2018 Winter: BIODS 215

Welcome to BIODS215 Topics in Biomedical Data Science: Large-scale inference!

Teaching team



Course content

# Date Lecturer Room Topic Lecture slides Readings Assignments
1 1/9/2018 Manuel M112 Overview of Methodology and Disease Genetics Slides D. Donoho. 50 years of Data Science  
2 1/11/2018 Julia M112 Overview of Methodology and Disease Genomics Slides Xiong et. al., 2015, Graveley, 2001, Rosenberg, et. al, 2015  
3 1/16/2018 James M112 An introduction to deep learning   Neural Nets and Deep learning primer, Deep learning for computational biology, Deep learning for healthcare: review, opportunities and challenges  
4 1/18/2018 Julia S M112 high dimensional RNA abundance estimation (Poisson models) Slides Jiang and Wong, 2009, IVT-seq, Statistical Model of RNA-seq data PSet1 out (due 1/30/2018)
5 1/23/2018 Julia S M112 Robust methods; rank testing permutation distributions Slides Zhang, Razaviyayn, and Tse, 2018, Lior Pachter blog post.  
6 1/25/2018 Julia S M114 Monte carlo techniques– intuition for mixing times ( markov chains); martingales and permutation testing Slides For review of Mann Whitney & Kruskall Walls test, please refer to Section 11.2.3. and 12.2.3 of J. Rice, 2007. Class project proposal due out (due 1/30/2018)
7 1/30/2018 Julia S M112 functional approximation: Neyman’s smooth testing, splines, fourier analysis; PCA and neural nets Slides Chung and Romano, 2013, Pimentel, et. al., 2017 PSet 1 due. We extend the deadline by a week.
8 2/1/2018 Yosuke M112 Data visualization Slides    
9 2/6/2018 Manuel M112 Multi level modeling Slides Efron, 2009; Gelman PSet1 due; PSet2 out (due 2/22/2018)
10 2/8/2018 Manuel M112 Mixture models Slides Rivas, et. al. 2015, PTVs; Rivas, et. al. 2016, IBD; Murphy 2007, Bayesian Priors  
11 2/13/2018 Manuel M112 Prediction with Bayesian models Slides Bayesian regression models using Stan in R ; Bayesian Basics; Conjugate prior (wikipedia)  
12 2/15/2018 Naras M112 Distributed and Privacy-Preserving Computations   Link to the tutorial  
13 2/20/2018 James Z M112       Class project milestone due
14 2/22/2018 James Z M112       PSet 2 due
15 2/27/2018 Daniel Rubin M112 Frontiers of Artificial Intelligence in AI in Imaging Slides    
16 3/1/2018            
17 3/6/2018 Manuel MSOB x303 High-dimensional inference methods on summary statistics Slides    
18 3/8/2018 All instructors presenting their research in lab M112 Frontier of Biomedical Data Science Research      
19 3/13/2018 Final project M112        
20 3/15/2018 Final project M112       Final project write up due