arXiv:2610.12745v1 Announce Type: new Abstract: We develop a neural transport framework for nonlinear, nonlocal aggregationdiffusion equations arising in chemotaxis, polymer dynamics, and related applications. Based on the Onsager variational principle, we reformulate the governing equation as a constrained optimal control problem, taking the velocity field as the control and evolving the density via the associated continuity equation. The velocity field is parameterized by a neural network trained on the variational objective evaluated along particle trajectories. By coupling the density and generalized score equations into a single system solved via the Euler method, the score function propagates efficiently for loss evaluation. Furthermore, we establish a rigorous error analysis that decomposes the total error into approximation, optimization, Monte Carlo sampling, and time-discretization components, and prove corresponding error bounds. Numerical experiments across several representative models demonstrate the accuracy and effectiveness of the proposed approach.