Generative epistatic landscapes show that evolutionary intermediate reconstruction works best via conditional sampling of ensembles rather than maximum-likelihood point predictions, with success limited by landscape topology and mutability.
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q-bio.PE 2years
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Review of generative sequence models and Direct Coupling Analysis for simulating protein evolutionary dynamics from extant data.
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Reconstructability of evolutionary intermediates in generative epistatic landscapes
Generative epistatic landscapes show that evolutionary intermediate reconstruction works best via conditional sampling of ensembles rather than maximum-likelihood point predictions, with success limited by landscape topology and mutability.
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Modeling Protein Evolution with Generative Models: from Extant Sequence Data to Evolutionary Dynamics
Review of generative sequence models and Direct Coupling Analysis for simulating protein evolutionary dynamics from extant data.