4 papers
Many Needles in a Haystack: Active Hit Discovery for Perturbation Experiments
Andrea Rubbi, Arpit Merchant, Samuel Ogden +4
High-throughput gene perturbation experiments can test several genetic interventions in parallel, yet experimental budgets remain limited. A central goal is hit discovery: identify…
A Standardized Framework For Evaluating Gene Expression Generative Models
Andrea Rubbi, Andrea Giuseppe Di Francesco, Mohammad Lotfollahi +1
The rapid development of generative models for single-cell gene expression data has created an urgent need for standardised evaluation frameworks. Current evaluation practices suff…
Differentiable Retrieval-Augmented Generation for Predicting Cellular Responses to Gene Perturbation
Andrea Giuseppe Di Francesco, Andrea Rubbi, Pietro Liò +1
Predicting transcriptional responses to genetic perturbations is fundamental to functional genomics and therapeutic discovery. Recent deep learning models have shown promise in sin…
Shortest-Path Flow Matching with Mixture-Conditioned Bases for OOD Generalization to Unseen Conditions
Andrea Rubbi, Amir Akbarnejad, Mohammad Vali Sanian +10
Robust generalization under distribution shift remains a key challenge for conditional generative modeling: conditional flow-based methods often fit the training conditions well bu…