MIA Talks Search

Spring 2021
Date	Speaker	Title
May 26	TBD	Primer: TBD
May 26	Lester Mackey Depts. of Statistics and Computer Science, Stanford University; Microsoft Research New England	TBD
May 19	Felix Dietlein Van Allen Lab, Dana-Farber Cancer Institute; Harvard Medical School	Primer: TBD
May 19	Haitham Elmarakeby Broad Institute; Harvard Medical School; Dana-Farber Cancer Institute	TBD
May 12	Michelle Li Bioinformatics and Integrative Genomics Program, Harvard Medical School	Primer: TBD
May 12	Marinka Zitnik Dept. of Biomedical Informatics, Harvard University; Broad Institute	TBD
May 5	Alan Amin Harvard University	Primer: TBD
May 5	Eli Weinstein Marks Lab, Harvard Medical School; Harvard University	TBD
Apr 29		No primer
Apr 29	Sara Mostafavi Paul G. Allen School of Computer Science and Engineering, University of Washington	Deep learning of immune differentiation (Note: 12pm start)
Apr 28		NO MEETING THIS WEEK
Apr 21		NO MEETING THIS WEEK
Apr 14		NO MEETING THIS WEEK
Apr 7		No primer
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]
Mar 31	Hoon Cho Broad Institute	Primer: Density-aware visualization and sketching of single-cell transcriptomic data [Video]
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]
Mar 24	Jung-Eun (June) Shin Marks Lab, Harvard Medical School	Primer: Generative models of antibodies for functionally optimized library design [Video]
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]
Mar 17		NO MEETING THIS WEEK

Spring 2021
Date	Speaker	Title
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]
Mar 10	David Hong Dept. of Statistics, Wharton School, University of Pennsylvania	Simple, flexible and effective pooled testing via hypergraph factorization [Video]
Mar 3	Emily Laubscher Van Valen Lab, California Institute of Technology	Primer: Integrating heterogeneous measurements in single cells [Video]
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]
Feb 24	Michael Mitzenmacher Dept. Computer Science, Harvard University	Primer: Locality sensitive hashing: A sort of history and introduction [Video]
Feb 24	Hayden Metsky Sabeti Lab, Broad Institute	Viral diagnostic design with model-based optimization [Video]
Feb 17		NO MEETING THIS WEEK
Feb 10		No primer
Feb 10	Martin Jankowiak Pyro Team, Broad Institute	Bayesian methods for adaptive experimental design [Video]
Feb 3		No primer
Feb 3	Christina Leslie Computational & Systems Biology Program, Memorial Sloan Kettering Cancer Center	The 3D genome and predictive models of gene regulation
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]
Jan 27	Gautam Reddy NSF-Simons Center for Mathematical and Statistical Analysis of Biology; Harvard University	Predictable patterns in phenotypic evolution [Video]

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]
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]
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]
Dec 2	Pankaj Mehta Dept. of Physics, Boston University	Toward a statistical mechanics of microbiomes [Video]
Nov 25		NO MEETING THIS WEEK
Nov 18		No primer
Nov 18	Asja Radja Mahadevan Group, Harvard University	Patterns on pollen: a polysaccharide phase transition process (Note: 11am start) [Video]

Fall 2020
Date	Speaker	Title
Nov 11		NO MEETING THIS WEEK
Nov 4		NO MEETING THIS WEEK
Oct 28	Will Townes Engelhardt Group, Princeton University	Primer: Generalized linear models and latent factor models [Video]
Oct 28	Jeff Miller Dept. of Biostatistics, Harvard University	Inference in generalized bilinear models [Video]
Oct 21	Eli Bingham Pyro team, Broad Institute	Primer: Stochastic gradient-based variational inference [Video]
Oct 21	Fritz Obermeyer Pyro team, Broad Institute	Deep probabilistic programming with Pyro [Video]
Oct 14		No primer
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]
Oct 7	Sam Sinai Dyno Therapeutics	Primer: Biological sequence design through machine-guided exploration [Video]
Oct 7	Eric Kelsic Dyno Therapeutics	Machine-guided capsid engineering for gene therapy [Video]
Sep 30	Daphne Schlesinger Research Laboratory of Electronics Computational Cardiovascular Research Group, Massachusetts Institute of Technology	Primer: Modeling cardiovascular physiology [Video]
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]
Sep 23	Mike Oberst Clinical Machine Learning Group, Massachusetts Institute of Technology	Primer: Learning personalized treatment policies from observational data [Video]
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]
Sep 16	Rohan Saha University of Alberta	Primer: Machines read, humans read: parallels between computer and human representations of meaning (Note: 11am start) [Video]
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]
Sep 9	Raj Agrawal Broderick Group, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology; ArbiLex	Primer: Gaussian processes: An introduction [Video]
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]

Spring 2020
Date	Speaker	Title
May 20		NO MEETING, SEE YOU NEXT SEMESTER!
May 13	TBD	Primer: TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)

Spring 2020
Date	Speaker	Title
May 13	Hayden Metsky Sabeti Lab, Broad Institute	TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)
May 6	TBD	Primer: TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)
May 6	Max Shen Massachusetts Institute of Technology	TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)
Apr 29	Megan Owen Dept. of Mathematics, Lehman College of the City University of New York	Primer: TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)
Apr 29	Katherine St. John Dept. of Computer Science, Hunter College of the City University of New York	TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)
Apr 22	TBD	Primer: TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)
Apr 22	Fritz Obermeyer Uber AI; Pyro	TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)
Apr 15		NO MEETING
Apr 8	TBD	Primer: TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)
Apr 8	Pankaj Mehta Dept. of Physics, Boston University	TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)
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]
Apr 1	Markus Kaiser Ek Group, Dept. of Computer Science, Technical University of Munich; Siemens AG	Primer: TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)
Apr 1	Carl Henrik Ek Dept. of Computer Science, University of Bristol	TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)
Mar 25		NO MEETING
Mar 18	TBD	Primer: TBD (NOTE: POSTPONED UNTIL FURTHER NOTICE)
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)
Mar 11	Sam Sinai Dyno Therapeutics	Primer: Biological sequence design through machine-guided exploration (NOTE: POSTPONED UNTIL FURTHER NOTICE)
Mar 11	Eric Kelsic Dyno Therapeutics	Machine-guided capsid engineering for gene therapy (NOTE: POSTPONED UNTIL FURTHER NOTICE)
Mar 4	Sam Friedman Data Sciences Platform, Broad Institute	Primer: Only connect: The variety and splendor of neural network architectures
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
Date	Speaker	Title
Feb 26	Alex Bloemendal Neale Lab, Lander Lab, Broad Institute; Analytic and Translational Genetics Unit, Massachusetts General Hospital	Primer: The multiple testing problem [Video]
Feb 26	Jackson Loper Paninski Lab, Blei Lab, Dept. of Statistics, Data Science Institute, Columbia University	Smoothed nested testing on directed acyclic graphs [Video]
Feb 19		NO MEETING
Feb 12	Roger Grosse Dept. of Computer Science, University of Toronto; Vector Institute	Primer: Enforcing Lipschitz constraints for neural networks [Video]
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]
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)
Jan 29		No primer
Jan 29	Aleksandrina Goeva Gopal Sarma Daniel King Patrick Schultz Alex Bloemendal Hilary Finucane Samuel Friedman	Topics Groups Nucleation Event (10-11am in Monadnock)

Fall 2019
Date	Speaker	Title
Dec 18	Holiday Mixer	Holiday Mixer (Note: 10am in Monadnock)
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]
Dec 4	Will Stephenson Computer Science & Artificial Intelligence Lab (CSAIL), Massachusetts Institute of Technology	Primer: An overview of some issues in Bayesian robustness [Video]
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]
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]
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]
Nov 13	CANCELLED	CANCELLED
Nov 13	CANCELLED	CANCELLED
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)
Nov 6	Emily Winn Crawford Lab, Brown University	Primer: Integrating topological data analysis (TDA) with statistical learning techniques [Video]
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]
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
Date	Speaker	Title
Oct 30	Andrew Gordon Wilson Courant Institute, New York University	Loss valleys, uncertainty, and generalization in deep learning [Video]
Oct 23	Adam Cohen Depts. of Chemistry and Chemical Biology, Physics, Harvard University	Primer: Computational challenges in optical electrophysiology (Note: Auditorium) [Video]
Oct 23	Sami Farhi Regev Lab, Broad Institute	New imaging data types and computational challenges at the optical profiling platform (Note: Auditorium) [Video]
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]
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]
Oct 16	Sam Lewallen Center for Brain Science, Harvard University	Manifold discovery of cognitive maps [Video]
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]
Oct 9	Gil Strang Dept. of Mathematics, Massachusetts Institute of Technology	Key ideas in linear algebra [Video]
Oct 2	Allen Goodman Carpenter Lab, Imaging Platform, Broad Institute	Primer: Intro to computer vision and its relationship to machine learning [Video]
Oct 2	Sam 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]
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]
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]
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]
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]
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]
Sep 11	Chang Liu Dept. of Biomedical Engineering, UC Irvine	Synthetic genetic systems for rapid mutation and continuous evolution in vivo [Video]

Spring 2019
Date	Speaker	Title
May 29	Peter Koo Eddy Lab, Harvard University	Interpretable convolutional networks for regulatory genomics [Video]
May 22	Aaron Kollasch Marks Lab, Harvard Medical School, Broad Institute	Primer: Generative models from NLP for sequence data [Video]
May 22	Debora Marks Dept. of Systems Biology, Harvard Medical School; Broad Institute	Alignment-free models for protein and antibody design [Video]
May 15	Natasha Jaques MIT Media Lab, Massachusetts Institute of Technology	Primer: Mechanisms for generalized learning across tasks and environments [Video]

Spring 2019
Date	Speaker	Title
May 15	Susan Murphy Depts. of Statistics, Computer Science, Harvard University	Personalized HeartSteps: A reinforcement learning algorithm for optimizing physical activity [Video]
May 8	Allon Klein Dept. of Systems Biology, Harvard Medical School	Primer: Inference of high-dimensional dynamics [Video]
May 8	Caleb Weinreb Dept. of Systems Biology, Harvard Medical School	Lineage tracing on transcriptional landscapes links state to fate during differentiation [Video]
May 6	Joshua Batson Chan Zuckerberg Biohub	Blind denoising by self-supervision [Video]
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]
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]
Apr 24	Wilder Wohns Dept. of Statistics, University of Oxford	Primer: Introduction to the tree sequence toolchain [Video]
Apr 24	Jerome Kelleher Big Data Institute, University of Oxford	Succinct tree sequences for megasample genomics [Video]
Apr 17	Galen Ballentine Drexel University College of Medicine	Primer: The human brain's default mode network [Video]
Apr 17	Danilo Bzdok Dept. of Psychiatry, Psychotherapy and Psychosomatics, RWTH Aachen University	Algorithms to understand default brain function [Video]
Apr 10	Alexander D'Amour Google Brain	Primer: Extracting causal signal from high-dimensional data: challenges and techniques [Video]
Apr 10	Wesley Tansey Rabadan Lab, Dept. of Systems Biology, Data Science Institute, Columbia University	Interpreting and learning from black box models [Video]
Apr 3	Harrison Specht Slavov Lab, Northeastern University	Primer: Quantifying proteins by mass-spec [Video]
Apr 3	Nikolai Slavov Dept. of Bioengineering, Northeastern University	Understanding biological systems: In search of direct causal mechanisms [Video]
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]
Mar 20	Ralph Peterson Datta Lab, Harvard Medical School	Primer: Learning structure in mouse behavior using motion sequenceing (MoSeq) [Video]
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]
Mar 13	Alex Bloemendal Neale Lab, Lander Lab, Broad Institute; Analytic and Translational Genetics Unit, Massachusetts General Hospital	Primer: Random matrix theory [Video]
Mar 13	Christina Chen Neale Lab, Broad Institute	Controlling for stratification in (meta-)GWAS with PCA: Theory, applications, and implications [Video]
Mar 6	Sergey Ovchinnikov Harvard University	Primer: Generative REgularized ModeLs of proteINs

Spring 2019
Date	Speaker	Title
Mar 6	Mohammed AlQuraishi Harvard Medical School	End-to-end differentiable learning of protein structure [Video]
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]
Feb 27	Daniel Kunin Stanford University Aleksandrina Goeva Macosko Lab, Broad Institute	Regularized linear autoencoders, probabilistic PCA, and backpropagation in the brain [Video]
Feb 13	Mor Nitzan Harvard University	Inferring geometric embeddings for single cell data [Video]
Feb 13	Joshua Weinstein Zhang Lab, Regev Lab, Broad Institute	Optics-free spatio-genetic imaging with DNA microscopy [Video]
Feb 6	Andrew J. Blumberg Dept. of Mathematics, University of Texas at Austin	Primer: Analyzing scientific data with topological data analysis [Video]
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]
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]
Jan 30	Katherine Gorman Talking Machines; Collective Next; Neural Information Processing Systems (neurIPS)	Group exercise: The story algorithm

Fall 2018
Date	Speaker	Title
Dec 12	Wenshuo Wang Dept. of Statistics, Harvard University	Primer: Challenges in high-dimensional variable selection [Video]
Dec 12	Lucas Janson Dept. of Statistics, Harvard University	Using knockoffs to find important variables with statistical guarantees [Video]
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]
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]
Nov 14	Aleksandrina Goeva Macosko Lab, Broad Institute	Primer: Intro to non-negative matrix factorization [Video]
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]
Nov 7	David Benjamin Data Sciences Platform, Broad Institute	Primer: Intro to topic models [Video]
Nov 7	Samantha Riesenfeld Regev Lab, Broad Institute; Kuchroo Lab, Harvard Medical School	Topic modeling the transcriptional spectrum in innate lymphoid cells [Video]
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]
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]
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
Date	Speaker	Title
Oct 24	Brian Cleary Regev Lab, Lander Lab, Broad Institute	Studying cell and tissue physiology with random composite experiments [Video]
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]
Oct 17	Smita Krishnaswamy Depts. of Genetics, Computer Science, Yale University	Manifold learning yields insight into cellular state space under complex experimental conditions [Video]
Oct 10	Hoon Cho Computer Science & Artificial Intelligence Lab, Massachusetts Institute of Technology	Biomedical data sharing and analysis with privacy [Video]
Oct 3	Dustin Tran Google Brain Chris Suter Google Brain	What might machine learners learn from probabilistic programming? [Video]
Sep 26	Adam Breuer Depts. of Computer Science and Government, Harvard University	Primer: Submodular maximization and machine learning [Video]
Sep 26	Yaron Singer Dept. of Computer Science, Harvard University	Maximizing submodular functions exponentially faster [Video]
Sep 19	David Rolnick University of Pennsylvania	Primer: Why is deep learning so deep? [Video]
Sep 19	David Rolnick University of Pennsylvania	Mapping the brain with machine learning [Video]
Jul 11	David Knowles Stanford Medicine	Transcriptomic modeling of chemotherapy side effects using human iPSC-derived cardiomyocytes [Video]

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]
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]
May 16	Larson Hogstrom Lander Lab, Broad Institute	Primer: How philosophy of science can help us better deploy machine learning in biology [Video]
May 16	Ray Jones Lander Lab, Broad Institute	Interpreting sequence models
May 9	James Zou Depts. of Biomedical Data Science, Computer Science, and Electrical Engineering, Stanford University	Primer: Contrastive PCA [Video]
May 9	James Zou Depts. of Biomedical Data Science, Computer Science, and Electrical Engineering, Stanford University	AI audit to uncover blind spots of data
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]
Apr 25	Martin Nowak Program for Evolutionary Dynamics, Harvard University	Primer: Hamilton's rule makes no prediction and cannot be tested empirically [Video]
Apr 25	Martin Nowak Program for Evolutionary Dynamics, Harvard University	Evolutionary dynamics [Video]
Apr 11	John Ingraham Marks Lab, Harvard Medical School	Learning protein structure with a differentiable simulator [Video]

Spring 2018
Date	Speaker	Title
Apr 4	Rich Bonneau Center for Genomics and Systems Biology, New York University	Primer: Inference of biological networks with biophysically motivated methods [Video]
Apr 4	Dayanne Castro Bonneau Lab, New York University	Multitask learning approaches to biological network inference: linking model estimation across diverse related datasets [Video]
Mar 28	Samuel Friedman Data Sciences Platform, Broad Institute	Variant filtering and calling with convolutional neural networks [Video]
Mar 21	Ben Allen Dept. of Mathematics, Emmanuel College; Program for Evolutionary Dynamics, Harvard University	Evolutionary dynamics on any population structure [Video]
Mar 7	Jacob Oppenheim Indigo Agriculture	Inferring microbial phenotypes through latent representations of biological diversity
Feb 28	Ray Jones Lander Lab, Broad Institute	Primer: Kernel methods and the kernel "trick" [Video]
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]
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
Feb 14	Fredrik Johansson Institute for Medical Engineering & Science, Massachusetts Institute of Technology	Primer: Causal inference [Video]
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]
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

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]
Dec 6	Vicky Yao Troyanskaya Lab, Lewis-Sigler Institute for Integrative Genomics, Princeton University	Primer: Integrated, tissue-specific analysis of biological data [Video]
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
Nov 29	Joseph Nasser Lander Lab, Broad Institute	Primer: Introduction to Hi-C
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
Nov 15	Jennifer Listgarten Microsoft Research	Machine-learning-based CRISPR guide design [Video]
Nov 8	Nicolo Fusi Microsoft Research	Automated Machine Learning [Video]
Nov 1	Alex Wein Dept. of Mathematics, Massachusetts Institute of Technology	Message passing algorithms for cryo-EM and synchronization [Video]
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
Date	Speaker	Title
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]
Oct 11	Michael Rooney Neon Therapeutics	Primer: Intro to tumor immunity [Video]
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]
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]
Sep 27		Primer: A tutorial on optimal transport [Video]
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]
Sep 20	Nick Patterson Broad Institute; Reich Lab, Harvard University	Learning phylogeny through f-statistics [Video]
Sep 13	Ran Cui Finucane Lab, Broad Institute	Primer: Generalized least squares [Video]
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]
Sep 6	David Kelley Calico Life Sciences	Reading the rules of gene regulation from the human noncoding genome [Video]
Sep 6	Samuel Friedman Data Sciences Platform, Broad Institute	Classifying genomic sequences with convolutional neural networks [Video]

Fall 2016
Date	Speaker	Title
Dec 14	Daniel King Hail Team, Neale Lab, Broad Institute	What is a compiler? [Video]
Dec 14	Daniel Huang The Programming Languages Group, Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS)	Compiling probabilistic programs [Video]
Dec 7	Karsten Krug Proteomics Platform, Broad Institute	Mass spectrometry-based proteomics [Video]
Dec 7	Ryan Peckner Proteomics Platform, Broad Institute	Spectral unmixing for next-generation mass spectrometry proteomics [Video]
Nov 16	Babak Ehteshami Bejnordi Beck Lab, Harvard Medical School	Practical recommendations for training convolutional neural nets [Video]
Nov 16	Dayong Wang Beck Lab, Harvard Medical School Andy Beck Dept. of Pathology, Harvard Medical School	Deep learning for computational pathology [Video]
Nov 9	David Benjamin Data Sciences Platform, Broad Institute	Dirichlet processes [Video]
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]
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
Date	Speaker	Title
Oct 26	Alex Wiltschko Twitter Cortex	Automatic differentiation, the algorithm behind all deep neural networks [Video]
Oct 26	Umut Eser Churchman Lab, Harvard Medical School	FIDDLE: An integrative deep learning framework for functional genomic data inference [Video]
Oct 12	Ann Sizemore Cancer Program, Broad Institute	Topological data analysis: What is persistent homology? [Video]
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]
Sep 28	Adrian Veres Dept. of Systems Biology, Harvard University; Harvard-MIT Health Sciences and Technology	Experimental and computational techniques underlying RNA-seq [Video]
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]
Sep 21	Rajesh Ranganath Dept. of Computer Science, Princeton University	Probabilistic generative models and posterior inference [Video]
Sep 21	Alp Kucukelbir Dept. of Computer Science, Columbia University	Automated inference and the promise of probabilistic programming [Video]
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]
Sep 14	Alex Bloemendal Hail Team, Neale Lab, Broad Institute; Analytic and Translational Genetics Unit, Massachusetts General Hospital	Introduction to compressed sensing

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
May 25		MIA Breakfast Social
May 18	Tim Poterba Hail Team, Neale Lab, Broad Institute Jon Bloom Hail Team, Neale Lab, Broad Institute	Basic introduction to distributed computation [Video]
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]
May 11	David Benjamin Data Sciences Platform, Broad Institute	Variational Bayesian inference [Video]
May 11	David Blei Depts. of Statistics and Computer Science, Data Science Institute, Columbia University	Scaling and generalizing variational inference [Video]
May 4	Yakir Reshef Harvard Intelligent Probabilistic Systems, Harvard University; Harvard Medical School; Massachusetts Institute of Technology	Gaussian processes [Video]
May 4	Barbara Engelhardt Dept. of Computer Science, Princeton University	Bayesian structured sparsity: Rethinking sparse regression [Video]
Apr 27	Ryan Peckner Genetic Perturbation Platform, Broad Institute	Linear codes [Video]
Apr 27	Yaniv Erlich Dept. of Computer Science, Columbia University; NY Genome Center	Compressed experiments [Video]

Spring 2016
Date	Speaker	Title
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]
Apr 20	Manuel Rivas Daly Lab, Massachusetts General Hospital; Broad Institute	Multiple testing and false discovery rate
Apr 20	Joshua Weinstein Zhang Lab, Broad Institute	DNA microscopy and the sequence-to-image inverse problem
Apr 13	Joseph Nasser Connectivity Map, Broad Institute	t-dist. stochastic neighbor embedding (t-SNE)
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
Apr 6	David Kelley Rinn Lab, Dept. of Stem Cell and Regenerative Biology, Harvard University	Convolutional neural nets
Apr 6	Abraham Heifets Atomwise	AtomNet: a deep convolutional neural net for bioactivity prediction in structure-based drug discovery
Mar 30	David Rolnick Dept. of Mathematics, Massachusetts Institute of Technology	Non-negative matrix factorization (NMF)
Mar 30	John Wakeley Dept. of Organismic and Evolutionary Biology, Harvard University	The effects of population pedigrees on gene genealogies
Mar 23	Alex Bloemendal Hail Team, Neale Lab, Broad Institute	Linear models III: regularization, LASSO and sparsity
Mar 23	D. Sculley Google Brain, Google Research Cambridge	A quick introduction to TensorFlow and related API's
Mar 16	Yakir Reshef Harvard Intelligent Probabilistic Systems, Harvard University; Harvard Medical School; Massachusetts Institute of Technology	Linear models II: Regularization and ridge
Mar 16	Jeremy Freeman Janelia Research Campus; Howard Hughes Medical Institute	Open source tools for large-scale neuroscience [Video]
Mar 9	Hilary Finucane Price Lab, Harvard School of Public Health; Dept. of Mathematics, Massachusetts Institute of Technology	Linear models I: Ordinary least squares
Mar 9	Po-Ru Loh Price Lab, Harvard School of Public Health	Haplotype phasing in large cohorts: Modeling, search, or both?
Mar 2	Giulio Genovese McCarrol Lab, Broad Institute; Dept. of Genetics, Harvard Medical School	Hidden Markov models II
Mar 2	Leonid Mirny Dept. of Physics, Institute for Medical Engineering and Science, Massachusetts Institute of Technology	Polymer models of chromosomes
Feb 24	Giulio Genovese McCarrol Lab, Broad Institute; Dept. of Genetics, Harvard Medical School	Hidden Markov models I
Feb 24	Geoffrey Schiebinger Dept. of Statistics, UC Berkeley	Sparse inverse problems
Feb 17	Jon Bloom Hail Team, Neale Lab, Broad Institute; Dept. of Mathematics, Massachusetts Institute of Technology	Frequentist vs Bayesian inference

Spring 2016
Date	Speaker	Title
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]
Feb 10	David Benjamin Data Sciences Platform, Broad Institute	Primer: Principal component analysis (PCA)
Feb 10	Jeremy Gunawardena Dept. of Systems Biology, Harvard University	Systems biology: Can mathematics lead experiments?
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
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?

Fall 2015
Date	Speaker	Title
Nov 30	Matthew Johnson Datta Lab, Harvard Intelligent Probabilistic Systems, Harvard University	TS II. Modeling structure in time series
Nov 23	Alex Wiltschko Datta Lab, Harvard Intelligent Probabilistic Systems, Harvard University; Twitter	TS I. Mapping sub-second structure in mouse behavior
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
Nov 12	Ryan Adams The Original HIPSter, Twitter Cortex, Talking Machines	Machine learning and the life sciences: Beyond data analysis [Video]
Nov 9	David Duvenaud Harvard Intelligent Probabilistic Systems, Harvard University	NN II. Convolutional networks on graphs for learning molecular fingerprints
Nov 2	Dougal Maclaurin Harvard Intelligent Probabilistic Systems, Harvard University	NN I. Reverse-mode differentiation and autograd
Oct 19	Scott Linderman Harvard Intelligent Probabilistic Systems, Harvard University	DM II. Discrete models with continuous latent structure: A new hope
Oct 13	Jon Bloom Broad Institute	DM I. Bayesian logistic regression and mixed models: Revenge of the Gibbs
Sep 21	Alex Bloemendal Broad Institute; Analytic and Translational Genetics Unit, Massachusetts General Hospital	CS2: Compressed sensing
Sep 21	Brendan Meade Dept. of Earth and Planetary Sciences, Harvard University; Google Research	CS1: Exploiting sparse and quantized signals to solve linear systems
Sep 14	Nikolai Slavov Dept. of Bioengineering, Northeastern University	Quantifying protein isoforms

Summer 2015
Date	Speaker	Title
Jul 27	Andrea Byrnes Broad Institute; Harvard Medical School; Massachusetts General Hospital	Challenges in normalization of RNAseq data
Jul 20	Brendan Bulik-Sullivan Broad Institute	LD score regression for distinguishing confounding from polygenicity
Jul 13	Mark Flaherty Data Sciences Platform, Broad Institute	Introduction to evolutionary algorithms and NEAT
Jul 6	David Benjamin Data Sciences Platform, Broad Institute	The Chinese restaurant process and Indian buffet process

Summer 2015
Date	Speaker	Title
Jun 29	David Benjamin Data Sciences Platform, Broad Institute	Introduction to Dirichlet processes
Jun 22	Bertrand Haas Broad Institute	Conjugate priors and Hardy-Weinberg equilibrium (Bishop, Ch2)
Jun 15	Jon Bloom Broad Institute	Discussion of Pachter's p-value prize
Jun 8	Bertrand Haas Broad Institute	Choosing priors in Bayesian inference
Jun 1	Heng Li Broad Institute	Graph-based genetic sequence representation

Spring 2015
Date	Speaker	Title
May 4	Jon Bloom Broad Institute	Introduction to Gaussian processes and Bayesian optimization (Bishop, Ch6)
Apr 28	Ian Smith Broad Institute	Connectivity map and challenges in data normalization
Apr 14	Brendan Bulik-Sullivan Broad Institute	Linear mixed models for genetic association analysis
Apr 7	Yossi Farjoun Data Sciences Platform, Broad Institute	Genetic fingerprints and contamination estimation
Mar 30	Alex Bloemendal Dept. of Mathematics, Harvard University	Markov Chain Monte Carlo and Gibbs sampling on Gaussian mixture models (Bishop, Ch11)
Mar 23	Laura Gauthier MacArthur Lab, Data Sciences Platform, Broad Institute Bertrand Haas Broad Institute	Variant quality score recalibration
Mar 16	Cotton Seed Dept. of Mathematics, Massachusetts Institute of Technology	Variational Bayes and inference on Gaussian mixture models (Bishop, Ch10)
Mar 9	Jon Bloom Dept. of Mathematics, Massachusetts Institute of Technology; Broad Institute	Expectation maximization and inference on Gaussian mixture models (Bishop, Ch9)
Mar 2	Jon Bloom Dept. of Mathematics, Massachusetts Institute of Technology; Broad Institute	Introduction to Bayesian graphical models: the Gaussian mixture model (Bishop, Ch8)
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
Jan 26	Bertrand Haas Broad Institute	Independent component analysis (ICA) and projection pursuit

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
Dec 8	Alex Bloemendal Dept. of Mathematics, Harvard University	Non-negative matrix factorization (NMF)
Nov 24	Alex Bloemendal Dept. of Mathematics, Harvard University	Principle component analysis (PCA) and the Marchenko-Pastur law
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
Date	Speaker	Title
Oct 27	Jon Bloom Dept. of Mathematics, Massachusetts Institute of Technology; Broad Institute	Optimal coverage in rare variant association studies
Oct 20	Yossi Farjoun Broad Institute	Detecting sample swap
Oct 6	Bertrand Haas Broad Institute	Contingency tables III: Examples in genetics
Sep 29	Bertrand Haas Broad Institute	Contingency tables II: Correlation, Pearson chi-squared test, and Fisher exact test
Sep 22	Bertrand Haas Broad Institute	Contingency tables I: t-test and z-test

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