Talk by Philip Versteeg

You are all cordially invited to the AMLab seminar on Tuesday April 18 at 16:00 in C3.163, where Philip Versteeg will give a talk titled “Prediction and validation of causal effects in gene knockout experiments”. Afterwards there are the usual drinks and snacks!

Abstract: Causal questions abound across the empirical sciences, including basic biology, epidemiology, psychology and economics. Molecular biology is a particularly interesting area due to the ability in that field to perform interventions via diverse experimental techniques, such as measurements of gene expression levels under single gene knockouts. Such experiments are a key tool for dissecting causal regulatory relationships and provide an opportunity to validate causal discovery methods using real experimental data. In this talk, we provide results of an empirical assessment of several causal discovery algorithms using large-scale data from knockout experiments. We discuss several measures of performance defined using held-out observational and interventional data and find that while discovering system-wide causal structure remains difficult, especially when using only observational data, predicting the set of strongest causal effects is more feasible. We report that predictions of the strongest total causal effects based on a combination of interventional and observational data can be stable across performance measures and consistently outperform non-causal baselines.