Sam Sinai Dyno Therapeutics	Primer: Biological sequence design through machine-guided exploration [Video]	Fall 2020
Oct 7	Eric Kelsic Dyno Therapeutics	Machine-guided capsid engineering for gene therapy [Video]	Fall 2020
Sep 30	Daphne Schlesinger Research Laboratory of Electronics Computational Cardiovascular Research Group, Massachusetts Institute of Technology	Primer: Modeling cardiovascular physiology [Video]	Fall 2020
Sep 30	Collin Stultz Dept. of Electrical Engineering and Computer Science, Institute for Medical Engineering and Science, Computer Science and Artificial Intelligence Laboratory, MIT; Massachusetts General Hospital	Physiology-inspired machine learning models for predicting adverse cardiovascular outcomes [Video]	Fall 2020
Sep 23	Mike Oberst Clinical Machine Learning Group, Massachusetts Institute of Technology	Primer: Learning personalized treatment policies from observational data [Video]	Fall 2020
Sep 23	David Sontag Dept. of Electrical Engineering and Computer Science, Institute for Medical Engineering & Science, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology	Going beyond diagnosis and prognosis: Machine learning to guide treatment suggestions [Video]	Fall 2020
Sep 16	Rohan Saha University of Alberta	Primer: Machines read, humans read: parallels between computer and human representations of meaning (Note: 11am start) [Video]	Fall 2020
Sep 16	Alona Fyshe Depts. of Computing Science, Psychology, University of Alberta; Canadian Institute for Advanced Research	Decoding word meaning from brain images collected during language production (Note: 12pm start) [Video]	Fall 2020
Sep 9	Raj Agrawal Broderick Group, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology; ArbiLex	Primer: Gaussian processes: An introduction [Video]	Fall 2020
Sep 9	Tamara Broderick Dept. of Electrical Engineering and Computer Science, Computer Science and Artificial Intelligence Laboratory, Statistics and Data Science Center, Massachusetts Institute of Technology	Fast discovery of pairwise interactions in high dimensions using Bayes [Video]	Fall 2020

Spring 2020
Date	Speaker	Title
May 20		NO MEETING, SEE YOU NEXT SEMESTER!	Spring 2020
May 13	TBD	Primer: TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)	Spring 2020
May 13	Hayden Metsky Sabeti Lab, Broad Institute	TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)	Spring 2020
May 6	TBD	Primer: TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)	Spring 2020
May 6	Max Shen Massachusetts Institute of Technology	TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)	Spring 2020
Apr 29	Megan Owen Dept. of Mathematics, Lehman College of the City University of New York	Primer: TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)	Spring 2020
Apr 29	Katherine St. John Dept. of Computer Science, Hunter College of the City University of New York	TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)	Spring 2020
Apr 22	TBD	Primer: TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)	Spring 2020

Spring 2020
Date	Speaker	Title
Apr 22	Fritz Obermeyer Uber AI; Pyro	TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)	Spring 2020
Apr 15		NO MEETING	Spring 2020
Apr 8	TBD	Primer: TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)	Spring 2020
Apr 8	Pankaj Mehta Dept. of Physics, Boston University	TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)	Spring 2020
Apr 6	Michael Bronstein Dept. of Computing, Imperial College London; Twitter	Geometric deep learning for functional protein design (Note: Joint CC&E/MIA Special Seminar, Monday at 9:30AM. See abstract for Zoom instructions) [Video]	Spring 2020
Apr 1	Markus Kaiser Ek Group, Dept. of Computer Science, Technical University of Munich; Siemens AG	Primer: TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)	Spring 2020
Apr 1	Carl Henrik Ek Dept. of Computer Science, University of Bristol	TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)	Spring 2020
Mar 25		NO MEETING	Spring 2020
Mar 18	TBD	Primer: TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)	Spring 2020
Mar 18	Tamara Broderick Dept. of Electrical Engineering and Computer Science, Computer Science and Artificial Intelligence Laboratory, Statistics and Data Science Center, Massachusetts Institute of Technology	TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)	Spring 2020
Mar 11	Sam Sinai Dyno Therapeutics	Primer: Biological sequence design through machine-guided exploration (NOTE: POSTPONED UNTIL FURTHER NOTICE)	Spring 2020
Mar 11	Eric Kelsic Dyno Therapeutics	Machine-guided capsid engineering for gene therapy (NOTE: POSTPONED UNTIL FURTHER NOTICE)	Spring 2020
Mar 4	Sam Freesun Friedman Data Sciences Platform, Broad Institute	Primer: Only connect: The variety and splendor of neural network architectures	Spring 2020
Mar 4	James Pirruccello Medical and Population Genetics, Broad Institute; Division of Cardiology, Massachusetts General Hospital	Deep learning enables efficient genetic analysis of the human thoracic aorta	Spring 2020
Feb 26	Alex Bloemendal Neale Lab, Lander Lab, Broad Institute; Analytic and Translational Genetics Unit, Massachusetts General Hospital	Primer: The multiple testing problem [Video]	Spring 2020
Feb 26	Jackson Loper Paninski Lab, Blei Lab, Dept. of Statistics, Data Science Institute, Columbia University	Smoothed nested testing on directed acyclic graphs [Video]	Spring 2020
Feb 19		NO MEETING	Spring 2020
Feb 12	Roger Grosse Dept. of Computer Science, University of Toronto; Vector Institute	Primer: Enforcing Lipschitz constraints for neural networks [Video]	Spring 2020
Feb 12	Cem Anil Grosse Group, University of Toronto; Vector Institute James Lucas Grosse Group, University of Toronto; Vector Institute	Efficient Lipschitz-constrained neural networks [Video]	Spring 2020
Feb 5	Max Welling (recording) University of Amsterdam; Qualcomm Technologies; Canadian Institute for Advanced Research Ray Jones Lander Lab, Broad Institute	Screening: VAEs & Deep Inverse Modeling (Note: 10-11am in the Auditorium)	Spring 2020

Spring 2020
Date	Speaker	Title
Jan 29		No primer	Spring 2020
Jan 29	Aleksandrina Goeva Gopal Sarma Daniel King Patrick Schultz Alex Bloemendal Hilary Finucane Sam Freesun Friedman	Topics Groups Nucleation Event (10-11am in Monadnock)	Spring 2020

Fall 2019
Date	Speaker	Title
Dec 18	Holiday Mixer	Holiday Mixer (Note: 10am in Monadnock)	Fall 2019
Dec 6	Volker Bergen Theis Lab, Institute of Computational Biology	RNA velocity generalized to transient cell states through dynamical modeling (Note: 2:30-3:30pm in Monadnock) [Video]	Fall 2019
Dec 4	Will Stephenson Computer Science & Artificial Intelligence Lab (CSAIL), Massachusetts Institute of Technology	Primer: An overview of some issues in Bayesian robustness [Video]	Fall 2019
Dec 4	Jonathan Huggins Dept. of Biostatistics, Harvard University; Dana-Farber Cancer Institute; Broad Institute	Using bagged posteriors for robust inference and model criticism [Video]	Fall 2019
Nov 20	Stephen Fleming Data Sciences Platform, Broad Institute	Primer: CellBender remove-background: A deep generative model for unsupervised removal of background noise from scRNA-seq datasets [Video]	Fall 2019
Nov 20	Mehrtash Babadi Data Sciences Platform, Broad Institute	CellBender droplet-time-machine: Reversing mixed-template cDNA amplification artifacts in droplet-based 3' scRNA-seq assays [Video]	Fall 2019
Nov 13	CANCELLED	CANCELLED	Fall 2019
Nov 13	CANCELLED	CANCELLED	Fall 2019
Nov 8	Romain Lopez Dept. of Electrical Engineering and Computer Sciences, UC Berkeley	Regev Lab, Cell Circuits and Epigenomics, and MIA special seminar: Deep generative modeling for single-cell transcriptomics (12:30-1:30pm in Monadnock)	Fall 2019
Nov 6	Emily Winn Crawford Lab, Brown University	Primer: Integrating topological data analysis (TDA) with statistical learning techniques [Video]	Fall 2019
Nov 6	Lorin Crawford Center for Statistical Sciences, Center for Computational Molecular Biology, Brown University	Statistical pipeline for identifying features that differentiate classes of 3D shapes [Video]	Fall 2019
Oct 30	Pavel Izmailov Courant Institute, New York University Polina Kirichenko Courant Institute, New York University	Primer: How do we build neural networks we can trust? [Video]	Fall 2019
Oct 30	Andrew Gordon Wilson Courant Institute, New York University	Loss valleys, uncertainty, and generalization in deep learning [Video]	Fall 2019
Oct 23	Adam Cohen Depts. of Chemistry and Chemical Biology, Physics, Harvard University	Primer: Computational challenges in optical electrophysiology (Note: Auditorium) [Video]	Fall 2019
Oct 23	Sami Farhi Regev Lab, Broad Institute	New imaging data types and computational challenges at the optical profiling platform (Note: Auditorium) [Video]	Fall 2019
Oct 22	David Duvenaud Depts. of Computer Science, Statistical Sciences, University of Toronto	It's time to talk about irregularly-sampled time series (Note: 12-1pm in Serengeti) [Video]	Fall 2019
Oct 16	Ila Fiete Dept. of Brain and Cognitive Science, McGovern Institute, Massachusetts Institute of Technology	Primer: Cognitive maps for navigation in the brain [Video]	Fall 2019
Oct 16	Sam Lewallen Center for Brain Science, Harvard University	Manifold discovery of cognitive maps [Video]	Fall 2019

Fall 2019
Date	Speaker	Title
Oct 9	Jon Bloom Hail Team, Neale Lab, Broad Institute Hoon Cho Broad Institute	Primer: The geometry of linear regression, privacy-preserving linear algebra, and multi-party GWAS [Video]	Fall 2019
Oct 9	Gil Strang Dept. of Mathematics, Massachusetts Institute of Technology	Key ideas in linear algebra [Video]	Fall 2019
Oct 2	Allen Goodman Carpenter Lab, Imaging Platform, Broad Institute	Primer: Intro to computer vision and its relationship to machine learning [Video]	Fall 2019
Oct 2	Sam Freesun Friedman Data Sciences Platform, Broad Institute Gregory Way Carpenter Lab, Imaging Platform, Broad Institute Beth Cimini Carpenter Lab, Imaging Platform, Broad Institute	Computer vision for hearts and cells [Video]	Fall 2019
Sep 25	Lauren Erdman Goldenberg Lab, SickKids Research Institute; Dept. of Computer Science, University of Toronto; Vector Institute	Primer: Learning biological patterns across domains: Investigating and integrating information across data types and sources [Video]	Fall 2019
Sep 25	Anna Goldenberg SickKids Research Institute; Dept. of Computer Science, University of Toronto; Vector Institute	From predicting to explaining biology using machine learning [Video]	Fall 2019
Sep 18	Vova (Vladimir) Seplyarskiy Sunyaev Lab, Dept. of Biomedical Informatics, Harvard Medical School; Division of Genetics, Brigham and Women's Hospital	Primer: DNA damage bypass is a major source of clustered mutations [Video]	Fall 2019
Sep 18	Ruslan Soldatov Kharchenko Lab, Dept. of Biomedical Informatics, Harvard Medical School	Population sequencing data reveal a compendium of mutational processes in human germline [Video]	Fall 2019
Sep 11	Ahmed Badran Infectious Disease & Microbiome Program, Chemical Biology & Therapeutic Sciences Program, Broad Institute	Primer: Impact of mutagenesis efficiency and selection stringency modulation during continuous directed evolution [Video]	Fall 2019
Sep 11	Chang Liu Dept. of Biomedical Engineering, UC Irvine	Synthetic genetic systems for rapid mutation and continuous evolution in vivo [Video]	Fall 2019

Spring 2019
Date	Speaker	Title
May 29	Peter Koo Eddy Lab, Harvard University	Interpretable convolutional networks for regulatory genomics [Video]	Spring 2019
May 22	Aaron Kollasch Marks Lab, Harvard Medical School, Broad Institute	Primer: Generative models from NLP for sequence data [Video]	Spring 2019
May 22	Debora Marks Dept. of Systems Biology, Harvard Medical School; Broad Institute	Alignment-free models for protein and antibody design [Video]	Spring 2019
May 15	Natasha Jaques MIT Media Lab, Massachusetts Institute of Technology	Primer: Mechanisms for generalized learning across tasks and environments [Video]	Spring 2019
May 15	Susan Murphy Depts. of Statistics, Computer Science, Harvard University	Personalized HeartSteps: A reinforcement learning algorithm for optimizing physical activity [Video]	Spring 2019
May 8	Allon Klein Dept. of Systems Biology, Harvard Medical School	Primer: Inference of high-dimensional dynamics [Video]	Spring 2019
May 8	Caleb Weinreb Dept. of Systems Biology, Harvard Medical School	Lineage tracing on transcriptional landscapes links state to fate during differentiation [Video]	Spring 2019
May 6	Joshua Batson Chan Zuckerberg Biohub	Blind denoising by self-supervision [Video]	Spring 2019
May 1	Po-Ru Loh Dept. of Medicine and Division of Genetics, Brigham and Women's Hospital, Harvard Medical School; Broad Institute	Primer: Hidden Markov models in phasing and imputation [Video]	Spring 2019
May 1	Ronen Mukamel Loh Lab, Dept. of Medicine and Division of Genetics, Brigham and Women's Hospital, Harvard Medical School; Broad Institute	Imputing genomic repeat variants and assessing their phenotypic effects [Video]	Spring 2019

Spring 2019
Date	Speaker	Title
Apr 24	Wilder Wohns Dept. of Statistics, University of Oxford	Primer: Introduction to the tree sequence toolchain [Video]	Spring 2019
Apr 24	Jerome Kelleher Big Data Institute, University of Oxford	Succinct tree sequences for megasample genomics [Video]	Spring 2019
Apr 17	Galen Ballentine Drexel University College of Medicine	Primer: The human brain's default mode network [Video]	Spring 2019
Apr 17	Danilo Bzdok Dept. of Psychiatry, Psychotherapy and Psychosomatics, RWTH Aachen University	Algorithms to understand default brain function [Video]	Spring 2019
Apr 10	Alexander D'Amour Google Brain	Primer: Extracting causal signal from high-dimensional data: challenges and techniques [Video]	Spring 2019
Apr 10	Wesley Tansey Rabadan Lab, Dept. of Systems Biology, Data Science Institute, Columbia University	Interpreting and learning from black box models [Video]	Spring 2019
Apr 3	Harrison Specht Slavov Lab, Northeastern University	Primer: Quantifying proteins by mass-spec [Video]	Spring 2019
Apr 3	Nikolai Slavov Dept. of Bioengineering, Northeastern University	Understanding biological systems: In search of direct causal mechanisms [Video]	Spring 2019
Mar 27	Alejandro Reyes Aryee Lab, Zhang Lab; Dana-Farber Cancer Institute, Harvard Medical School, Massachusetts General Hospital	Modeling the 3D organization of chromosomes in the cancer cell nucleus [Video]	Spring 2019
Mar 20	Ralph Peterson Datta Lab, Harvard Medical School	Primer: Learning structure in mouse behavior using motion sequenceing (MoSeq) [Video]	Spring 2019
Mar 20	Jeffrey Markowitz Datta Lab, Sabatini Lab, Harvard Medical School	Using machine learning to understand how the brain implements moment-to-moment action selection [Video]	Spring 2019
Mar 13	Alex Bloemendal Neale Lab, Lander Lab, Broad Institute; Analytic and Translational Genetics Unit, Massachusetts General Hospital	Primer: Random matrix theory [Video]	Spring 2019
Mar 13	Christina Chen Neale Lab, Broad Institute	Controlling for stratification in (meta-)GWAS with PCA: Theory, applications, and implications [Video]	Spring 2019
Mar 6	Sergey Ovchinnikov Harvard University	Primer: Generative REgularized ModeLs of proteINs	Spring 2019
Mar 6	Mohammed AlQuraishi Harvard Medical School	End-to-end differentiable learning of protein structure [Video]	Spring 2019
Feb 27	Cotton Seed Hail Team, Neale Lab, Broad Institute Jon Bloom Hail Team, Neale Lab, Broad Institute	Primer: From Morse theory to geometric ensembling via the topology of PCA [Video]	Spring 2019
Feb 27	Daniel Kunin Stanford University Aleksandrina Goeva Macosko Lab, Broad Institute	Regularized linear autoencoders, probabilistic PCA, and backpropagation in the brain [Video]	Spring 2019
Feb 13	Mor Nitzan Harvard University	Inferring geometric embeddings for single cell data [Video]	Spring 2019
Feb 13	Joshua Weinstein Zhang Lab, Regev Lab, Broad Institute	Optics-free spatio-genetic imaging with DNA microscopy [Video]	Spring 2019
Feb 6	Andrew J. Blumberg Dept. of Mathematics, University of Texas at Austin	Primer: Analyzing scientific data with topological data analysis [Video]	Spring 2019

Spring 2019
Date	Speaker	Title
Feb 6	Andrew J. Blumberg Dept. of Mathematics, University of Texas at Austin	Using random matrix theory to extract signals from single-cell expression data [Video]	Spring 2019
Jan 30	Katherine Gorman Talking Machines; Collective Next; Neural Information Processing Systems (neurIPS)	Primer: Super deep generative networks for cat robots: or how I learned to start worrying more about the public conversation [Video]	Spring 2019
Jan 30	Katherine Gorman Talking Machines; Collective Next; Neural Information Processing Systems (neurIPS)	Group exercise: The story algorithm	Spring 2019

Fall 2018
Date	Speaker	Title
Dec 12	Wenshuo Wang Dept. of Statistics, Harvard University	Primer: Challenges in high-dimensional variable selection [Video]	Fall 2018
Dec 12	Lucas Janson Dept. of Statistics, Harvard University	Using knockoffs to find important variables with statistical guarantees [Video]	Fall 2018
Dec 5	Luca Pinello Massachusetts General Hospital; Harvard Medical School; Broad Institute Jonathan Hsu Pinello Lab, Massachusetts General Hospital (MGH); Joung Lab, MGH, Harvard Medical School; Collins Lab, Massachusetts Institute of Technology	Primer: A deconvolution framework for the analysis of CRISPR tiling screen data [Video]	Fall 2018
Dec 5	Luca Pinello Massachusetts General Hospital; Harvard Medical School; Broad Institute Huidong Chen Pinello Lab, Massachusetts General Hospital; Harvard Medical School	Single-cell trajectory reconstruction, exploration and mapping from omics data [Video]	Fall 2018
Nov 14	Aleksandrina Goeva Macosko Lab, Broad Institute	Primer: Intro to non-negative matrix factorization [Video]	Fall 2018
Nov 14	Dylan Kotliar Sabeti Lab, Dept. of Systems Biology, Harvard Medical School	Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq [Video]	Fall 2018
Nov 7	David Benjamin Data Sciences Platform, Broad Institute	Primer: Intro to topic models [Video]	Fall 2018
Nov 7	Samantha Riesenfeld Regev Lab, Broad Institute; Kuchroo Lab, Harvard Medical School	Topic modeling the transcriptional spectrum in innate lymphoid cells [Video]	Fall 2018
Oct 31	Archit Verma Engelhardt Group, Depts. of Computer Science, Quantitative and Computational Biology, Princeton University	Primer: Robust nonlinear manifold learning for single cell RNA-seq data [Video]	Fall 2018
Oct 31	Bianca Dumitrascu Engelhardt Group, Depts. of Computer Science, Quantitative and Computational Biology, Princeton University	Experimental design for maximizing cell-type discovery in single-cell data [Video]	Fall 2018
Oct 24	Miriam Shiffman Broderick Lab, Machine Learning Group, Massachusetts Institute of Technology; Regev Lab, Broad Institute Miriam Udler Florez Lab, Massachusetts General Hospital, Broad Institute Brian Trippe Broderick Lab, Computer Science & Artificial Intelligence Lab, Massachusetts Institute of Technology Eli Weinstein Marks Lab, The Biophysics Graduate Program, Harvard University	Lightning talk social	Fall 2018
Oct 24	Brian Cleary Regev Lab, Lander Lab, Broad Institute	Studying cell and tissue physiology with random composite experiments [Video]	Fall 2018
Oct 17	David van Dijk Krishnaswamy Lab, Depts. of Genetics, Computer Science, Yale University	Primer: Manifold learning and graph signal processing of high-dimensional, high-throughput biological data [Video]	Fall 2018
Oct 17	Smita Krishnaswamy Depts. of Genetics, Computer Science, Yale University	Manifold learning yields insight into cellular state space under complex experimental conditions [Video]	Fall 2018
Oct 10	Hoon Cho Computer Science & Artificial Intelligence Lab, Massachusetts Institute of Technology	Biomedical data sharing and analysis with privacy [Video]	Fall 2018
Oct 3	Dustin Tran Google Brain Chris Suter Google Brain	What might machine learners learn from probabilistic programming? [Video]	Fall 2018
Sep 26	Adam Breuer Depts. of Computer Science and Government, Harvard University	Primer: Submodular maximization and machine learning [Video]	Fall 2018

Fall 2018
Date	Speaker	Title
Sep 26	Yaron Singer Dept. of Computer Science, Harvard University	Maximizing submodular functions exponentially faster [Video]	Fall 2018
Sep 19	David Rolnick University of Pennsylvania	Primer: Why is deep learning so deep? [Video]	Fall 2018
Sep 19	David Rolnick University of Pennsylvania	Mapping the brain with machine learning [Video]	Fall 2018
Jul 11	David Knowles Stanford Medicine	Transcriptomic modeling of chemotherapy side effects using human iPSC-derived cardiomyocytes [Video]	Fall 2018

Spring 2018
Date	Speaker	Title
May 23	Wouter Boomsma Depts. of Computer Science, University of Copenhagen and IT University of Copenhagen Jes Frellsen Depts. of Computer Science, University of Copenhagen and IT University of Copenhagen	Primer: Learning from molecular structure [Video]	Spring 2018
May 23	Wouter Boomsma Depts. of Computer Science, University of Copenhagen and IT University of Copenhagen Jes Frellsen Depts. of Computer Science, University of Copenhagen and IT University of Copenhagen	Convolutional models of molecular structure [Video]	Spring 2018
May 16	Larson Hogstrom Lander Lab, Broad Institute	Primer: How philosophy of science can help us better deploy machine learning in biology [Video]	Spring 2018
May 16	Ray Jones Lander Lab, Broad Institute	Interpreting sequence models	Spring 2018
May 9	James Zou Depts. of Biomedical Data Science, Computer Science, and Electrical Engineering, Stanford University	Primer: Contrastive PCA [Video]	Spring 2018
May 9	James Zou Depts. of Biomedical Data Science, Computer Science, and Electrical Engineering, Stanford University	AI audit to uncover blind spots of data	Spring 2018
May 2	Shantanu Singh Carpenter Lab, Imaging Platform, Broad Institute Jane Hung Carpenter Lab, Imaging Platform, Broad Institute Juan Caicedo Carpenter Lab, Imaging Platform, Broad Institute Mohammad Rohban Carpenter Lab, Imaging Platform, Broad Institute	How to make a picture worth a thousand numbers: Models and methods in biological image analysis [Video]	Spring 2018
Apr 25	Martin Nowak Program for Evolutionary Dynamics, Harvard University	Primer: Hamilton's rule makes no prediction and cannot be tested empirically [Video]	Spring 2018
Apr 25	Martin Nowak Program for Evolutionary Dynamics, Harvard University	Evolutionary dynamics [Video]	Spring 2018
Apr 11	John Ingraham Marks Lab, Harvard Medical School	Learning protein structure with a differentiable simulator [Video]	Spring 2018
Apr 4	Rich Bonneau Center for Genomics and Systems Biology, New York University	Primer: Inference of biological networks with biophysically motivated methods [Video]	Spring 2018
Apr 4	Dayanne Castro Bonneau Lab, New York University	Multitask learning approaches to biological network inference: linking model estimation across diverse related datasets [Video]	Spring 2018
Mar 28	Sam Freesun Friedman Data Sciences Platform, Broad Institute	Variant filtering and calling with convolutional neural networks [Video]	Spring 2018
Mar 21	Ben Allen Dept. of Mathematics, Emmanuel College; Program for Evolutionary Dynamics, Harvard University	Evolutionary dynamics on any population structure [Video]	Spring 2018
Mar 7	Jacob Oppenheim Indigo Agriculture	Inferring microbial phenotypes through latent representations of biological diversity	Spring 2018
Feb 28	Ray Jones Lander Lab, Broad Institute	Primer: Kernel methods and the kernel "trick" [Video]	Spring 2018

Spring 2018
Date	Speaker	Title
Feb 28	Omer Weissbrod Price Group, Harvard School of Public Health	Linking gut microbiomes, genomes and phenotypes via linear mixed models and kernel methods [Video]	Spring 2018
Feb 21	Po-Ru Loh Dept. of Medicine and Division of Genetics, Brigham and Women's Hospital, Harvard Medical School; Broad Institute Giulio Genovese McCarrol Lab, Broad Institute; Dept. of Genetics, Harvard Medical School	Leveraging long range phasing to detect mosaicism in blood at ultra-low allelic fractions	Spring 2018
Feb 14	Fredrik Johansson Institute for Medical Engineering & Science, Massachusetts Institute of Technology	Primer: Causal inference [Video]	Spring 2018
Feb 14	David Sontag Dept. of Electrical Engineering and Computer Science, Institute for Medical Engineering & Science, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology	AI for health needs causality [Video]	Spring 2018
Feb 7	Tami Lieberman Institute for Medical Engineering and Science, Dept. of Civil and Environmental Engineering, Massachusetts Institute of Technology	Rapid bacterial adaptation within individual human microbiomes	Spring 2018

Fall 2017
Date	Speaker	Title
Dec 13	Cheng-Zhong Zhang Dept. of Biomedical Informatics, Harvard Medical School; Dept. of Biostatistics and Computational Biology, Dana-Farber Cancer Institute Rick Tourdot Harvard Medical School; Dana-Farber Cancer Institute	In search of lost time: Reconstructing the evolutionary history of cancer genomes [Video]	Fall 2017
Dec 6	Vicky Yao Troyanskaya Lab, Lewis-Sigler Institute for Integrative Genomics, Princeton University	Primer: Integrated, tissue-specific analysis of biological data [Video]	Fall 2017
Dec 6	Olga Troyanskaya Lewis-Sigler Institute for Integrative Genomics, Princeton University; Center for Computational Biology, Flatiron Institute	From genome to networks: A data-driven, tissue-specific view of human disease	Fall 2017
Nov 29	Joseph Nasser Lander Lab, Broad Institute	Primer: Introduction to Hi-C	Fall 2017
Nov 29	Erez Lieberman Aiden Center for Genomic Architecture, Baylor College of Medicine; Depts. of Computational and Applied Mathematics and Computer Science, Rice University	A 3D Code in the human genome	Fall 2017
Nov 15	Jennifer Listgarten Microsoft Research	Machine-learning-based CRISPR guide design [Video]	Fall 2017
Nov 8	Nicolo Fusi Microsoft Research	Automated Machine Learning [Video]	Fall 2017
Nov 1	Alex Wein Dept. of Mathematics, Massachusetts Institute of Technology	Message passing algorithms for cryo-EM and synchronization [Video]	Fall 2017
Oct 25	David Reshef MIT CSAIL, HMS, Harvard CS Yakir Reshef Dept. of Computer Science, Harvard University; Harvard/MIT MD-PhD Program, Harvard Medical School	Primer: Hypothesis testing and measures of dependence [Video]	Fall 2017
Oct 25	David Reshef MIT CSAIL, HMS, Harvard CS Yakir Reshef Dept. of Computer Science, Harvard University; Harvard/MIT MD-PhD Program, Harvard Medical School	Detecting novel associations in large data sets [Video]	Fall 2017
Oct 11	Michael Rooney Neon Therapeutics	Primer: Intro to tumor immunity [Video]	Fall 2017
Oct 11	Sisi Sarkizova Hacohen Lab, Broad Institute, Massachusetts General Hospital Michael Rooney Neon Therapeutics	Improving endogenous antigen prediction to support personalized cancer vaccine development [Video]	Fall 2017
Oct 4	Hilary Finucane Medical and Population Genetics, Broad Institute	Insight into the biology of common diseases using summary statistics of large genome-wide association studies [Video]	Fall 2017
Sep 27	Lénaïc Chizat Dept. of Mathematics, Ecole Normale Supérieure Paris	Primer: A tutorial on optimal transport [Video]	Fall 2017
Sep 27	Geoffrey Schiebinger Broad Institute; Statistics and Data Science Center, Massachusetts Institute of Technology	Learning developmental landscapes from single-cell gene expression with optimal transport [Video]	Fall 2017

Fall 2017
Date	Speaker	Title
Sep 20	Nick Patterson Broad Institute; Reich Lab, Harvard University	Learning phylogeny through f-statistics [Video]	Fall 2017
Sep 13	Ran Cui Finucane Lab, Broad Institute	Primer: Generalized least squares [Video]	Fall 2017
Sep 13	Yakir Reshef Dept. of Computer Science, Harvard University; Harvard/MIT MD-PhD Program, Harvard Medical School	Detecting effects of transcription factors on disease [Video]	Fall 2017
Sep 6	Sam Freesun Friedman Data Sciences Platform, Broad Institute	Primer: Classifying genomic sequences with convolutional neural networks [Video]	Fall 2017
Sep 6	David Kelley Calico Life Sciences	Reading the rules of gene regulation from the human noncoding genome [Video]	Fall 2017

Fall 2016
Date	Speaker	Title
Dec 14	Daniel King Hail Team, Neale Lab, Broad Institute	What is a compiler? [Video]	Fall 2016
Dec 14	Daniel Huang The Programming Languages Group, Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS)	Compiling probabilistic programs [Video]	Fall 2016
Dec 7	Karsten Krug Proteomics Platform, Broad Institute	Mass spectrometry-based proteomics [Video]	Fall 2016
Dec 7	Ryan Peckner Proteomics Platform, Broad Institute	Spectral unmixing for next-generation mass spectrometry proteomics [Video]	Fall 2016
Nov 16	Babak Ehteshami Bejnordi Beck Lab, Harvard Medical School	Practical recommendations for training convolutional neural nets [Video]	Fall 2016
Nov 16	Dayong Wang Beck Lab, Harvard Medical School Andy Beck Dept. of Pathology, Harvard Medical School	Deep learning for computational pathology [Video]	Fall 2016
Nov 9	David Benjamin Data Sciences Platform, Broad Institute	Dirichlet processes [Video]	Fall 2016
Nov 9	Quaid Morris Donnelly Centre for Cellular and Biomedical Research, Depts. of Molecular Genetics, Computer Science, and Electrical and Computer Engineering, University of Toronto	Algorithms for reconstructing tumor evolution [Video]	Fall 2016
Nov 2	Anshul Kundaje Depts. of Genetics and Computer Science, Stanford University	Integrative, interpretable deep learning frameworks for regulatory genomics and epigenomics [Video]	Fall 2016
Oct 26	Alex Wiltschko Twitter Cortex	Automatic differentiation, the algorithm behind all deep neural networks [Video]	Fall 2016
Oct 26	Umut Eser Churchman Lab, Harvard Medical School	FIDDLE: An integrative deep learning framework for functional genomic data inference [Video]	Fall 2016
Oct 12	Ann Sizemore Cancer Program, Broad Institute	Topological data analysis: What is persistent homology? [Video]	Fall 2016
Oct 12	Chad Giusti Dept. of Mathematics, Warren Center for Network and Data Sciences, University of Pennsylvania	Topological data analysis: What can persistent homology see? [Video]	Fall 2016
Sep 28	Adrian Veres Dept. of Systems Biology, Harvard University; Harvard-MIT Health Sciences and Technology	Experimental and computational techniques underlying RNA-seq [Video]	Fall 2016
Sep 28	Rafael Irizarry Dept. of Data Sciences, Dana-Farber Cancer Institute; Dept. of Biostatistics, Harvard School Public Health	Overcoming bias and batch effects in high-throughput data [Video]	Fall 2016

Fall 2016
Date	Speaker	Title
Sep 21	Rajesh Ranganath Dept. of Computer Science, Princeton University	Probabilistic generative models and posterior inference [Video]	Fall 2016
Sep 21	Alp Kucukelbir Dept. of Computer Science, Columbia University	Automated inference and the promise of probabilistic programming [Video]	Fall 2016
Sep 14	Brian Cleary Regev Lab, Lander Lab, Broad Institute; Dept. of Computational and Systems Biology, Massachusetts Institute of Technology	Composite measurements and molecular compressed sensing for efficient transcriptomics at scale [Video]	Fall 2016
Sep 14	Alex Bloemendal Hail Team, Neale Lab, Broad Institute; Analytic and Translational Genetics Unit, Massachusetts General Hospital	Introduction to compressed sensing	Fall 2016

Spring 2016
Date	Speaker	Title
Jun 1	Su-In Lee Depts. of Genome Sciences, Electrical Engineering, and Computer Science, University of Washington	Identifying molecular markers for cancer treatment from big data	Spring 2016
May 25		MIA Breakfast Social	Spring 2016
May 18	Tim Poterba Hail Team, Neale Lab, Broad Institute Jon Bloom Hail Team, Neale Lab, Broad Institute	Basic introduction to distributed computation [Video]	Spring 2016
May 18	Matei Zaharia Dept. of Electrical Engineering and Computer Science, Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology; Databricks	Scaling data analysis with Apache Spark [Video]	Spring 2016
May 11	David Benjamin Data Sciences Platform, Broad Institute	Variational Bayesian inference [Video]	Spring 2016
May 11	David Blei Depts. of Statistics and Computer Science, Data Science Institute, Columbia University	Scaling and generalizing variational inference [Video]	Spring 2016
May 4	Yakir Reshef Harvard Intelligent Probabilistic Systems, Harvard University; Harvard Medical School; Massachusetts Institute of Technology	Gaussian processes [Video]	Spring 2016
May 4	Barbara Engelhardt Dept. of Computer Science, Princeton University	Bayesian structured sparsity: Rethinking sparse regression [Video]	Spring 2016
Apr 27	Ryan Peckner Genetic Perturbation Platform, Broad Institute	Linear codes [Video]	Spring 2016
Apr 27	Yaniv Erlich Dept. of Computer Science, Columbia University; NY Genome Center	Compressed experiments [Video]	Spring 2016
Apr 27	David Tse Dept. of Electrical Engineering, Stanford University; Dept. of Electrical Engineering and Computer Sciences, UC Berkeley	The science of information: Case studies from DNA and RNA assembly [Video]	Spring 2016
Apr 20	Manuel Rivas Daly Lab, Massachusetts General Hospital; Broad Institute	Multiple testing and false discovery rate	Spring 2016
Apr 20	Joshua Weinstein Zhang Lab, Broad Institute	DNA microscopy and the sequence-to-image inverse problem	Spring 2016
Apr 13	Joseph Nasser Connectivity Map, Broad Institute	t-dist. stochastic neighbor embedding (t-SNE)	Spring 2016
Apr 13	Shantanu Singh Carpenter Lab, Broad Institute Anne Carpenter Imaging Platform, Broad Institute Mohammad Rohban Carpenter Lab, Broad Institute	Information in cell images: Targeting diseases and characterizing compounds	Spring 2016
Apr 6	David Kelley Rinn Lab, Dept. of Stem Cell and Regenerative Biology, Harvard University	Convolutional neural nets	Spring 2016

Spring 2016
Date	Speaker	Title
Apr 6	Abraham Heifets Atomwise	AtomNet: a deep convolutional neural net for bioactivity prediction in structure-based drug discovery	Spring 2016
Mar 30	David Rolnick Dept. of Mathematics, Massachusetts Institute of Technology	Non-negative matrix factorization (NMF)	Spring 2016
Mar 30	John Wakeley Dept. of Organismic and Evolutionary Biology, Harvard University	The effects of population pedigrees on gene genealogies	Spring 2016
Mar 23	Alex Bloemendal Hail Team, Neale Lab, Broad Institute	Linear models III: regularization, LASSO and sparsity	Spring 2016
Mar 23	D. Sculley Google Brain, Google Research Cambridge	A quick introduction to TensorFlow and related API's	Spring 2016
Mar 16	Yakir Reshef Harvard Intelligent Probabilistic Systems, Harvard University; Harvard Medical School; Massachusetts Institute of Technology	Linear models II: Regularization and ridge	Spring 2016
Mar 16	Jeremy Freeman Janelia Research Campus; Howard Hughes Medical Institute	Open source tools for large-scale neuroscience [Video]	Spring 2016
Mar 9	Hilary Finucane Price Lab, Harvard School of Public Health; Dept. of Mathematics, Massachusetts Institute of Technology	Linear models I: Ordinary least squares	Spring 2016
Mar 9	Po-Ru Loh Price Lab, Harvard School of Public Health	Haplotype phasing in large cohorts: Modeling, search, or both?	Spring 2016
Mar 2	Giulio Genovese McCarrol Lab, Broad Institute; Dept. of Genetics, Harvard Medical School	Hidden Markov models II	Spring 2016
Mar 2	Leonid Mirny Dept. of Physics, Institute for Medical Engineering and Science, Massachusetts Institute of Technology	Polymer models of chromosomes	Spring 2016
Feb 24	Giulio Genovese McCarrol Lab, Broad Institute; Dept. of Genetics, Harvard Medical School	Hidden Markov models I	Spring 2016
Feb 24	Geoffrey Schiebinger Dept. of Statistics, UC Berkeley	Sparse inverse problems	Spring 2016
Feb 17	Jon Bloom Hail Team, Neale Lab, Broad Institute; Dept. of Mathematics, Massachusetts Institute of Technology	Frequentist vs Bayesian inference	Spring 2016
Feb 17	Caroline Uhler Dept. of Electrical Engineering and Computer Science, Institute for Data, Systems and Society (IDSS), Massachusetts Institute of Technology	Gene regulation in space and time [Video]	Spring 2016
Feb 10	David Benjamin Data Sciences Platform, Broad Institute	Primer: Principal component analysis (PCA)	Spring 2016
Feb 10	Jeremy Gunawardena Dept. of Systems Biology, Harvard University	Systems biology: Can mathematics lead experiments?	Spring 2016
Feb 3	Shamil Sunyaev Dept. of Biomedical Informatics, Harvard University; Brigham and Women's Hospital; Broad Institute	Judging the importance of human mutations using evolutionary models	Spring 2016
Jan 27	Brendan Frey Depts. of Electrical and Computer Engineering, Computer Science, and Medical Research, University of Toronto; Deep Genomics	Genomic medicine: Will software eat bio?	Spring 2016

Fall 2015
Date	Speaker	Title
Nov 30	Matthew Johnson Datta Lab, Harvard Intelligent Probabilistic Systems, Harvard University	TS II. Modeling structure in time series	Fall 2015

Fall 2015
Date	Speaker	Title
Nov 23	Alex Wiltschko Datta Lab, Harvard Intelligent Probabilistic Systems, Harvard University; Twitter	TS I. Mapping sub-second structure in mouse behavior	Fall 2015
Nov 16	David Kelley Rinn Lab, Dept. of Stem Cell and Regenerative Biology, Harvard University	Harvard Stem Cell NN III. Learning the regulatory code of the accessible genome with deep convolutional neural nets	Fall 2015
Nov 12	Ryan Adams The Original HIPSter, Twitter Cortex, Talking Machines	Machine learning and the life sciences: Beyond data analysis [Video]	Fall 2015
Nov 9	David Duvenaud Harvard Intelligent Probabilistic Systems, Harvard University	NN II. Convolutional networks on graphs for learning molecular fingerprints	Fall 2015
Nov 2	Dougal Maclaurin Harvard Intelligent Probabilistic Systems, Harvard University	NN I. Reverse-mode differentiation and autograd	Fall 2015
Oct 19	Scott Linderman Harvard Intelligent Probabilistic Systems, Harvard University	DM II. Discrete models with continuous latent structure: A new hope	Fall 2015
Oct 13	Jon Bloom Broad Institute	DM I. Bayesian logistic regression and mixed models: Revenge of the Gibbs	Fall 2015
Sep 21	Alex Bloemendal Broad Institute; Analytic and Translational Genetics Unit, Massachusetts General Hospital	CS2: Compressed sensing	Fall 2015
Sep 21	Brendan Meade Dept. of Earth and Planetary Sciences, Harvard University; Google Research	CS1: Exploiting sparse and quantized signals to solve linear systems	Fall 2015
Sep 14	Nikolai Slavov Dept. of Bioengineering, Northeastern University	Quantifying protein isoforms	Fall 2015

Summer 2015
Date	Speaker	Title
Jul 27	Andrea Byrnes Broad Institute; Harvard Medical School; Massachusetts General Hospital	Challenges in normalization of RNAseq data	Summer 2015
Jul 20	Brendan Bulik-Sullivan Broad Institute	LD score regression for distinguishing confounding from polygenicity	Summer 2015
Jul 13	Mark Flaherty Data Sciences Platform, Broad Institute	Introduction to evolutionary algorithms and NEAT	Summer 2015
Jul 6	David Benjamin Data Sciences Platform, Broad Institute	The Chinese restaurant process and Indian buffet process	Summer 2015
Jun 29	David Benjamin Data Sciences Platform, Broad Institute	Introduction to Dirichlet processes	Summer 2015
Jun 22	Bertrand Haas Broad Institute	Conjugate priors and Hardy-Weinberg equilibrium (Bishop, Ch2)	Summer 2015
Jun 15	Jon Bloom Broad Institute	Discussion of Pachter's p-value prize	Summer 2015
Jun 8	Bertrand Haas Broad Institute	Choosing priors in Bayesian inference	Summer 2015
Jun 1	Heng Li Broad Institute	Graph-based genetic sequence representation	Summer 2015

Spring 2015
Date	Speaker	Title
May 4	Jon Bloom Broad Institute	Introduction to Gaussian processes and Bayesian optimization (Bishop, Ch6)	Spring 2015

Spring 2015
Date	Speaker	Title
Apr 28	Ian Smith Broad Institute	Connectivity map and challenges in data normalization	Spring 2015
Apr 14	Brendan Bulik-Sullivan Broad Institute	Linear mixed models for genetic association analysis	Spring 2015
Apr 7	Yossi Farjoun Data Sciences Platform, Broad Institute	Genetic fingerprints and contamination estimation	Spring 2015
Mar 30	Alex Bloemendal Dept. of Mathematics, Harvard University	Markov Chain Monte Carlo and Gibbs sampling on Gaussian mixture models (Bishop, Ch11)	Spring 2015
Mar 23	Laura Gauthier MacArthur Lab, Data Sciences Platform, Broad Institute Bertrand Haas Broad Institute	Variant quality score recalibration	Spring 2015
Mar 16	Cotton Seed Dept. of Mathematics, Massachusetts Institute of Technology	Variational Bayes and inference on Gaussian mixture models (Bishop, Ch10)	Spring 2015
Mar 9	Jon Bloom Dept. of Mathematics, Massachusetts Institute of Technology; Broad Institute	Expectation maximization and inference on Gaussian mixture models (Bishop, Ch9)	Spring 2015
Mar 2	Jon Bloom Dept. of Mathematics, Massachusetts Institute of Technology; Broad Institute	Introduction to Bayesian graphical models: the Gaussian mixture model (Bishop, Ch8)	Spring 2015
Feb 24	Alex Bloemendal Dept. of Mathematics, Harvard University Jon Bloom Dept. of Mathematics, Massachusetts Institute of Technology; Broad Institute Bertrand Haas Broad Institute Cotton Seed Dept. of Mathematics, Massachusetts Institute of Technology	Comparison of dimensional reduction methods: PCA, ICA, NMF, tSNE, and diffusion maps	Spring 2015
Jan 26	Bertrand Haas Broad Institute	Independent component analysis (ICA) and projection pursuit	Spring 2015

Fall 2014
Date	Speaker	Title
Dec 15	Jon Bloom Dept. of Mathematics, Massachusetts Institute of Technology; Broad Institute Cotton Seed Dept. of Mathematics, Massachusetts Institute of Technology	Non-linear dimensional reduction: tSNE and diffusion maps	Fall 2014
Dec 8	Alex Bloemendal Dept. of Mathematics, Harvard University	Non-negative matrix factorization (NMF)	Fall 2014
Nov 24	Alex Bloemendal Dept. of Mathematics, Harvard University	Principle component analysis (PCA) and the Marchenko-Pastur law	Fall 2014
Nov 3	Jon Bloom Dept. of Mathematics, Massachusetts Institute of Technology; Broad Institute Bertrand Haas Broad Institute	Puzzle day: Drunk Monty Hall, the two envelopes, the bloody crime scene, and Simpson's paradox	Fall 2014
Oct 27	Jon Bloom Dept. of Mathematics, Massachusetts Institute of Technology; Broad Institute	Optimal coverage in rare variant association studies	Fall 2014
Oct 20	Yossi Farjoun Broad Institute	Detecting sample swap	Fall 2014
Oct 6	Bertrand Haas Broad Institute	Contingency tables III: Examples in genetics	Fall 2014
Sep 29	Bertrand Haas Broad Institute	Contingency tables II: Correlation, Pearson chi-squared test, and Fisher exact test	Fall 2014
Sep 22	Bertrand Haas Broad Institute	Contingency tables I: t-test and z-test	Fall 2014