Cross-task interpretability through unified modeling reveals a universal shortcut bias in neoantigen prediction

This repository contains the implementation of ImmUni, the unified transformer-based framework introduced in our manuscript “Cross-task interpretability through unified modeling reveals a universal shortcut bias in neoantigen prediction.” An earlier version of this framework was presented under the name ImmuBPI at RECOMB 2024 (https://doi.org/10.1007/978-1-0716-3989-4_28). To maintain continuity and avoid fragmenting the codebase, we retain the original repository name ImmuBPI, while the current manuscript refers to the unified model as ImmUni. No functional changes were made to the implementation for this renaming; the code here corresponds to the version used in both the RECOMB presentation and the current manuscript.