3 papers
cs.LG2026
One pool, many targets: a conservation layer and what archival data can identify
Zahra Khodagholi, Niloofar Yousefi
Pairwise guide--transcript scores do not enforce conservation of a finite guide-loaded RISC pool when they are interpreted independently as occupancies. We formulate a differentiab…
cs.LG2026
Representable but Unlearned: Encoding Rank and the Interaction-Prediction Floor
Zahra Khodagholi, Niloofar Yousefi
Input encodings can restrict which measured contrasts a predictor can jointly reproduce, even when no single contrast is forced to vanish. We compute the attainable contrast space…
q-bio.GN2026
Validating Interpretability in siRNA Efficacy Prediction: A Perturbation-Based, Dataset-Aware Protocol
Zahra Khodagholi, Niloofar Yousefi
Saliency maps are increasingly used as design guidance in siRNA efficacy prediction, yet attribution methods are rarely validated before motivating sequence edits. We introduce a p…