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

Frequent Co-Authors

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

Activity by Year

2025-2025 · peak 1/yr

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4 top collaborators · 6 mutual co-author links

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1 shared paperBioinformatics

Andrew ShenORCID

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1 paper

Recent·Most cited

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

Yasha Ektefaie, Andrew Shen, Lavik Jain, Maha Farhat, 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.

neural information processing systems · Jan 1, 2025Peer-reviewedBioinformatics