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Traditional bi-level origin-destination (OD) matrix estimation process adjusts the matrix (at the upper level) based on the deviation between the observed and simulated traffic counts. The problem is mathematically under-determined, and the quality of the solution can be enhanced by restricting the upper level search space with information from other sources. This paper presents a methodology that assimilates sub-path flows in the upper level objective function. The contributions of the study are two-fold: first, it proposes the idea of “structural comparison of sub-path flows” to relax the requirement of “known” penetration rate of vehicles’ trajectories; second, it proposes an innovative upper level formulation where the structural difference between the observed and assigned sub-path flows is integrated with the traditional deviations between the observed and assigned link flows. The sub-path flows can be estimated …