Section outline

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  • Thursday, July 22, 2021; 1:00 PM to 1:45 PM

    Lecture 1: Introduction to the course

    What is data science/big data?  What makes it different from non-big data?  What big data can and cannot do.  Phases of data science:  getting data, merging and cleaning data, storing and accessing data, visualizing or telling stories with data, drawing conclusions from data.

    Faculty:  Aaron Wolfe Scheffler

    • Lecture Slides:

    • Biostat 202 Lecture 1 - in class File
    • Biostat 202 Lecture 1 - in class File
    • Biostat 202 Lecture 1: Introduction File
    • Biostat 202 Lecture 1: Introduction File
    • Biostat 202: Orange Data Mining Download Guide File
    • Biostat 202 Syllabus File

    • Pre-recorded lecture - watch before live Zoom class session (Access restricted to registered students):

    • Prerecorded Lecture 1 - module 1 Media Resource
      Not available unless: You belong to Registered Students Only
    • Prerecorded Lecture 1 - module 2 Media Resource
      Not available unless: You belong to Registered Students Only
    • Prerecorded Lecture 1 - module 3 Media Resource
      Not available unless: You belong to Registered Students Only
    • Prerecorded Lecture 1 - module 4 Media Resource
      Not available unless: You belong to Registered Students Only
    • Prerecorded Lecture 1 - module 5 Media Resource
      Not available unless: You belong to Registered Students Only
    • Prerecorded Lecture 1 - module 6 Media Resource
      Not available unless: You belong to Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Biostat 202 Lecture 1 - RECORDED Zoom Session URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 1 - RECORDED Zoom Session Media Resource
      Not available unless: You belong to Registered Students Only

    • Final Project

    • Final Project Folder
    • Component 1 - upload here (Due Sunday, Aug 8 @ 11:55 PM) Assignment
    • Component 2 - upload here (Due Sunday, August 15 @ 11:55 PM) Assignment
    • Component 3 - upload here (Due Sunday, August 22 @ 11:55 PM) Assignment
    • Final Project - upload here (Due Tuesday, Sep 2 @ 11:55 PM) Assignment

    • Optional Reading:

      An Introduction to Statistical Learning. Gareth James, Daniela Witten, Trevor Hastie, and Robert Tibshirani. New York: Springer, 2013 and is available for free via http://faculty.marshall.usc.edu/gareth-james/ISL/ISLR%20Seventh%20Printing.pdf . Largely a data mining book. The book is technical in places, but strives to explain things in text. The book provides accompanying code in R to illustrate concepts, but the R material is restricted to lab sections at the end of each chapter; understanding R is not necessary for following the general concepts in the book.

  • Thursday, July 22, 2021; 2:00 PM - 3:45 PM

    Lab 1: Introduction to software

    Students have access to course faculty for questions on current or prior curriculum, assignments and software implementation. This session will be given in-person at Mission Hall.

    Faculty:  Aaron Wolfe Scheffler

    Location:     MH-1400

  • Thursday, July 22, 2021; 4:00 PM - 5:00 PM

    Drop-In Help

    Course faculty are available to address questions. This session will be given via web-conferencing software and in-person.

    Faculty:  Aaron Wolfe Scheffler

    Location (Access restricted to registered students):  Zoom and MH-1400

  • Monday, July 26, 2021; 1:00 PM - 1:45 PM

    Lecture 2: Getting data from large databases


    Faculty:  Aaron Wolfe Scheffler

    • Lecture Slides:

    • Biostat 202 Lecture 2 - in class File
    • Biostat 202 Lecture 2: Getting Data File
    • BSI_Exercise Data File
    • Biostat 202 Lecture 2: Getting Data File
    • Biostat 202 Lecture 2 - in class File

    • Pre-recorded lecture - watch before live Zoom class session (Access restricted to registered students):

    • Prerecorded Lecture 2 - module 1 Media Resource
      Not available unless: You belong to Registered Students Only
    • Prerecorded Lecture 2 - module 2 Media Resource
      Not available unless: You belong to Registered Students Only
    • Prerecorded Lecture 2 - module 3 Media Resource
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 2 - 2021 UPDATE [WATCH ME] URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 2 - 2021 UPDATE [WATCH ME] Media Resource
      Not available unless: You belong to Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Biostat 202 Lecture 2 - RECORDED Zoom Session URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 2 - RECORDED Zoom Session Media Resource
      Not available unless: You belong to Registered Students Only

  • Thursday, July 29, 2021; 1:00 PM - 1:45 PM

    Lecture 3: Managing data and data storage

    Data management, cleaning, and storage.

    Faculty: Aaron Wolfe Scheffler

    • Lecture Slides:

    • Biostat 202 Lecture 3 - class File
    • Biostat 202 Lecture 3 - class File
    • Biostat 202 Lecture 3 - Orange Imputation Demo File
    • Biostat 202 Lecture 3 - Orange Outlier Demo File

    • Pre-recorded lecture - watch before live Zoom class session (Access restricted to registered students):

    • Prerecorded Lecture 3 - module 1 Media Resource
      Not available unless: You belong to Registered Students Only
    • Prerecorded Lecture 3 - module 2 Media Resource
      Not available unless: You belong to Registered Students Only
    • Prerecorded Lecture 3 - module 3 Media Resource
      Not available unless: You belong to Registered Students Only
    • Prerecorded Lecture 3 - module 4 Media Resource
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 3: Data Management, Storage, & Cleaning File
    • Biostat 202 Lecture 3: Data Management, Storage, & Cleaning File

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Biostat 202 Lecture 3 - RECORDED Zoom Session URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 3 - RECORDED Zoom Session Media Resource
      Not available unless: You belong to Registered Students Only

    • Optional readings:

    • Your data is your fingerprint URL
    • How anonymous is anonymizing? URL
    • Data Cleaning File

  • Thursday, July 29, 2021; 2:00 PM - 3:45 PM

    Lab 2: Managing data and data storage

    Students have access to course faculty for questions on current or prior curriculum, assignments and software implementation. This session will be given in-person at Mission Hall.

    Faculty:  Aaron Wolfe Scheffler

    Location:     MH-1400

  • Thursday, July 29, 2021; 4:00 PM - 5:00 PM

    Drop-In Help

    Course faculty are available to address questions. This session will be given via web-conferencing software and in-person.

    Faculty:  Aaron Wolfe Scheffler

    Location (Access restricted to registered students):  Zoom and MH-1400

  • Monday, August 2, 2021; 1:00 PM - 1:45 PM

    Lecture 4: Machine Learning

    Introduction and supervised learning [regression]

    Faculty:  Aaron Wolfe Scheffler

    • Lecture Slides:

    • Biostat 202 Lecture 4: Machine Learning 1 File
    • Biostat 202 Lecture 4: Machine Learning 1 File
    • Heart disease dataset File
    • Biostat 202 Lecture 4 - class File
    • Biostat 202 Lecture 4 - class File
    • Biostat 202 Lecture 4 - Orange Linear Regression Demo File

    • Pre-recorded lecture - watch before live Zoom class session (Access restricted to registered students):

    • Prerecorded Lecture 4 - module 1 Media Resource
      Not available unless: You belong to Registered Students Only
    • Prerecorded Lecture 4 - module 2 Media Resource
      Not available unless: You belong to Registered Students Only
    • Prerecorded Lecture 4 - module 3 Media Resource
      Not available unless: You belong to Registered Students Only
    • Prerecorded Lecture 4 - module 4 Media Resource
      Not available unless: You belong to Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Biostat 202 Lecture 4 - RECORDED Zoom Session URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 4 - RECORDED Zoom Session Media Resource
      Not available unless: You belong to Registered Students Only

  • Thursday, August 5, 2021; 1:00 PM - 1:45 PM

    Lecture 5: Machine Learning 2

    Supervised learning [classification]

    Faculty:  Aaron Wolfe Scheffler

  • Thursday, August 5, 2021; 2:00 PM - 3:45 PM

    Lab 3: Machine Learning

    Students have access to course faculty for questions on current or prior curriculum, assignments and software implementation. This session will be given in-person at Mission Hall.

    Faculty:  Aaron Wolfe Scheffler

    Location:     MH-1400

    • Biostat 202 Lab 3 - RECORDED Zoom Session 1/2 URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lab 3 - RECORDED Zoom Session 1/2 Media Resource
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lab 3 - RECORDED Zoom Session 2/2 URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lab 3 - RECORDED Zoom Session 2/2 Media Resource
      Not available unless: You belong to Registered Students Only

    • Assignment:  

    • Biostat 202 Homework 3 - upload here (Due Thursday, August 12 @ 11:55 PM) Assignment
    • Biostat 202 Assignment 3 File

    • Datasets:

    • framingham.csv File

  • Thursday, August 5, 2021; 4:00 PM - 5:00 PM

    Drop-In Help

    Course faculty are available to address questions. This session will be given via web-conferencing software and in-person.

    Faculty:  Aaron Wolfe Scheffler

    Location (Access restricted to registered students):  Zoom and MH-1400

  • Monday, August 9, 2021; 1:00 PM - 1:45 PM

    Lecture 6: Machine Learning 3

    Supervised learning, cont. [classification]

    Faculty:  Aaron Wolfe Scheffler

    • Lecture Slides:

    • Biostat 202 Lecture 6: Machine Learning 3 File
    • Biostat 202 Lecture 6: Machine Learning 3 File

    • Pre-recorded lecture - watch before live Zoom class session (Access restricted to registered students):

    • Prerecorded Lecture 6 - module 1 Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Biostat 202 Lecture 6 - module 2 URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 6 - module 3 URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 6 - module 4 URL
      Not available unless: You belong to Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Biostat 202 Lecture 6 - RECORDED Zoom Session URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 6 - RECORDED Zoom Session Media Resource
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 6 - class File
    • Biostat 202 Lecture 6 - class File
    • Heart disease dataset File
    • Lecture 6 - KNN Orange Demo File
    • Lecture 6 - Decision Tree Orange Demo File
    • Lecture 6 - SVM Orange Demo File
    • Lecture 6 - Neural Network Orange Demo File

    • Readings:

    • AI is learning from humans. Many humans. URL

  • Thursday, August 12, 2021; 1:00 PM - 1:45 PM

    Lecture 7: Machine Learning 4

    Cross-validation, ensemble methods, and feature importance

    Faculty:  Aaron Wolfe Scheffler

    • Lecture Slides:

    • Biostat 202 Lecture 7: Machine Learning 4 File
    • Biostat 202 Lecture 7: Machine Learning 4 File

    • Pre-recorded lecture - watch before live Zoom class session (Access restricted to registered students):

    • Biostat 202 Lecture 7 - module 1 URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 7 - module 2 URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 7 - module 3 URL
      Not available unless: You belong to Registered Students Only
    • laheart File
    • Lecture 7 Orange Demo File

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Biostat 202 Lecture 7 - class File
    • Biostat 202 Lecture 7 - class File
    • Biostat 202 Lecture 7- RECORDED Zoom Session URL
      Not available unless: You belong to Registered Students Only

  • Thursday, August 12, 2021; 2:00 PM - 3:45 PM

    Lab 4: Machine Learning Competition

    Students have access to course faculty for questions on current or prior curriculum, assignments and software implementation. This session will be given in-person at Mission Hall.

    Faculty:  Aaron Wolfe Scheffler

    Location:      REMOTE via ZOOM

  • Thursday, August 12, 2021; 4:00 PM - 5:00 PM

    Drop-In Help

    Course faculty are available to address questions. This session will be given via web-conferencing software and in-person.

    Faculty:  Aaron Wolfe Scheffler

    Location (Access restricted to registered students):  Zoom 

  • Monday, August 16, 2021; 1:00 PM - 1:45 PM

    Lecture 8: Machine Learning 5

    Unsupervised learning, clustering, and dimension reduction

    Faculty:  Aaron Wolfe Scheffler

    • Lecture Slides:

    • Biostat 202 Lecture 8 - Machine Learning 5 File
    • Biostat 202 Lecture 8 - Machine Learning 5 File

    • Pre-recorded lecture - watch before live Zoom class session (Access restricted to registered students):

    • Biostat 202 Lecture 8 - module 1 URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 8 - module 2 URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 8 - module 3 URL
      Not available unless: You belong to Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Biostat 202 Lecture 8 - RECORDED Zoom Session URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 8 - CLASS File
    • Biostat 202 Lecture 8 - CLASS File
    • Biostat 202 Lecture 8 - Orange Clustering Demo File
    • Biostat 202 Lecture 8 - Orange PCA Demo File
    • Biostat 202 Lecture 8 - Orange t-SNE Demo File
    • Biostat 202 ML Guide File

  • Thursday, August 19, 2021; 1:00 PM - 1:45 PM

    Lecture 9: Causal Inference in ''Big Data''

    Issues of bias and how to minimize. Selection bias. Methods to minimize bias in observational studies.

    Faculty:  Aaron Wolfe Scheffler

    • Lecture Slides:

    • Biostat 202 Lecture 9: Causation vs Prediction File
    • Biostat 202 Lecture 9: Causation vs Prediction File

    • Pre-recorded lecture - watch before live Zoom class session (Access restricted to registered students):

    • Biostat 202 Lecture 9 - module 1 URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 9 - module 2 URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 9 - module 3 URL
      Not available unless: You belong to Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Biostat 202 Lecture 9 - RECORDED Zoom Session URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 9 - CLASS File
    • Biostat 202 Lecture 9 - CLASS File

    • Optional Reading:  Pragmatic trials lecture from 2016 by Mark Pletcher

    • Biostat 202 Pragmatic Trials File
    • Biostat 202 Pragmatic Trials File
    • NEJM Review - Pragmatic Trials File

    • Tool Files:

    • Biostat 202 Lecture 9 Potential Outcomes Orange Demo File
    • Biostat 202 Lecture 9 Propensity Score Analysis Orange Demo File

    • Datasets:

    • Propensity score example data File
    • Subgroup example data File

  • Thursday, August 19, 2021; 2:00 PM - 3:45 PM

    Lab 5: Unsupervised Learning

    Students have access to course faculty for questions on current or prior curriculum, assignments and software implementation. This session will be given in-person at Mission Hall.

    Faculty:  Aaron Wolfe Scheffler

    Location:     MH-1400

  • Thursday, August 19, 2021; 4:00 PM - 5:00 PM

    Drop-In Help

    Course faculty are available to address questions. This session will be given via web-conferencing software and in-person.

    Faculty:  Aaron Wolfe Scheffler

    Location (Access restricted to registered students):  Zoom and MH-1400

  • Monday, August 23, 2021; 1:00 PM - 1:45 PM

    Lecture 10: Data visualization/storytelling

    Graphical and tabular methods for displaying data to uncover/understand associations.

    Faculty:  Aaron Wolfe Scheffler

    • Lecture Slides:

    • Biostat 202 lecture: Data Visualization (.pptx) File
    • Biostat 202 lecture: Data Visualization (.pdf) File

    • Pre-recorded lecture - watch before live Zoom class session (Access restricted to registered students):

    • Biostat 202 Lecture 10 - module 1 URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 10 - module 2 URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 10 - module 3 URL
      Not available unless: You belong to Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Biostat 202 Lecture 10 - RECORDED Zoom Session URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202 Lecture 10 - CLASS File
    • Biostat 202 Lecture 10 - CLASS File
    • Graph/Table Exercise File
    • Graph/Table Exercise File

  • Thursday, August 26, 2021; 1:00 PM - 1:45 PM

    Lecture 11: Case studies in "Big Data"

    Taking a step back, we will review what we learned and run through several case studies in "Big Data" and identify the possible ways to analyze the data.

    Faculty:  Aaron Wolfe Scheffler

    • Lecture Slides:

    • Biostat 202 Lecture: Review and Case Studies File
    • Biostat 202: Review and Case Studies File
    • Orange model validation template File

    • Pre-recorded lecture - watch before live Zoom class session (Access restricted to registered students):

    • Big Data in Preterm Birth - Marina Sirota Case Study URL
      Not available unless: You belong to Registered Students Only
    • Biostat 202: Digital Health - Dr. Mark Pletcher Case Study File
    • Digital Health - Mark Pletcher Case Study URL
      Not available unless: You belong to Registered Students Only
    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.
    • Biostat 202 Lecture 11 - RECORDED Zoom URL
      Not available unless: You belong to Registered Students Only

  • Thursday, August 26, 2021; 2:00 PM - 3:45 PM

    Highlighted

    Extended Project Office Hours

    Lab 6: Data Visualization

    Students have access to course faculty for questions on current or prior curriculum, assignments and software implementation. This session will be given in-person at Mission Hall.

    Faculty:  Aaron Wolfe Scheffler

    Location:     MH-1400

  • Thursday, August 26, 2021; 4:00 PM- 5:00 PM

    Drop-In Help

    Course faculty are available to address questions. This session will be given via web-conferencing software and in-person.

    Faculty:  Aaron Wolfe Scheffler

    Location (Access restricted to registered students):  Zoom and MH-1400

  • Monday, August 30, 2021; 1:00 PM - 1:45 PM

    Lecture 12: Case Studies

    Faculty:  Aaron Wolfe Scheffler

    We will explore some case studies to practice our skills in drawing up a machine learning analysis plan, much as you would for your own future projects. Some materials discussing ethics in Big Data are linked below for those curious. 

    Ethics in Big Data

    Ethical application of machine learning to big data is an important topic and I would like to provide some resources for you to archive and peruse at your own leisure. As clinical researchers, the approaches and considerations we take when analyzing data have implications on treatment and health outcomes. Even the most well intended applications of machine learning to big data can have unanticipated consequences that produce bias or even discrimination. Therefore, please keep these topics in mind as you develop your future research projects.

    Resources:

    Online courses: 
    • Practical data ethics: an online short course on data ethics by https://ethics.fast.ai/. Very organized structure with recorded video lectures.
    Books:
    • Cathy O'Neil. Weapons of Math Destruction: How Big Data Increases Inequality and Threatens Democracy. New York: Crown Publishers, 2016.
    • Broussard, M. (2018). Artificial Unintelligence: How Computers Misunderstand the World. MIT Press.

    Journal articles with discussion of bias in machine learning with clinical applications:

    • Vyas DA, Eisenstein LG, Jones DS. Hidden in Plain Sight - Reconsidering the Use of Race Correction in Clinical Algorithms. N Engl J Med. 2020;383(9):874-882. doi:10.1056/NEJMms2004740
    • Ziad Obermeyer and Sendhil Mullainathan. 2019. Dissecting Racial Bias in an Algorithm that Guides Health Decisions for 70 Million People. In Proceedings of the Conference on Fairness, Accountability, and Transparency (FAT* '19). Association for Computing Machinery, New York, NY, USA, 89. DOI:https://ucsf.idm.oclc.org/login?url=https://doi.org/10.1145/3287560.3287593

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Biostat 202 Lecture 12 - RECORDED Zoom URL
      Not available unless: You belong to Registered Students Only