Correspondence modelling between low-dimensional breathing signals and internal organ motion is a prerequisite for application of advanced techniques in radiotherapy of moving targets. Patient-specific correspondence models can, for example, be built prior to treatment based on a planning 4D CT and simultaneously acquired breathing signals. Reliability of pre-treatment-built models depends, however, on the degree of patient-specific inter-fraction motion variations. This study investigates whether motion estimation accuracy in the presence of inter-fraction motion variations can be improved using correspondence models that incorporate motion information from different patients. The underlying assumption is that inter-patient motion variations resemble patient-specific inter-fraction motion variations for subpopulations of patients with similar breathing characteristics. The hypothesis is tested by integrating a sparse manifold clustering approach into a regression-based correspondence modelling framework that allows for automated identification of patient subpopulations. The evaluation is based on a total of 73 lung 4D CT data sets, including two cohorts of patients with repeat 4D CT scans (cohort 1: 14 patients; cohort 2: ten patients). The results are consistent for both cohorts: The subpopulation-based modelling approach outperforms general population modelling (models built on all data sets available) as well as pre-treatment-built models trained on only the patient-specific motion information. The results thereby support the hypothesis and illustrate the potential of subpopulation-based correspondence modelling.