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bioRxiv · 10.64898/2026.02.19.706811

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models

Larey, A.·Dahan, E.·Amit Bleiweiss, A. B.·Kellerman, R.·Leib, G.·Nayshool, O.·Ofer, D.·Zinger, T.·Dominissini, D.·Rechavi, G.·Bussola, N.·Lee, S.·O'Connell, S.·Hoang, D.·Wirth, M.·W. Charney, A.·Shavit, Y.·Daniel, N.
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Abstract

The rapid scaling of Genomic Foundation Models (GFMs) has created a critical need for standardized evaluation frameworks. Current benchmarking practices are often fragmented, relying on model-specific preprocessing and inconsistent metric implementations that hinder reproducible comparisons. We present GFMBench-API, a high-level Python interface designed to unify the evaluation lifecycle of GFMs. GFMBench-API provides a modular "middleware" architecture that decouples model-specific tokenization and embedding logic from task-specific data streams and performance metrics. By standardizing the input/output schemas for common genomic tasks, such as regulatory element prediction, variant effect scoring, and long-range interaction mapping, GFMBench-API enables researchers to integrate new models or tasks with minimal "glue code." Our interface ensures mathematical consistency across evaluations, providing a robust foundation for the transparent and systematic benchmarking of GFMs.

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Larey, A., Dahan, E., Amit Bleiweiss, A. B., Kellerman, R., Leib, G., Nayshool, O., Ofer, D., Zinger, T., Dominissini, D., Rechavi, G., Bussola, N., Lee, S., O'Connell, S., Hoang, D., Wirth, M., W. Charney, A., Shavit, Y., Daniel, N.. 2026-02-19. GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models. https://doi.org/10.64898/2026.02.19.706811

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