Starkly Speaking reading group: Identifying perturbation targets through causal differential networks

[Hannes Stärk]

Hi together,

Tomorrow we will have:

Paper:
Identifying perturbation targets through causal differential networks https://arxiv.org/abs/2410.03380 (Menghua Wu, Umesh Padia, Sean H. Murphy, Regina Barzilay, Tommi Jaakkola)
Identifying variables responsible for changes to a biological system enables applications in drug target discovery and cell engineering. Given a pair of observational and interventional datasets, the goal is to isolate the subset of observed variables that were the targets of the intervention. Directly applying causal discovery algorithms is challenging: the data may contain thousands of variables with as few as tens of samples per intervention, and biological systems do not adhere to classical causality assumptions. We propose a causality-inspired approach to address this practical setting. First, we infer noisy causal graphs from the observational and interventional data. Then, we learn to map the differences between these graphs, along with additional statistical features, to sets of variables that were intervened upon. Both modules are jointly trained in a supervised framework, on simulated and real data that reflect the nature of biological interventions. This approach consistently outperforms baselines for perturbation modeling on seven single-cell transcriptomics datasets. We also demonstrate significant improvements over current causal discovery methods for predicting soft and hard intervention targets across a variety of synthetic data.

Speaker:
Rachel Wu from Regina Barzilay and Tommi Jaakkola's groups at MIT. 

Meeting Details:
Every Monday at 12:00 ET / 9:00 PT / 18:00 CE(S)T.  
https://zoom.us/j/5775722530?pwd=ZzlGTXlDNThhUDZOdU4vN2JRMm5pQT09

Add it to your calendar:
Subscribe via Google Calendar, or subscribe via iCal.
Alternatively, add the events, or add this single event.

Slack Workspace for discussion and paper voting:
https://join.slack.com/t/logag/shared_invite/zt-2zuxi7gd1-rLUgxg6gnCkhO7WlRsyElg

All information: Schedule of upcoming papers, recordings, etc.:
https://portal.valencelabs.com/starklyspeaking