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Distinguished Speaker Seminar Series 2021

29 Apr - 18 Jun 21
Thursday 18th February,              3.30 pm Distinguished Speaker Seminar

Title:         Veridical Data Science for biomedical discovery: detecting epistatic interactions with epiTree

Abstract: “A.I. is like nuclear energy — both promising and dangerous” — Bill Gates, 2019.

Data Science is a pillar of A.I. and has driven most of recent cutting-edge discoveries in biomedical research. In practice, Data Science has a life cycle (DSLC) that includes problem formulation, data collection, data cleaning, modeling, result interpretation and the drawing of conclusions. Human judgement calls are ubiquitous at every step of this process, e.g., in choosing data cleaning methods, predictive algorithms and data perturbations. Such judgment calls are often responsible for the “dangers” of A.I. To maximally mitigate these dangers, we developed a framework based on three core principles: Predictability, Computability and Stability (PCS). Through a workflow and documentation (in R Markdown or Jupyter Notebook) that allows one to manage the whole DSLC, the PCS framework unifies, streamlines and expands on the best practices of machine learning and statistics – bringing us a step forward towards veridical Data Science.

In this lecture, we will illustrate the PCS framework through the epiTree; a pipeline to discover epistasis interactions from genomics data. epiTree addresses issues of scaling of penetrance through decision trees, significance calling through PCS p-values, and combinatorial search over interactions through iterative random forests (which is a special case of PCS). Using UK  Biobank data, we validate the epiTree pipeline through an application to the red-hair phenotype, where several genes are known to display epistatic interactions.

Bin Yu,                               Chancellor’s Professor, Departments of Statistics and Electrical Engineering & Computer Science, UC Berkeley

Thursday 29th April, 3.30 pm Distinguished Speaker Seminar Sara van der Geer                Professor at the Seminar for Statistics, ETH Zurich
Friday 18th June, 3.30 pm Distinguished Speaker Seminar Susan Murphy,                      Professor of statistics and  computer science at Harvard John A. Paulson School of Engineering and Applied Sciences