Author

Ilaria Alfisi

University of Florence

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Biology Disciplines

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Genomics· 1

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Research Focus:benchmarking· 1 Approach:deep learning· 1 Assay:DNA methylation· 1 Organism:human· 1 Organism:multiple species· 1 Approach:transformer / foundation model· 1 Research Focus:variant effect prediction· 1 Assay:whole-genome sequencing· 1

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Alberto MagiiD· 1 shared Francesca Ciapi· 1 shared Marta Baragli· 1 shared

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2025-2025 · peak 1/yr

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1 shared paperGenomics

Alberto MagiORCID

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1 paper

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GenomicsbioRxivPreprintJun 15, 2025

Benchmarking DNA Foundation Models for zero-shot variant effect prediction: the role of context, training, and architecture

Ilaria Alfisi, Francesca Ciapi, Marta Baragli, Alberto Magi

This study benchmarks DNA foundation models for zero-shot variant effect prediction, showing that large multi-species models outperform human-only models in capturing contextual effects.

DOI 10.1101/2025.06.15.659748

humanmultiple species

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