We are excited to announce that the Center for Causal Discovery will be hosting their Summer Short Course and Datathon this year from June 11-14, 2018.

 Registration is CLOSED

Causal Discovery from Biomedical Data – June 11-14, 2018, Carnegie Mellon University, Pittsburgh, PA
Course Director: Richard Scheines, PhD

Causal Discovery Datathon – June 14-15, 2018, Carnegie Mellon University, Pittsburgh, PA
Datathon Director: Jeremy Espino, MD, MS


Our short course on causal discovery with biomedical data is appropriate for both biomedical and data scientists at the level of graduate students on up who seek training in causal discovery and graphical modeling of biomedical data. Attendees, either biomedical or data scientists, are expected to have knowledge of basic statistical principles, but no prior graphical modeling experience is needed. You can review the 2017 Summer Short Course on Causal Discoverypresentations from the 2016 Summer Short Course on Causal Discovery from Biomedical Data and the Causal and Statistical Reasoning online course to prepare for the 2018 Short Course and better understand the material to be presented.

Details about the Datathon will be announced later on this site.

There is no charge to attend the Summer Short Course.


A block of Carnegie Mellon University dorm rooms are available for reservation. Dorm rooms must be reserved by May 21, 2018.

 

CMU dorm rates:

Single Occupancy in a Single Room: $65.00

Double Occupancy in a Double Room: $50.00

Single Occupancy in a Double Room: $91.00

Mon, June 11Tues, June 12Wed, June 13Thurs, June 14Fri, June 15

MONDAY
Causal Graphical Models
Giant Eagle Auditorium, Baker Hall

Morning (9:00 am – 12:00 pm) – Richard Scheines, PhD
Registration will be open at 8:00 am

  • Welcome and Overview of CCD – Greg Cooper, PhD, Director of CCD
  • Introduction
    • Overview of causal graphical models
    • Loading Tetrad
    • Causal graphs/interventions
  • Building Models
    • Parametric models: Bayes nets, SEM, other (e.g., generalized SEM)
    • Instantiated models: Bayes net, SEM, generalized SEM

Lunch (12:00 – 1:30 pm) – on your own

Afternoon (1:30 – 4:00 pm) – Richard Scheines, PhD

  • Estimation and Model Fit
    • Estimation
    • Inference
    • Model fit
  • Hands-on Real-Data Examples

Dinner on your own.

TUESDAY
Causal Graphical Models
Giant Eagle Auditorium, Baker Hall

Morning (9am – 12:00 pm) – Search I – Richard Scheines, PhD

  • D-Separation
  • Model equivalence
  • Basic search algorithms
  • Hands-on real-data examples

Lunch (12:00 – 1:30 pm) – on your own

Afternoon (1:30 – 4:00 pm)– Breakout Groups

  • 1:30 – 1:50 – Introduction to additional software and Bridges supercomputer – Jeremy Espino, MD, MS
  • 1:50 – 2:00 – Breakout into workshop groups by interest and data type
  • 2:00 – 3:00 – Instructor led group breakout
    • Load data, specify and test a hypothesis
  • 3:00 – 4:00 – student free time with breakout instructor and TA(s)

4:00 – 6:00 Short Course Welcome Reception with hors d’oeuvres (included with registration)
Giant Eagle Auditorium Baker Hall CMU

Dinner on your own

WEDNESDAY
Biomedical Causal Discovery Overview
Giant Eagle Auditorium, Baker Hall

Morning (9:00 am – 12:00 pm) Search II – Richard Scheines, PhD

  • Latent variable search algorithms
  • Working with mixed data types (discrete and continuous in one set)

Lunch (12:00 – 1:30 pm) – on your own

Afternoon (1:30 – 4:00 pm) – Breakout Groups

  • 1:30 – 2:30 – instructor led group breakout
    • Enter background knowledge
    • Perform basic searches
  • 2:30 – 4:00 – student free time with breakout instructor and TA(s)

Dinner on your own

THURSDAY
Case Studies
Giant Eagle Auditorium, Baker Hall

Morning (9am – 12:00 pm) – Biomedical Case Studies

  • fMRI (brain functional connectome) – Clark Glymour, PhD
  • Cancer genomic drivers – Xinghua Lu, MD, PhD
  • Lung disease pathways (susceptibility & progression) Takis Benos, PhD
  • Single cell pathways – Shyam Visweswaran, MD, PhD
  • Sign up for Consultation sessions after the short Course
  • Course question-and-answer period, discussion, and wrap-up
  • Evaluations

Box Lunch (12:00 – 1:00 pm) – provided by us

Afternoon: Causal Discovery Datathon Begins at 1:00 pm in the same location

Jeremy Espino, MD, MS, Director

Immediately following the Short Course, we will hold a Datathon designed to instruct and challenge biomedical researchers on the use and application of causal modeling and discovery tools in a “bring your own data event”.  You will be required to use our CCD software, including our API (Java, R, Python) and command-line interfaces for Fast Greedy Search (FGS) and any other causal discovery algorithms available for use in June.

A panel of data scientists from our CCD Driving Biomedical Project teams will judge the analyses and award prizes based on size and complexity of data, impact with regard to the causal hypotheses generated, and innovation in the use of CCD tools.

You will need to download CCD software and perform preliminary data formatting in advance of the Datathon. If you attend the Short Course, you will have already completed this process. If you are attending only the Datathon, we will send you formatting specifications for your data so that you can prepare them in advance.

Causal Discovery Datathon

1:00 pm Datathon introduction
1:30 pm Team introductions and pairing of teams with support staff
2:00 pm Data preparation discussion – discretization, data filtering, distributions
3:00 pm Instruction on supercomputing resources available to Datathon teams
3:30-5:45 pm Data analysis using CCD tools
6:00-8:00 pm Group dinner & networking

FRIDAY
Causal Discovery Datathon
Giant Eagle Auditorium, Baker Hall

9:00 am Breakfast with question and answer session
10:00 am – noon Data hacking
12:00 pm – 1:00 pm Lunch (on your own)
1:00 – 3:00 pm Data hacking & visualization
3:00 Participant presentations