ClockBridge: Partial Identification of Cross-Modal Disease Timing across Unpaired Cohorts

Biomedical cohorts often measure different modalities in different individuals and at different disease stages, so stage labels that appear comparable can still admit multiple incompatible cross-modal timelines. We formulate cross-modal disease timing across unpaired cohorts as a partial identification problem. ClockBridge places each cohort on its own disease clock, retains the synchronizations compatible with the observed stage-resolved evidence in a synchronization equivalence set (SES), and reports a temporal direction only when it is invariant over the resulting identified interval. Otherwise the claim remains unresolved. On hidden-pair synchronization, ClockBridge substantially lowers selective false-order risk relative to shared-protocol forced-map references and a same-loss point estimator. FO@40 is 12.3% on ADNI versus 52.2–53.5% for forced maps and 17.7% for Point-L, and 3.3% on PD versus 20.8–49.6% and 7.2%, respectively, while decision coverage at low error remains higher. Under degraded stage evidence, unresolved claims increase and unstable directions are withheld. On fully unpaired molecular and imaging cohorts, ClockBridge yields lower aggregate contradiction under cohort replacement and abstains more often on unstable claims. These results support set-valued identification as a principled alternative to forcing a single cross-modal disease timeline when the available stage evidence does not uniquely determine one.