The fundamental diagram serves as the foundation of traffic flow modeling for almost a century. With the increasing availability of road sensor data, deterministic parametric models have proved inadequate in describing the variability of real-world data, especially in congested area of the density-flow diagram. In this paper we estimate the stochastic density-flow relation introducing a nonparametric method called convex quantile regression. The proposed method does not depend on any prior functional form assumptions, but thanks to the concavity constraints, the estimated function satisfies the theoretical properties of the fundamental diagram. The second contribution is to develop the new convex quantile regression with bags (CQRb) approach to facilitate practical implementation of CQR to the real-world data. We illustrate the CQRb estimation process using the road sensor data from Finland in years 2016-2018. Our third contribution is to demonstrate the excellent out-of-sample predictive power of the proposed CQRb method in comparison to the standard parametric deterministic approach.