Across 13 protein language models and 15 downstream tasks, the last layer is rarely the best source of embeddings; intermediate layers work better, and the best layer is set by dataset structure rather than by the task alone.
Language mod- els can identify enzymatic binding sites in pro- tein sequences.Computational and structural biotechnology journal, 23:1929–1937, 2024
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Task- and dataset-specific information in protein language models
Across 13 protein language models and 15 downstream tasks, the last layer is rarely the best source of embeddings; intermediate layers work better, and the best layer is set by dataset structure rather than by the task alone.