Radiomics-Guided Multi-Sequence Learning for Pathological Complete Response Prediction from Breast MRI with Missing Auxiliary Sequences

Pathological complete response (pCR) after neoadjuvant chemotherapy (NACT) provides an endpoint for treatment evaluation in breast cancer. Multi-sequence breast MRI can support pCR prediction, but routine examinations may lack usable T1-weighted or T2-weighted sequences. Many models merge radiomic and deep features by concatenation, leaving the interaction between handcrafted descriptors and learned representations weakly specified. We developed a radiomics-guided framework for pCR prediction from multi-sequence breast MRI. The model uses a multi-branch 2.5D encoder for sequence-specific features, radiomics-guided channel recalibration, and masked token fusion to aggregate available sequence tokens. We evaluated the framework on 157 patients from the I-SPY1 Trial cohort with patient-level five-fold cross-validation, fixed sequence-combination analysis, and slice-window sensitivity analysis. The full model achieved 78.4% accuracy and 0.809 AUC, compared with 75.8% accuracy and 0.788 AUC for the strongest channel-concatenation baseline. In this cohort, radiomics-guided multi-sequence learning was feasible, with external validation required before clinical interpretation.