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Embedding sequences with ESMC
Embed protein sequences and explore how different transformer layers encode structural and
functional information.
Embed multiple sequences with ESMC
Use the esm SDK parallel executor to generate ESMC representations for multiple protein
sequences.
Zero-shot entropy and mutation analysis
Compute per-position entropy and log-likelihood ratios to identify constrained vs.
mutation-tolerant sites.
Layer sweep for enzyme function classification
Sweep all layers to find the best one, using enzyme classification as the task.
Understanding proteins with SAE features
Extract and visualize sparse autoencoder features, rank by peak activation, and map activations
onto 3D structures.
Fine-tuning ESMC
Fine-tune a classification or regression head for your dataset on top of ESMC using parameter-efficient
fine-tuning (PEFT).