Author

Mehrdad Shoeibi

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Preprint Jul 2026

Pre-Registered External Evaluation Yields a Consistent Partial-Replication Category across Three Transcriptomic Foundation Models

A pre-registered, final-test-once evaluation framework that locks the outcome rule, seeds, and target-gene-grouped splits before any test data are seen, and scores each frozen representation against a strong expression baseline, a matched-capacity Gaussian control, and a within-split row-identity (shuffle) control.

Mehrdad Shoeibi, Niloofar Yousefi · 0 citations

#artificial intelligence Preprint Jul 2026

Can We Trust In-Distribution Success? Locked Evaluation Reveals Transfer Failure and Sampling-Depth Entanglement in CRISPRi Perturbation Prediction

This case study shows how locking the evaluation, harmonizing the measured endpoint, and separating primary from secondary evidence can change the inference supported by an AI benchmark.

Mehrdad Shoeibi, Niloofar Yousefi · 1 citation