Author

Lavik Jain

Harvard University

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Bioinformatics· 1

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Research Focus:benchmarking· 1 Approach:deep learning· 1 Research Focus:gene regulatory network inference· 1 Research Focus:phylogenetics / evolution· 1 Assay:protein sequence· 1 Approach:transformer / foundation model· 1

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Andrew SheniD· 1 shared Maha FarhatiD· 1 shared Marinka ŽitnikiD· 1 shared Yasha EktefaieiD· 1 shared

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2025-2025 · peak 1/yr

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1 paper

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Bioinformaticsneural information processing systemsPeer-reviewedJan 1, 2025

Evolutionary Reasoning Does Not Arise in Standard Usage of Protein Language Models

Yasha Ektefaie, Andrew Shen, Lavik Jain…·Marinka Žitnik

This paper shows that standard protein language models do not support evolutionary reasoning, but a new model trained with phylogenetic supervision performs better on tree reconstruction and clustering.

DOI 10.52202/085713-4356

protein sequencedeep learning

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