The evolution of neutrino flavor in dense environments such as core-collapse supernovae and binary compact object mergers constitutes an important and unsolved problem. Its solution has potential implications for the dynamics and heavy-element nucleosynthesis in these environments. In this paper, we build upon recent work to explore inference-based techniques for estimation of model parameters and neutrino flavor evolution histories. We combine data assimilation, ordinary differential equation solvers, and neural networks to craft an inference approach tailored for non-linear dynamical systems. Using this architecture, and a simple two-neutrino, two-flavor model, we test various optimization algorithms with the help of four experimental setups. We find that employing this new architecture, together with evolutionary optimization algorithms, accurately captures flavor histories in the four experiments. This work provides more options for extending inference techniques to large numbers of neutrinos.