Author

Zahra Khodagholi

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Review Open access Aug 2026

From rules to foundation models: a comprehensive review of machine learning approaches for siRNA design

Abstract Small interfering RNAs (siRNAs) are a clinically validated therapeutic modality with eight FDA-approved drugs, yet designing effective siRNAs remains computationally challenging due to complex dependencies on sequence composition, thermodynamic properties, target-site accessibility, and off-target interactions...

Zahra Khodagholi, Niloofar Yousefi · NAR Genomics and Bioinformat... · 0 citations

#machine learning Preprint Sep 2026

One pool, many targets: a conservation layer and what archival data can identify

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 differentiable scalar equilibrium layer: one conservation equation with a unique positive root and exact implicit gradients. It yields a redistribution...

Zahra Khodagholi, Niloofar Yousefi · 0 citations

#artificial intelligence Preprint Sep 2026

Representable but Unlearned: Encoding Rank and the Interaction-Prediction Floor

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 from an encoder's equivalence classes and a fixed contrast design, without labels, loss, or a fitted model; projecting the recorded contrast...

Zahra Khodagholi, Niloofar Yousefi · 0 citations