# 2018 Winter: BIODS 215

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

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### Teaching team

#### Instructors

#### TA

### 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 | |

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 |