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Expose the latest changes to the PeptDeepKontext (PDK) interfaces and configuration.
Add the hybrid adaptation method: Combines test-time optimization (TTO) with a subsequent fine-tuning run of the downstream model. Both steps are executed and managed by PeptDeepKontext.
Expose PDK configuration options: As PDK's configuration has grown, AlphaDIA now surfaces a subset of commonly adjusted options for users to configure directly. For advanced use cases, users can also provide a separate path to a PDK configuration file for further customization.
To-do list (outside contributers only)