3 papers
cs.LG2026
Can We Trust In-Distribution Success? Locked Evaluation Reveals Transfer Failure and Sampling-Depth Entanglement in CRISPRi Perturbation Prediction
Mehrdad Shoeibi, Niloofar Yousefi
AI evaluation can support the wrong inference when an in-domain benchmark success does not survive distribution shift, or when the benchmark endpoint is entangled with a design fac…
q-bio.OT2026
Pre-Registered External Evaluation Yields a Consistent Partial-Replication Category across Three Transcriptomic Foundation Models
Mehrdad Shoeibi, Niloofar Yousefi
Transcriptomic foundation models are increasingly used as reusable cell and gene representations, but validating them on new data under weak supervision and distribution shift is h…
q-bio.QM2025
BIOGEN: Evidence-Grounded Multi-Agent Reasoning Framework for Transcriptomic Interpretation in Antimicrobial Resistance
Elias Hossain, Mehrdad Shoeibi, Ivan Garibay +1
Interpreting gene clusters from RNA sequencing (RNA-seq) remains challenging, especially in antimicrobial resistance studies where mechanistic insight is important for hypothesis g…