The Protocol Genome A Self Supervised Learning Framework from DICOM Headers
This addresses generalization issues in medical imaging AI across sites and protocols, with incremental gains over existing SSL methods.
The paper tackles the problem of latent confounders in clinical imaging from DICOM headers that impede generalization of image-only networks, achieving AUROC improvements of +0.046 to +0.058 across tasks and 25-37% calibration improvements on external validation.
In this paper, we introduce the Protocol Genome, a self-supervised learning system that learns correlations from DICOM headers and achieves AUROC 0.901 (vs 0.847 baseline) and ECE 0.036 (vs 0.058) on fully held-out external validation. Our method also improves calibration and robustness across modalities (CT, MRI, CXR) and vendors. Clinical imaging is funneled through PACS/DICOM, where procedure choices (scanner make/model, sequence, kernel, kVp, TR/TE, and slice thickness) have consequences for contrast, noise, and artifact. These latent confounders impede the generalization of image-only networks across sites. We consider structured DICOM headers as a label and learn protocol-aware but clinically robust image representations. Protocol Genome obtains tokenized embeddings of de-identified header fields and models them along with image features using: (1) protocol-image contrastive learning, (2) masked protocol prediction, and (3) protocol-protocol translation. With 1.26M studies (7 health systems, 31 scanners, 3 vendors; CT, MR, CR/DR), we experiment on: (A) chest CT triage for PE, (B) brain MRI glioma grading, and (C) chest radiograph cardiomegaly detection. Relative to strong SSL baselines (SimCLR, MAE) as well as ImageNet transfer, Protocol Genome (+0.046: PE, +0.058: glioma, +0.041: cardiomegaly) is associated with higher external AUROC; 25-37% calibration improvements are obtained (p < 0.01, DeLong tests). While the gains may be task-dependent, they are preserved with 10-20% of labeled data. From a clinical point of view, the technique reduces false positives at protocol borders and is applicable in a PACS (DICOM C-FIND/C-MOVE, DICOMweb QIDO/WADO). We publish a model card and deployment guide, complete with both de-identification and bias audits.